Effects of diet on the bacterial and eukaryotic microbiota across the gastrointestinal tract of healthy rabbits (Oryctolagus cuniculus)

OBJECTIVE

This study aimed to characterize the bacterial and eukaryotic microbiota of the gastrointestinal (GI) tract in domestic rabbits and to evaluate the effect of different diet characteristics, such as pelleting, extrusion, and hay supplementation.

ANIMALS

30 New Zealand White rabbits (15 male and 15 female; 6 to 7 months old) were fed 1 of 6 diets (5 rabbits per diet) for 30 days after an initial acclimation period. At the end of the trial, samples were collected from the stomach, small intestine, cecum, large intestine, and hard feces.

METHODS

The samples were analyzed using 16S rRNA and internal transcribed spacer 1 region-targeted amplicon sequencing.

RESULTS

The bacterial microbiota was distinct between the foregut and hindgut. The most abundant bacterial genera included an unclassified genus in the Bacteroidales order and Alistipes. Candida was the most abundant genus in the eukaryotic dataset. In the bacterial dataset, diet No Hay/Pellet E was shown to have lower diversity (Shannon diversity, P < .05) compared to all diet groups except for No Hay/Pellet M. Few significant differences in alpha-diversity indexes between diet groups were detected in the eukaryotic dataset.

CLINICAL RELEVANCE

Our findings demonstrated that feeding hay had a significant effect on the beta diversity of the bacterial microbiota. Given the prevalence of gastrointestinal disease in the domestic rabbit population, furthering our understanding of what constitutes a healthy rabbit microbiota and the effects of different diets on the microbial community can help veterinarians implement better intervention strategies and allow pet owners to provide the best level of care.

Temporal changes in ewe vaginal microbiota throughout gestation

Introduction

Numerous factors are known to influence reproductive efficiency in ewes, but few studies have investigated the potential role of vaginal microbiota in sheep reproductive success. The objective of this study was to thoroughly characterize the ewe vaginal microbiota throughout the course of pregnancy.

Methods

Vaginal samples were collected from 31 pregnant Hampshire and Hampshire X Suffolk crossbred ewes on a weekly basis from pre-breeding to pregnancy testing and then biweekly until just after lambing. To characterize the vaginal microbial communities, DNA was extracted and 16S rRNA gene Illumina MiSeq amplicon sequencing was performed.

Results and Discussion

Alpha diversity metrics indicated an increase in species richness, evenness, and overall diversity throughout gestation. Distinct shifts in the bacterial communities were observed during gestation and were segregated into three periods: early gestation, a transitional period and mid/late gestation. During early gestation, Actinobacillus, Histophilus, and unclassified Leptotrichiaceae were found in greater relative abundance. During the transitional period, a population shift occurred characterized by increasing relative abundance of Streptococcus and Staphylococcus. During mid/late gestation, Staphylococcus, Streptococcus, and Ureaplasma had the greatest relative abundance. These shifts in the microbial population throughout the ewe's gestation are likely related to hormonal changes triggered by the growing conceptus, specifically increasing blood concentration of progesterone. The transitional period shift in vaginal microbial communities potentially aligns with the placental take-over of progesterone production from the corpus luteum at approximately day 50 after conception (gestational week 7). Understanding the observed variability of the vaginal microbiota throughout pregnancy will allow for future comparison of ewes that did not become pregnant or had abnormal pregnancies, which could lead to the discovery of potential bacterial biomarkers for pregnancy outcome; this understanding could also lead to development of probiotics to improve sheep reproductive success.

Fecal and vaginal microbiota of vaccinated and non-vaccinated pregnant elk challenged with Brucella abortus

Introduction

Brucella abortus is the causative agent of brucellosis in cattle and in humans, resulting in economic losses in the agricultural sector and representing a major threat to public health. Elk populations in the American Northwest are reservoirs for this bacterium and transmit the agent to domestic cattle herds. One potential strategy to mitigate the transmission of brucellosis by elk is vaccination of elk populations against B. abortus; however, elk appear to be immunologically distinct from cattle in their responses to current vaccination strategies. The differences in host response to B. abortus between cattle and elk could be attributed to differences between the cattle and elk innate and adaptive immune responses. Because species-specific interactions between the host microbiome and the immune system are also known to affect immunity, we sought to investigate interactions between the elk microbiome and B. abortus infection and vaccination.

Methods

We analyzed the fecal and vaginal microbial communities of B. abortus-vaccinated and unvaccinated elk which were challenged with B. abortus during the periparturient period.

Results

We observed that the elk fecal and vaginal microbiota are similar to those of other ruminants, and these microbial communities were affected both by time of sampling and by vaccination status. Notably, we observed that taxa representing ruminant reproductive tract pathogens tended to increase in abundance in the elk vaginal microbiome following parturition. Furthermore, many of these taxa differed significantly in abundance depending on vaccination status, indicating that vaccination against B. abortus affects the elk vaginal microbiota with potential implications for animal reproductive health.

Discussion

This study is the first to analyze the vaginal microbiota of any species of the genus Cervus and is also the first to assess the effects of B. abortus vaccination and challenge on the vaginal microbiome.

Dietary peptide-specific antibodies against interleukin-4 differentially alter systemic immune cell responses during Eimeria challenge with minimal impacts on the cecal microbiota

Eimeria spp. induce host interleukin (IL)-4 production, a potent immune regulator, during coccidiosis to evade immune responses. Dietary anti-IL-4 may preserve bird performance during challenge; however, specific mechanisms have not been investigated. Study objectives were to develop peptide-specific anti-IL-4 antibodies and evaluate immune cell profiles and the cecal microbiota during Eimeria challenge. Four candidate IL-4 peptides were selected based on antigenicity and location. Hens were injected with conjugated peptide or carrier-only control (3/injection), eggs were collected post-vaccination and yolks were pooled by peptide before freeze-drying. On d 0, 300 Ross 708 broilers were placed in floor pens (10/pen) and assigned to 5 diets consisting of basal diet + 2% egg yolk powder containing antibodies against 1 of 4 target peptides or carrier-only control for 14-d starter and grower periods (28 d total). Baseline blood and cecal contents were collected on d 14 (6 birds/diet) before half the remainder were inoculated with 10X Coccivac-B52 (Merck Animal Health, Kenilworth, NJ). Body weight (BW) and feed intake (FI) were recorded weekly and blood and cecal samples were collected at 3, 7, and 14 d post-inoculation (pi; 3/treatment). Immune cell profiles in peripheral blood mononuclear cells (PBMC) were evaluated flow cytometrically and cecal microbial communities determined by 16S/18S rRNA gene amplicon sequencing. Data were log-transformed when necessary and analyzed with diet, Eimeria, and timepoint fixed effects plus associated interactions (SAS 9.4; P ≤ 0.05). Anti-IL-4 did not alter baseline performance but generally increased PBMC Bu-1+ B cells 38.0 to 55.4% (P < 0.0001). Eimeria challenge reduced FI and BWG 16.1 and 30.3%, respectively, regardless of diet (P < 0.0001) with only birds fed peptide 4 antibodies not recovering feed conversion by d 28. Minimal diet-associated cecal microbiota changes were observed, indicating that anti-IL-4 effects were likely host-specific. Eimeria-challenged birds fed peptide 3 antibodies displayed minimal immune cell fluctuations compared to unchallenged counterparts, suggesting these antibodies potentially modulated intestinal immune responses to minimize systemic requirements, making them good candidates for further research.

Dietary alfalfa hay or lipid-soluble alfalfa extract may improve broiler growth, but fiber presence may be detrimental during Eimeria vaccine challenge

Lipid-soluble components in late-cutting alfalfa are linked to beneficial immune and microbiota responses in mouse challenge models; therefore, responses in a comparative poultry Eimeria challenge model were investigated. The study objective was to evaluate performance, immunity, and the cecal microbiota in broilers fed ground hay or lipid-soluble extract from late (fifth) cutting alfalfa during Eimeria challenge. At hatch, 432 Ross 708 broilers were placed in 24 floor pens (18 birds/pen) and assigned to 3 isocaloric/isonitrogenous dietary treatments consisting of control, 5% ground hay, or 0.25% lipid-soluble extract for a 42-d trial divided into 14 d starter, grower, and finisher periods. On d 14, 4 birds/treatment were euthanized to collect blood and cecal contents before half the remainder were inoculated with 10X Merck Coccivac-B52 (Kenilworth, NJ). Tissue samples were collected at 3, 7, 14, and 28 d postinoculation (pi; 4 birds/diet × Eimeria group) with body weight (BW) and feed intake (FI) recorded weekly. Immune populations within peripheral blood mononuclear cells were characterized by flow cytometry while cecal microbial communities were profiled by 16S rRNA gene amplicon sequencing. Data were normalized when appropriate and analyzed to evaluate the effects of diet, Eimeria challenge, and timepoint (SAS 9.4; P ≤ 0.05). Before challenge, dietary alfalfa hay or extract increased FI 6.9 to 8.0% and increased CD3+ T cells 19.3 to 24.9% compared to control-fed birds (P ≤ 0.007). Alfalfa did not significantly affect post-Eimeria performance, but Eimeria-challenged birds fed hay showed the greatest numeric reduction in final BW compared to their unchallenged counterparts (0.17 kg) vs. control and extract-fed birds (0.02-0.04 kg). Immune cell changes did not indicate recruitment from peripheral blood to local infection sites; however, alfalfa hay may have accelerated Bu-1+ B cell development by 7 d in unchallenged birds (P < 0.0001). During Eimeria-challenge, dietary alfalfa extract preserved alpha diversity measures related to species richness (P ≤ 0.007). Collectively, these results indicate potential benefits of feeding lipid-soluble extract from late cutting alfalfa to broilers during Eimeria challenge.

Closed genome sequences of two Listeria monocytogenes ST121 strains

We performed Oxford Nanopore and Illumina sequencing to generate accurate, closed genomes for the Listeria monocytogenes strains 6179 and L58-55. The new assemblies were generally similar to the previous Illumina-based assemblies, but additional rRNA operons and repeat regions were identified in the new assembly for strain 6179.

Complete genome sequences generated using hybrid Nanopore-Illumina assembly of two non-typical Avibacterium paragallinarum strains isolated from clinically normal chicken flocks

We report the complete genome sequences of two non-typical Avibacterium paragallinarum (AP) strains isolated from chickens in the absence of clinical signs. The availability of these genomes can aid scientists in improving current diagnostics and increase our understanding of AP epidemiology and pathogenicity in chickens.

Characterization of the eukaryotic microbial communities in the chicken ileum in cage-free and conventional commercial housing systems

The current shift from conventional cage (CC) hen housing facilities towards cage-free (CF) hen housing in the egg industry has left many questions regarding how level of fecal exposure and exposure to other hens may influence the hen intestinal microbiota. In a previous publication we reported differences in the bacterial ileal communities and ileal morphology between hens in CC and CF production environments at a single commercial site. Here, we present the first 18S rRNA gene amplicon sequencing-based characterization of the eukaryotic ileal microbiota of adult layer hens, and their associations with intestinal health parameters and the bacterial microbiota. DNA was extracted from the ileal digesta of hens (n = 32 CC, n = 48 CF) using the Qiagen Powerlyzer Powersoil kit, followed by amplification of the V9 region of the 18S rRNA gene. Paired end sequencing was performed with the Illumina MiSeq platform, and the resulting reads were processed according to the Mothur MiSeq protocol in Mothur v1.43.0. De novo operational taxonomic unit (OTU) clustering was performed in mothur with a 99% similarity threshold, and OTUs were taxonomically classified with the SILVA SSU v138 reference database. OTUs classified as vertebrate, plant, or arthropod were removed, resulting in 3,136,400 high quality reads and 1,370 OTUs. Associations between OTUs and intestinal parameters were calculated using PROC GLIMMIX. PERMANOVA over Bray-Curtis distances revealed differences between CC and CF eukaryotic ileal microbiota at the whole community level, but no OTUs were differentially abundant after correcting for false discovery (P > 0.05; q > 0.1). Kazachstania and Saccharomyces, closely related genera of yeast, represented 77.1% and 9.7% of sequences respectively. Two Kazachstania OTUs and 1 Saccharomycetaceae OTU were positively correlated with intestinal permeability (r² ≥ 0.35). Eimeria accounted for 7.6% of sequences across all samples. Intriguingly, 15 OTUs classified as Eimeria were inversely associated with intestinal permeability (r² ≤ -0.35), suggesting Eimeria may play a more complex role in the microbiota of healthy birds than has been observed in disease challenges.

Evaluating a potential model to analyze the function of the gut microbiota of the giant panda

To contribute to the conservation of endangered animals, the utilization of model systems is critical to analyze the function of their gut microbiota. In this study, the results of a fecal microbial transplantation (FMT) experiment with germ-free (GF) mice receiving giant panda or horse fecal microbiota showed a clear clustering by donor microbial communities in GF mice, which was consistent with the results of blood metabolites from these mice. At the genus level, FMT re-established approximately 9% of the giant panda donor microbiota in GF mice compared to about 32% for the horse donor microbiota. In line with this, the difference between the panda donor microbiota and panda-mice microbiota on whole-community level was significantly larger than that between the horse donor microbiota and the horse-mice microbiota. These results were consistent with source tracking analysis that found a significantly higher retention rate of the horse donor microbiota (30.9%) than the giant panda donor microbiota (4.0%) in GF mice where the microbiota remained stable after FMT. Further analyzes indicated that the possible reason for the low retention rate of the panda donor microbiota in GF mice was a low relative abundance of Clostridiaceae in the panda donor microbiota. Our results indicate that the donor microbiota has a large effect on GF mice microbiota after FMT.

Influence of a sodium-saccharin sweetener on the rumen content and rumen epithelium microbiota in dairy cattle during heat stress

The effect of a saccharin-based artificial sweetener was tested on animal performance measures and on the microbial communities associated with the rumen content and with the rumen epithelium during heat stress. Ten cannulated Holstein-Friesian milking dairy cattle were supplemented with 2 g of saccharin-based sweetener per day, top-dressed into individual feeders for a 7-day adaptation period followed by a 14-day heat stress period. A control group of ten additional cows subjected to the same environmental conditions but not supplemented with sweetener were included for comparison. 16S rRNA gene amplicon sequencing was performed on rumen content and rumen epithelium samples from all animals, and comparisons of rumen content microbiota and rumen epithelial microbiota were made between supplemented and control populations. Supplementation of the saccharin-based sweetener did not affect the rumen content microbiota, but differences in the rumen epithelial microbiota beta-diversity (PERMANOVA, P = 0.003, R2 = 0.12) and alpha-diversity (Chao species richness, P = 0.06 and Shannon diversity, P = 0.034) were detected between the supplemented and control experimental groups. Despite the changes detected in the microbial community, animal performance metrics including feed intake, milk yield, and short-chain fatty acid (acetic, propionic, and butyric acid) concentrations were not different between experimental groups. Thus, under the conditions applied, supplementation with a saccharin-based sweetener does not appear to affect animal performance under heat stress. Additionally, we detected differences in the rumen epithelial microbiota due to heat stress when comparing initial, prestressed microbial communities to the communities after heat stress. Importantly, the changes occurring in the rumen epithelial microbiota may have implications on barrier integrity, oxygen scavenging, and urease activity. This research adds insight into the impact of saccharin-based sweeteners on the rumen microbiota and the responsivity of the rumen epithelial microbiota to different stimuli, providing novel hypotheses for future research.

Genome analysis of Erwinia persicina reveals implications for soft rot pathogenicity in plants

Soft rot disease causes devastating losses to crop plants all over the world, with up to 90% loss in tropical climates. To better understand this economically important disease, we isolated four soft rot-causing Erwinia persicina strains from rotted vegetables. Notably, E. persicina has only recently been identified as a soft rot pathogen and a comprehensive genomic analysis and comparison has yet to be conducted. Here, we provide the first genomic analysis of E. persicina, compared to Pectobacterium carotovorum, P. carotovorum, and associated Erwinia plant pathogens. We found that E. persicina shares common genomic features with other Erwinia species and P. carotovorum, while having its own unique characteristics as well. The E. persicina strains examined here lack Type II and Type III secretion systems, commonly used to secrete pectolytic enzymes and evade the host immune response, respectively. E. persicina contains fewer putative pectolytic enzymes than P. carotovorum and lacks the Out cluster of the Type II secretion system while harboring a siderophore that causes a unique pink pigmentation during soft rot infections. Interestingly, a putative phenolic acid decarboxylase is present in the E. persicina strains and some soft rot pathogens, but absent in other Erwinia species, thus potentially providing an important factor for soft rot. All four E. persicina isolates obtained here and many other E. persicina genomes contain plasmids larger than 100 kbp that encode proteins likely important for adaptation to plant hosts. This research provides new insights into the possible mechanisms of soft rot disease by E. persicina and potential targets for diagnostic tools and control measures.

Sex-based de novo transcriptome assemblies of the parasitoid wasp Encarsia suzannae, a host of the manipulative heritable symbiont Cardinium hertigii

Parasitoid wasps in the genus Encarsia are commonly used as biological pest control agents of whiteflies and armored scale insects in greenhouses or the field. They are also hosts of the bacterial endosymbiont Cardinium hertigii, which can cause reproductive manipulation phenotypes, including parthenogenesis, feminization, and cytoplasmic incompatibility (the last is mainly studied in Encarsia suzannae). Despite their biological and economic importance, there are no published Encarsia genomes and only one public transcriptome. Here, we applied a mapping-and-removal approach to eliminate known contaminants from previously-obtained Illumina sequencing data. We generated de novo transcriptome assemblies for both female and male E. suzannae which contain 45,986 and 54,762 final coding sequences, respectively. Benchmarking Single-Copy Orthologs results indicate both assemblies are highly complete. Preliminary analyses revealed the presence of homologs of sex-determination genes characterized in other insects and putative venom proteins. Our male and female transcriptomes will be valuable tools to better understand the biology of Encarsia and their evolutionary relatives, particularly in studies involving insects of only one sex.

Tardigrade Community Microbiomes in North American Orchards Include Putative Endosymbionts and Plant Pathogens

The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, United States, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades vs. their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.

The validation of the existence of the entero-mammary pathway and the assessment of the differences of the pathway between first and third parity sows

Forty sows (PIC Camborough 1050) from a single farm were randomly selected at 112 days of gestation to evaluate if gut bacteria transverse the blood system of the sow to deposit gut microbiota into colostrum for piglet gut inoculation via the entero-mammary pathway. Fourteen first-parity gilts and twenty third-parity sows were used for the study. At the time of farrowing, colostrum, fecal samples and blood samples were collected to evaluate the presence of bacteria in each sample. Colostrum and blood samples were processed via centrifugation to separate the immune cell fraction. Total deoxyribonucleic acid (DNA) was extracted from fecal, colostrum and white blood cell fractions. 16S ribosomal ribonucleic acid (rRNA) gene amplicon sequencing was conducted at the Iowa State University DNA Facility (Ames, IA) to further characterize the bacterial and archaeal taxa present within each sample. Data were analyzed using Mothur and using R v4.0.3 (R Core Team, 2020). The experimental unit was the sow. Tables were generated to demonstrate the relative abundances of bacteria and archaea present in each type of sample and also identify organisms differentially abundant between sample types. Firmicutes was the most abundant phylum in colostrum and fecal samples and Tenericutes had the greatest abundance in blood comparative to other phyla. Further evaluation of the classification of bacteria present demonstrated that a few genera of bacteria are present in all three samples. Clostridum_sensu_stricto 1 was present in high relative abundance in colostrum and in moderate abundance in the feces while also being present within the blood. Other genera present in all three sample types includes Ruminococcus and Mycoplasma. In conclusion, the data suggest that there are bacteria present in all three locations of the sow at the time of farrowing and that first parity sows have different microbial populations than third parity sows.

183 Circulating Biomarkers and Leukocyte Profiles in Agalactic Sows

Agalactia is characterized by reduced milk production after farrowing, resulting in economic losses due to increased piglet mortality. Although a variety of management factors have been associated with the etiology of agalactia, a specific causative mechanism has not been identified. Since clinical signs of agalactia develop in the days following farrowing, the objective of the current study was to determine if periparturient immune cell profiles and circulating biomarkers are predictive of future agalactia. Blood samples and litter weights were collected from sows (n = 374) within 24-36 hours after farrowing (timepoint 1) and sows were subsequently monitored for symptoms of agalactia and gaunt piglets. When a sow was designated as agalactic (n = 36) blood samples and litter weights were collected again (timepoint 2) and also from a parity matched healthy control sow (n = 46) of the same day of lactation. Agalactia diagnosis occurred on average 9.25 ± 2.67 d after farrowing. Average daily gain (ADG) of piglets from agalactic sows was 55% less (P &lt; 0.01) than ADG of piglets from controls. Additionally, piglet mortality was substantially greater (P &lt; 0.01) in litters from agalactic sows compared with controls. Circulating immune cells and metabolites were determined. Cholesterol, blood urea nitrogen, and globulin were increased 22.3, 17.8, and 34.1%, respectively, in agalactic compared with control sows at timepoint 2 (P ≤ 0.01). Aspartate aminotransferase tended to increase in agalactic sows compared with control at timepoint 1 (P = 0.08). No differences in immune cell profiles were observed between agalactic and control sows at either timepoint (P ≥ 0.14). Collectively, these data suggest metabolic changes are occurring in sows experiencing agalactia compared with healthy herd mates, but that very few of the metrics analyzed at timepoint 1 predicted future agalactia. This project was supported by Zoetis; TI-07023.

185 The Validation of the Existence of the Entero-Mammary Pathway and the Assessment of the Differences of the Pathway Between Gilts and Sows

Forty sows (PIC Camborough 1050) from a single farm were randomly selected at 112 d of gestation to evaluate if gut bacteria transverse the blood system of the sow to deposit gut microbiota into colostrum for piglet gut inoculation via the entero-mammary pathway. Fourteen first-parity gilts and twenty third-parity sows were used for the study. At the time of farrowing, colostrum, fecal samples and blood samples were collected to evaluate the presence of bacteria in each sample. Colostrum and blood samples were processed via centrifugation to separate the immune cell fraction. Total deoxyribonucleic acid (DNA) was extracted from fecal, colostrum and white blood cell fractions. 16S ribosomal ribonucleic acid (rRNA) gene amplicon sequencing was conducted at the Iowa State University DNA Facility (Ames, IA) to further characterize the bacterial and archaeal taxa present within each sample. Data were analyzed using Mothur and using R v4.0.3 (R Core Team, 2020). The experimental unit was the female. Tables were generated to demonstrate the relative abundances of bacteria and archaea present in each type of sample and also identify organisms differentially abundant between sample types. Firmicutes was the most abundant phylum in colostrum and fecal samples and Tenericutes had the greatest abundance in blood comparative to other phyla. Further evaluation of the classification of bacteria present demonstrated that a few genera of bacteria are present in all 3 samples. Clostridum_sensu_stricto 1 was present in high relative abundance in colostrum and in moderate abundance in the feces while also being present within the blood. Other genera present in all 3 sample types includes Ruminococcus and Mycoplasma. In conclusion, the data suggests that there are bacteria present in all 3 locations of the sow at the time of farrowing and that gilts have different microbial populations than sows.

41 Differential Gene Expression of the Bovine Rumen Epithelial Microbiota During a Sub-acute Ruminal Acidosis (SARA) Challenge

Sub-Acute Ruminal Acidosis (SARA) is a metabolic disorder in dairy cattle characterized by a lowered ruminal pH, as a result of high grain diets. Dairy cows experiencing SARA show decreased milk production and impaired health; thus, SARA has major economic impacts. SARA has been associated with changes in the rumen epithelial microbiota. Previously, we performed meta-transcriptome sequencing on rumen epithelial biopsy samples from 3 fistulated Holstein cows before (baseline) and after switching to high concentrate feed to induce SARA to analyze the gene expression of the rumen epithelial microbiota. In this previous analysis, 1,607 features were detected using the KEGG Ontology reference database, including a wide variety of metabolic genes, as well as stress response, motility, and other functions. However, only 3 features were differentially expressed between baseline and SARA conditions using this approach. Here, we present a re-analysis of the meta-transcriptomics data using an improved bioinformatics pipeline to reveal additional genetic diversity and differentially expressed genes. We performed a de novo transcriptome co-assembly with Trinity, mapped reads to the assembled contigs, used RSEM to determine read counts, and DESEQ2 for detection of differentially expressed genes (Q &lt; 0.05). Features were annotated using EggNOG, providing taxonomic predictions and GO, COG, and KEGG-based functional prediction. Using this method, a total of 76,861 transcripts were assembled, and 4,935 genes were differentially expressed between baseline and SARA conditions, representing a substantial improvement over the previous analysis. Our preliminary analysis indicates high expression levels of central metabolism and housekeeping genes, as well as oxidative stress response genes, and outer membrane proteins among rumen epithelial bacteria. Differentially expressed archaeal genes were primarily upregulated under SARA conditions and included genes involved in methanogenesis. Further analyses are ongoing and will provide insight into gene expression of the rumen epithelial microbiota, and their association with SARA.

181 Evaluation of the Fecal Microbiota in Commercial Sows with Variable Risk for Pelvic Organ Prolapse During Late Gestation

Sow mortality has increased during the last decade with a large portion due to pelvic organ prolapse (POP) manifesting during late gestation and early lactation. Approximately 21% of sow mortality is attributed to POP, creating a significant economic and animal welfare concern. The study objective was to identify differences in sow fecal microbiota associated with POP risk and to determine if fecal and vaginal microbial communities are correlated. Using an established perineal scoring (PS) system, 2,864 sows were assigned PS1 (low), PS2 (moderate), or PS3 (high) based on phenotypic observations and presumed POP risk during gestation week 15. Of those sows scored, 1.0%, 2.7%, and 23.4% of PS1, PS2, and PS3 assigned sows, respectively, subsequently experienced POP. At the time of scoring, fecal swabs were collected from sows (n = 213) and DNA was extracted for 16S rRNA gene Illumina MiSeq sequencing, and analyzed using mothur, phyloseq and SAS. Additionally, co-occurrence networks were constructed between fecal and vaginal microbial communities using CoNet (V1.1.1), to identify correlations in taxa abundance. Differences in fecal community composition (PERMANOVA; P &lt; 0.05), structure (alpha diversity measurements; P &lt; 0.05), and 13 individual operational taxonomic units (OTU; Q &lt; 0.05) were detected between PS1 and PS3 sows. The abundance of several taxa were correlated across sample collection sites, suggesting the fecal and vaginal microbial communities may influence one another. Collectively, fewer differences exist in fecal microbiota in sows differing risk for POP than previously observed in vaginal microbiota, suggesting the vaginal microbial communities may be a better indicator of POP risk. Understanding correlations between the fecal and vaginal microbial communities may provide strategies or targets for combatting POP. This project was supported by the National Pork Board and the Foundation for Food and Agriculture Research.

184 Correlating Microbial Community Membership of Cervical Fluid, Vagina and Feces in Post-Partum Sows

Postpartum metritis, or the inflammation of the uterus after parturition, is often a direct result of bacterial infection and considered to contribute to agalactia / dysgalactia in multiple species. Diagnosing metritis has included evaluation of vaginal and cervical fluid (CF) discharge for signs of infection (i.e., purulent discharge, strong odor, and discoloration). Metritis in sows results in economic losses for the swine industry due to increased numbers of sows requiring repeat inseminations to establish pregnancy, longer weaning to estrus intervals, association with increased abortions, and is also linked to agalactia. This study aimed to compare the microbial communities of the CF, the vaginal cavity, and feces from sows shortly after parturition, to identify similarities and differences in relative microorganism abundance between these body sites. Fecal and vaginal swabs were collected from 82 sows within 24-36 hours post-parturition. Additionally, CF was collected from each sow and classified based on color and consistency. Extraction of DNA was performed from all 246 samples and used for 16S rRNA gene Illumina MiSeq sequencing. Sequence analysis was conducted using MOTHUR (V1.43.0). No changes in CF microbial community composition or structure were determined related to CF color but differences (P &lt; 0.05) were detected relative to CF consistency. Taxa were compared across body sites to identify correlated phylotypes using CoNet (V1.1.1). The abundances of several phylotypes harboring metritis-relevant pathogens were correlated with common commensal microorganisms across body sites (including Fusobacterium, Streptococcus, Escherichia, and Staphylococcus) suggesting interactions between these body sites exist. This work provides initial insights into postpartum sow CF microbial communities, and the interconnectedness with the vaginal and fecal microbiota. This project was supported by Zoetis (TI-07021).

Metatranscriptomic Analyses Unravel Dynamic Changes in the Microbial and Metabolic Transcriptional Profiles in Artisanal Austrian Hard-Cheeses During Ripening

Vorarlberger Bergkäse (VB) is an artisanal Austrian washed-rind hard cheese produced from alpine cows' raw milk without the addition of ripening cultures. Ripening time is a key factor in VB, as it strongly influences the microbial communities present in the cheeses and the organoleptic properties of the product. In this study, the microbial and metabolic transcriptional profiles in VB rinds at different ripening times were investigated. VB products before (30 days of ripening) and after (90 days of ripening) selling were selected, RNA was extracted and subjected to shotgun metatranscriptomic sequencing. The analysis revealed some of the previously described abundant bacterial taxa of Brevibacterium, Corynebacterium, Halomonas, Psychrobacter, and Staphylococcus to be highly active in VB rinds. Additionally, the investigation of most important metabolic pathways in cheese ripening clearly showed differences in the gene transcription profiles and the active microbiota between the two ripening points investigated. At 30 days of ripening, metabolic events related with the degradation of residual lactose, lactate, citrate, proteolysis, and lipolysis were significantly more transcribed and mainly associated with Staphylococcus. On the other hand, genes involved in the degradation of smaller compounds derived from previous metabolism (i.e., metabolism of free amino acids and fatty acids) were significantly more expressed in VB rinds with 90 of ripening, and mainly associated with Brevibacterium and Corynebacterium. These latter metabolic activities are responsible of the generation of compounds, such as methanethiol and 2,3-butanediol, that are very important for the flavor and aroma characteristics of cheeses. This study shows the dynamic changes in the gene transcriptional profiles associated with energy substrates metabolism and the generation of organoleptic compounds during VB ripening and uncovers bacterial taxa as key drivers of the ripening process. These taxa might be the target for future studies toward an accelerated cheese ripening and the enhancement of its organoleptic properties.

Quality over quantity: unraveling the contributions to cytoplasmic incompatibility caused by two coinfecting Cardinium symbionts

Cytoplasmic incompatibility (CI) is a common form of reproductive sabotage caused by maternally inherited bacterial symbionts of arthropods. CI is a two-step manipulation: first, the symbiont modifies sperm in male hosts which results in the death of fertilized, uninfected embryos. Second, when females are infected with a compatible strain, the symbiont reverses sperm modification in the fertilized egg, allowing offspring of infected females to survive and spread the symbiont to high frequencies in a population. Although CI plays a role in arthropod evolution, the mechanism of CI is unknown for many symbionts. Cardinium hertigii is a common CI-inducing symbiont of arthropods, including parasitoid wasps like Encarsia partenopea. This wasp harbors two Cardinium strains, cEina2 and cEina3, and exhibits strong CI. The strains infect wasps at different densities, with the cEina3 present at a lower density than cEina2, and it was previously not known which strain caused CI. By differentially curing wasps of cEina3, we found that this low-density symbiont is responsible for CI and modifies males during their pupal stage. cEina2 does not modify host reproduction and may spread by 'hitchhiking' with cEina3 CI or by conferring an unknown benefit. The cEina3 strain also shows a unique localization pattern in male reproductive tissues. Instead of infecting sperm like other CI-inducing symbionts, cEina3 cells are found in somatic cells at the testis base and around the seminal vesicle. This may allow the low-density cEina3 to efficiently modify host males and suggests that cEina3 uses a different modification strategy than sperm-infecting CI symbionts.

The life cycle-dependent transcriptional profile of the obligate intracellular amoeba symbiont Amoebophilus asiaticus

Free-living amoebae often harbor obligate intracellular bacterial symbionts. Amoebophilus (A.) asiaticus is a representative of a lineage of amoeba symbionts in the phylum Bacteroidota. Here, we analyse the transcriptome of A. asiaticus strain 5a2 at four time points during its infection cycle and replication within the Acanthamoeba host using RNA sequencing. Our results reveal a dynamic transcriptional landscape throughout different A. asiaticus life cycle stages. Many intracellular bacteria and pathogens utilize eukaryotic-like proteins (ELPs) for host cell interaction and the A. asiaticus 5a2 genome shows a particularly high abundance of ELPs. We show the expression of all genes encoding ELPs and found many ELPs to be differentially expressed. At the replicative stage of A. asiaticus, ankyrin repeat proteins and tetratricopeptide/Sel1-like repeat proteins were upregulated. At the later time points, high expression levels of a type 6 secretion system that likely prepares for a new infection cycle after lysing its host, were found. This study reveals comprehensive insights into the intracellular lifestyle of A. asiaticus and highlights candidate genes for host cell interaction. The results from this study have implications for other intracellular bacteria such as other amoeba-associated bacteria and the arthropod symbionts Cardinium forming the sister lineage of A. asiaticus.

Ewe Vaginal Microbiota: Associations With Pregnancy Outcome and Changes During Gestation

Reproductive performance is paramount to the success of livestock production enterprises focused on lamb meat production. Reproductive success is influenced by various factors, possibly including the reproductive tract microbial communities present at the time of copulation and throughout pregnancy. There are few publications that identify the vaginal microbial communities of livestock, and even fewer exist for sheep. To compare ewe vaginal microbial communities, vaginal swabs were taken from 67 Hampshire and Hampshire X Suffolk crossbred ewes from the Iowa State University sheep farm at a pre-breeding time point (S1) and after pregnancy testing (S2). Animals that were determined pregnant were sampled again within a few days of expected parturition (S3). DNA was extracted from these swabs, and 16S rRNA gene Illumina MiSeq amplicon sequencing was conducted to fingerprint the bacterial communities found within this system. Pre-breeding time point samples showed no differences in community structure between animals later found to be pregnant or non-pregnant, but significant changes were detected in species richness (Chao; P < 0.001) and species diversity (Shannon; P < 0.001) at the second sampling time point. A higher microbial diversity within the S2 time point samples may suggest a more stable environment driven by pregnancy, as this increased diversity is maintained in pregnant animals from the S2 to the S3 time point. Additionally, several bacterial phylotypes, such as Mannheimia, Oscillospiraceae-like OTUs and Alistipes, were more abundant at either the S1 or S2 time points in animals that established pregnancy, suggesting a beneficial effect on pregnancy outcome. This study identifies changes within the microbial communities of the ewe vagina before and during gestation and offers inferences on how these changes may impact pregnancy outcome. Information presented herein offers new knowledge about sheep vaginal microbial communities and serves as a starting point to help guide researchers to improve sheep reproductive performance in the future.

Certain Listeria monocytogenes plasmids contribute to increased UVC ultraviolet light stress

Listeria monocytogenes is the causative agent of the highly fatal foodborne disease listeriosis and can persist in food production environments. Recent research highlights the involvement of L. monocytogenes plasmids in different stress response mechanisms, which contribute to its survival in food production facilities. Ultraviolet (UV) light in the UVC spectrum (200–280 nm) is used in food production to control microbial contamination. Although plasmid-encoded UV resistance mechanisms have been described in other bacteria, no research indicates that L. monocytogenes plasmids contribute to the UV stress response. The plasmids of L. monocytogenes strains 6179, 4KSM and R479a are genetically distinct and were utilized to study the roles of plasmids in the UV response. Wild-type and plasmid-cured variant cells were grown to logarithmic or late-stationary phase, plated on agar plates and exposed to UVC for 60 or 90 s, and colony-forming units (CFUs) were determined. CFUs of 6179 and 4KSM, bearing pLM6179 and p4KSM, respectively, were significantly (P-value < 0.05) higher than those of the plasmid-cured strains in both logarithmic and stationary phases. No difference in survival was observed for the R479a strain. Our data show for the first time that certain L. monocytogenes plasmids contribute to the survival of UVC light stress.

Vaginal microbiota differences associated with pelvic organ prolapse risk during late gestation in commercial sows

During the last decade, sow mortality due to pelvic organ prolapse (POP) has increased. To better understand the biology associated with POP, sows were phenotypically assessed and assigned a perineal score (PS) based on presumed POP risk and categorized as PS1 (low), PS2 (moderate), or PS3 (high). The study objective was to identify changes in sow vaginal microbiota that may be associated with POP. The hypothesis is that vaginal microbiota differs between sows with variable risk for POP, and changes in microbiota during late gestation exist between sows with differing risk. Of the 2864 sows scored during gestation week 15, 1.0, 2.7, and 23.4% of PS1, PS2, and PS3 sows, respectively, subsequently experienced POP. Vaginal swabs subjected to 16S rRNA gene sequencing revealed differences in community composition (Bray–Curtis; P < 0.05) and individual operational taxonomic unit (OTU) comparisons between vaginal microbiota of PS1 and PS3 sows at gestation week 15. Further, differences (P < 0.05) in community composition and OTUs (Q < 0.05) were observed in PS3 sows that either did or did not subsequently experience POP. Differences in community structure (alpha diversity measurements; P < 0.05), composition (P < 0.05), and OTUs (Q < 0.05) were observed in gestation week 12 sows scored PS1 compared to week 15 sows scored PS1 or PS3, suggesting that sow vaginal microbiota shifts during late gestation differently as POP risk changes. Collectively, these data demonstrate that sows with greater POP risk have unique vaginal microflora, for which a better understanding could aid in the development of mitigation strategies.

The Rumen Epithelial Microbiota: Possible Gatekeepers of the Rumen Epithelium and Its Potential Contributions to Epithelial Barrier Function and Animal Health and Performance

Ruminants are characterized by their unique mode of digesting cellulose-rich plant material in their forestomach, the rumen, which is densely populated by diverse microorganisms that are crucial for the breakdown of plant material. Among ruminal microbial communities, the microorganisms in the rumen fluid or attached to feed particles have attracted considerable research interest. However, comparatively less is known about the microorganisms attached to the rumen epithelium. Generally, the tissue lining the gastrointestinal tract serves the dual role of absorbing nutrients while preventing the infiltration of unwanted compounds and molecules as well as microorganisms. The rumen epithelium fulfills critical physiological functions for the ruminant host in energy absorption, metabolism, and nutrient transport. Essential host metabolites, such as short-chain fatty acids, ammonia, urea, and minerals, are exchanged across the rumen wall, thereby exposing the rumen epithelial microbiota to these nutrients. The integrity of the gastrointestinal barrier is central to animal health and productivity. The integrity of the rumen epithelium can be compromised by high ruminal microbial fermentation activity resulting in decreased rumen pH or by stress conditions such as heat stress or feed restriction. It is important to keep in mind that feeding strategies in cattle have changed over the last decades in favor of energy- and nutrient-rich concentrates instead of fiber-rich forages. These dietary shifts support high milk yields and growth rates but raised concerns regarding a possibly compromised rumen function. This paper will provide an overview of the composition of rumen epithelial microbial communities under physiological and disease conditions and will provide insights into the knowledge about the function and in situ activity of rumen epithelial microorganisms and their relevance for animal health and production. Given that an impaired intestinal barrier will negatively affect economically significant phenotypes, a better understanding of rumen wall microbiota is urgently needed.

Xylanase Supplementation Modulates the Microbiota of the Large Intestine of Pigs Fed Corn-Based Fiber by Means of a Stimbiotic Mechanism of Action

This research tested the hypothesis that xylanase modulates microbial communities within the large intestine of growing pigs fed corn-based fiber through a stimbiotic mechanism(s) of action (MOA). Sixty gilts were blocked by initial body weight, individually housed, and randomly assigned to one of four dietary treatments (n = 15): a low-fiber (LF) control, a high-fiber (HF) control containing 30% corn bran, HF+100 mg/kg xylanase (HF+XY), and HF+50 mg/kg arabinoxylan-oligosaccharide (HF+AX). Pigs were fed dietary treatments for 46 days. On day 46, pigs were euthanized, and mucosa and lumen contents were collected from the cecum and the colon. The V4 region of 16S rRNA genes was sequenced and clustered into 5,889, 4,657, 2,822, and 4,516 operational taxonomic units (OTUs), in the cecal contents and mucosa and colonic contents and mucosa, respectively. In cecal contents, HF+XY increased measures of α-diversity compared to LF (p < 0.001). Relative to LF, HF increased the prevalence of 44, 36, 26, and 8, and decreased 19, 9, 21, and 10, of the 200 most abundant OTUs from the cecal contents and mucosa and colonic contents and mucosa, respectively (Q < 0.05). Compared to LF, HF increased the abundance of OTUs from the Treponema_2, Ruminococcus_1 genera, from the Lachnospiraceae, Ruminococcaceae, and Prevotellaceae families. In contrast, relative to LF, HF decreased Turicibacter and Lactobacillus in the cecal contents, and Megasphaera and Streptococcus in the mucosa. Relative to HF, HF+XY increased 32, 16, 29, and 19 and decreased 27, 11, 15, and 10 of the 200 most abundant OTUs from the cecal contents and mucosa and colonic contents and mucosa, respectively (Q < 0.05). The addition of xylanase to HF further increased the abundance of OTUs from the Lachnospiraceae and Ruminococcaceae families across the large intestine. Compared to HF, HF+XY increased the abundance of Lactobacillus, Bifidobacterium, and Faecalibacterium among all locations (Q < 0.05). However, HF+AX did not increase the prevalence of these genera in the large intestine. Supplementing xylanase to HF increased hidden-state predictions of microbial enzymes associated with arabinoxylan degradation, xylose metabolism, and short-chain fatty acid production. These data suggest xylanase elicits a stimbiotic MOA in the large intestine of pigs fed corn-based fiber.

Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets

In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.

A Large-Scale Sequencing-Based Survey of Plasmids in Listeria monocytogenes Reveals Global Dissemination of Plasmids

The food-borne pathogen Listeria monocytogenes is known for its capacity to cope with multiple stress conditions occurring in food and food production environments (FPEs). Plasmids can provide benefits to their host strains, and it is known that various Listeria strains contain plasmids. However, the current understanding of plasmid frequency and function in L. monocytogenes strains remains rather limited. To determine the presence of plasmids among L. monocytogenes strains and their potential contribution to stress survival, a comprehensive dataset was established based on 1,921 published genomes from strains representing 14 L. monocytogenes sequence types (STs). Our results show that an average of 54% of all L. monocytogenes strains in the dataset contained a putative plasmid. The presence of plasmids was highly variable between different STs. While some STs, such as ST1, ST2, and ST4, contained few plasmid-bearing strains (<15% of the strains per ST), other STs, such as ST121, ST5, ST8, ST3, and ST204, possessed a higher proportion of plasmid-bearing strains with plasmids found in >71% of the strains within each ST. Overall, the sizes of plasmids analyzed in this study ranged from 4 to 170 kbp with a median plasmid size of 61 kbp. We also identified two novel groups of putative Listeria plasmids based on the amino acid sequences of the plasmid replication protein, RepA. We show that highly conserved plasmids are shared among Listeria strains which have been isolated from around the world over the last few decades. To investigate the potential roles of plasmids, nine genes related to stress-response were selected for an assessment of their abundance and conservation among L. monocytogenes plasmids. The results demonstrated that these plasmid genes exhibited high sequence conservation but that their presence in plasmids was highly variable. Additionally, we identified a novel transposon, Tn7075, predicted to be involved in mercury-resistance. Here, we provide the largest plasmid survey of L. monocytogenes to date with a comprehensive examination of the distribution of plasmids among L. monocytogenes strains. Our results significantly increase our knowledge about the distribution, composition, and conservation of L. monocytogenes plasmids and suggest that plasmids are likely important for the survival of L. monocytogenes in food and FPEs.

Comparison of intestinal permeability, morphology, and ileal microbial communities of commercial hens housed in conventional cages and cage-free housing systems

The gastrointestinal health of poultry can be impacted by a variety of factors including their environment. As egg production moves from conventional cage housing (CC) toward cage-free housing (CF), it is important to understand this impact on intestinal health. This study was conducted to determine if housing type impacted intestinal permeability, morphology, and microbial communities in commercial hens across housing systems. Hens were randomly selected from 2 rooms of CC (n = 25) and CF (n = 25) at a commercial facility. Birds were given fluorescein isothiocyanate dextran (FITC-D) by oral gavage to measure intestinal permeability. Jejunal and ileal samples were collected to evaluate villus height, crypt depth, and their ratio. Ileal contents were collected for bacterial DNA isolation and 16S rRNA gene sequencing. Serum FITC-D was similar between housing type (P = 0.709). Hens housed in the CF had increased jejunal villus height and crypt depth compared with hens from the CC (P < 0.002). Hens from the CC tended to have a greater villus height to crypt depth ratio in both the jejunum and ileum compared with the CF (P = 0.064; P = 0.091, respectively). Microbial community diversity measurements favored hens housed in the CC as ileal contents tended to have increased species richness (P = 0.059), had greater alpha diversity (P = 0.044), and had an increased number of over represented operational taxonomic units (46/64), including Romboutsia sp. (30.80%), Lactobacillus kitasatonis (17.16%), and Lactobacillus aviarius (11.15%). Correlations between microbial communities with intestinal traits identified significant association with the greatest number of correlations with FITC-D and ileal morphology. Many of these correlations identified microbial communities associated with expected traits; thus, providing limited functional data to microbial communities with limited information. The greater number of correlations of ileal morphology with ileal microbial communities suggesting local microbial communities contribute to the intestinal environment distant. In this limited study, several parameters favored hens from CC suggesting an advantage of this system for intestinal health. However, the lower intestinal health parameters observed in CF were not at levels to indicate detrimental effects.

Xylanase modulates the microbiota of ileal mucosa and digesta of pigs fed corn-based arabinoxylans likely through both a stimbiotic and prebiotic mechanism

The experimental objective was to characterize the impact of insoluble corn-based fiber, xylanase, and an arabinoxylan-oligosaccharide on ileal digesta and mucosa microbiome of pigs. Three replicates of 20 gilts were blocked by initial body weight, individually-housed, and assigned to 1 of 4 dietary treatments: a low-fiber control (LF), a 30% corn bran high-fiber control (HF), HF+100 mg/kg xylanase (HF+XY), and HF+50 mg/kg arabinoxylan oligosaccharide (HF+AX). Gilts were fed their respective treatments for 46 days. On day 46, pigs were euthanized and ileal digesta and mucosa were collected. The V4 region of the 16S rRNA was amplified and sequenced, generating a total of 2,413,572 and 1,739,013 high-quality sequences from the digesta and mucosa, respectively. Sequences were classified into 1,538 mucosa and 2,495 digesta operational taxonomic units (OTU). Hidden-state predictions of 25 enzymes were made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUST2). Compared to LF, HF increased Erysipelotrichaceae_UCG-002, and Turicibacter in the digesta, Lachnospiraceae_unclassified in the mucosa, and decreased Actinobacillus in both (Q<0.05). Relative to HF, HF+XY increased 19 and 14 of the 100 most abundant OTUs characterized from digesta and mucosa, respectively (Q<0.05). Notably, HF+XY increased the OTU_23_Faecalibacterium by nearly 6 log2-fold change, compared to HF. Relative to HF, HF+XY increased genera Bifidobacterium, and Lactobacillus, and decreased Streptococcus and Turicibacter in digesta (Q<0.05), and increased Bifidobacterium and decreased Escherichia-Shigella in the mucosa (Q<0.05). Compared to HF, HF+AX increased 5 and 6 of the 100 most abundant OTUs characterized from digesta and mucosa, respectively, (Q<0.05), but HF+AX did not modulate similar taxa as HF+XY. The PICRUST2 predictions revealed HF+XY increased gene-predictions for enzymes associated with arabinoxylan degradation and xylose metabolism in the digesta, and increased enzymes related to short-chain fatty acid production in the mucosa. Collectively, these data suggest xylanase elicits a stimbiotic and prebiotic mechanism.

Cardinium Localization During Its Parasitoid Wasp Host's Development Provides Insights Into Cytoplasmic Incompatibility

Arthropods harbor heritable intracellular symbionts that may manipulate host reproduction to favor symbiont transmission. In cytoplasmic incompatibility (CI), the symbiont sabotages the reproduction of infected males such that high levels of offspring mortality result when they mate with uninfected females. In crosses with infected males and infected females, however (the “rescue” cross), normal numbers of offspring are produced. A common CI-inducing symbiont, Cardinium hertigii, causes variable levels of CI mortality in the parasitoid wasp, Encarsia suzannae. Previous work correlated CI-induced mortality with male development time in this system, although the timing of Cardinium CI-induction and the relationship between development time and CI mortality was not well understood. Here, using a combination of crosses, manipulation of development time, and fluorescence microscopy, we identify the localization and the timing of the CI-induction step in the Cardinium-E. suzannae system. Antibiotic treatment of adult Cardinium-infected males did not reduce the mortality associated with the CI phenotype, suggesting that CI-alteration occurs prior to adulthood. Our results suggest that the alteration step occurs during the pupal period, and is limited by the duration of pupal development: 1) Encarsia produces most sperm prior to adulthood, 2) FISH localization of Cardinium in testes showed an association with sperm nuclei throughout spermatogenesis but not with mature sperm, and 3) two methods of prolonging the pupal period (cool temperatures and the juvenile hormone analog methoprene) both caused greater CI mortality, suggesting the degree of alteration is limited by the duration of the pupal stage. Based on these results, we compare two models for potential mechanisms of Cardinium sperm modification in the context of what is known about analogous mechanisms of Wolbachia, a more extensively studied CI-inducing symbiont.

High-Fat Diets Led to OTU-Level Shifts in Fecal Samples of Healthy Adult Dogs

High fat diets have been reported to negatively affect the microbiota in both mice and humans. However, there is a lack of studies in canine models. The variation among the gastrointestinal (GI) tract anatomy/physiology and typical diet compositions of these animal species may lead to vastly different results. Due to the large inclusion rate of dietary fat in pet food, it is critical to understand its effects in a canine model. Therefore, the study objective was to report the effects of high fat, low carbohydrate diets on the fecal microbiota in healthy adult dogs. Eight adult beagles were randomly assigned to one of four dietary treatments within each 15-day period of a replicated 4x4 Latin Square design. Diets contained 32% (T1), 37% (T2), 42% (T3), and 47% (T4) fat. T2, T3, and T4 were created by adding increasing levels of canola oil to T1, a commercially manufactured canned canine diet, which served as the control diet. Fresh fecal samples were collected during the last 5 days of each period for microbial analysis. DNA was extracted from fecal samples and paired-end 16S rRNA gene amplicon sequencing was performed using the Illumina MiSeq platform. When comparing whole microbial communities using PERMANOVA, no significant differences were observed among treatments (P = 0.735). Individual OTUs were analyzed using the GLIMMIX procedure of SAS with fixed effects of diet and room, and the random effects of period and animal. Out of the 100 most abundant individual OTUs, 36 showed significant differences in abundance based on treatment (q < 0.05). Overall, OTUs assigned to genera related to fat digestion increased while OTUs assigned to genera involved in carbohydrate digestion decreased. In conclusion, the microbial community adapted to dietary intervention without jeopardizing the health of the animals, evaluated by body condition score, fecal characteristics, and blood parameters.

PSVIII-3 Can the fermentation of insoluble corn fiber be improved in the pig? – An investigation into the in vivo mode of action of xylanase

Xylanase may improve fermentability of corn co-products through the alteration of hemicellulose, but the mode of action (MOA) is incompletely understood. The experimental objective was to investigate the in vivo MOA of xylanase in growing pigs fed insoluble fiber. Sixty gilts (25.4 ± 0.9 kg BW; L337 X Camborough), were blocked by weight, housed individually, and randomly assigned to one of four dietary treatments: a low-fiber control (LF; 8.45% NDF), a 30% corn bran high-fiber control (HF; 24.5% NDF), HF + 100 mg of xylanase/kg (HF+XY; Econase XT 25P; AB Vista, Marlborough, UK), and HF + 50 mg of arabinoxylan-oligosaccharide/kg (HF+AX; 3-7 degrees of polymerization). Gilts were fed ad libitum for 36 d, followed by 10-d of metabolism crate housing and limit feeding (80% of average ad libitum intake). On d 46, pigs were necropsied and ileal, cecal, and colonic digesta were collected for short-chain fatty acid (SCFA) analysis, and 16s rRNA gene amplicon sequencing. Data were analyzed as a mixed model with random effects of replicate and block, and fixed effect of treatment. Differences in individual operational taxonomic units (OTUs) were compared using Linear Discriminant Analysis Effect Size. Acetate, propionate, butyrate, and total SCFA in the ileum did not differ (P &gt;0.05), but HF+XY had 10 significantly different OTUs compared to HF in the ileum (P&lt; 0.05). In the cecum, compared to LF, HF reduced total SCFA concentration (91.7 vs. 82.8 mM/L; P&lt; 0.01). However, HF+XY and HF+AX increased total SCFA concentration by 23% and 12% over HF, respectively (P&lt; 0.05). This is likely due to increased cecal acetate concentration (54.0, 53.2, 74.4, 61.2 mM/L for LF, HF, HF+XY, and HF+AX, respectively; P&lt; 0.01). Total colonic SCFA concentration did not differ (P=0.72), but xylanase increased molar proportions of butyrate (P&lt; 0.01). One MOA of xylanase could be the release of fermentable substrates from insoluble fiber.

20 Vaginal microbiome composition is associated with sow longevity

The vaginal microbiome of gilts vaccinated for porcine reproductive and respiratory syndrome (PRRS) has been previously associated with first-parity reproductive performance in absence of PRRS outbreak. However, associations using multiparous sows have not been investigated. The objective of this study was to associate the vaginal microbiota of PRRS-vaccinated gilts with longevity. Vaginal swabs from 251 commercial F1 gilts (Landrace/Large-White) were collected on days 4 and 52 after PRRS vaccination (dpv) for 16S rRNA sequencing. Sequences were clustered into operational taxonomic unit (OTU). Sows were assigned to one of four groups according to the maximum parity reached (number of animals): without parity (13), first-parity (45), second-parity (47), and 3 or more parities (146). A negative binomial mixed model including fixed effects of group, dpv, group*dpv, and collection age (covariate), and random effect of animal, was used to identify OTUs with differential abundance. The false discovery rate method was used for multiple test correction. Canonical discriminant analysis (CDA) was performed to classify animals into the four parity groups by including significant OTUs in stepwise selection (P &lt; 0.05) using the whole data. A leave-one-out-cross-validation was used to assess the predictive ability of OTUs to correctly classify animals into the parity groups. Abundance of five and four OTUs was associated (q &lt; 0.05) with group and with group*dpv (q &lt; 0.05), respectively. In the CDA analysis, 220 OTUs identified in the vaginal microbiome were included (P &lt; 0.05). The first and second canonical variables explained 96.6 and 3.4% of the variation, respectively. All animals were correctly classified into their respective parity groups. This study indicates that the vaginal microbiome composition of gilts collected after PRRS-vaccination may be used to predict longevity in commercial sow herds. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brazil (Capes) – Finance Code 001.

The Cobalamin-Dependent Gene Cluster of Listeria monocytogenes: Implications for Virulence, Stress Response, and Food Safety

Several genes of the eut, pdu, and cob/cbi operons are responsible for the metabolism of ethanolamine (EA) and 1,2-propanediol (PD) and are essential during the pathogenic lifecycles of various enteric pathogens. Studies concerning EA and PD metabolism have primarily focused on bacterial genera from the family Enterobacteriaceae, especially the genus Salmonella. Listeria monocytogenes is a member of the Firmicutes phylum and is the causative agent of the rare but highly fatal foodborne disease listeriosis. The eut, pdu, and cob/cbi operons are organized as a single large locus collectively referred to as the cobalamin-dependent gene cluster (CDGC). The CDGC is well conserved in L. monocytogenes; however, functional characterization of the genes in this cluster and how they may contribute to Listeria virulence and stress tolerance in food production environments is highly limited. Previous work suggests that the degradation pathway of PD is essential for L. monocytogenes establishment in the gastrointestinal tract. In contrast, EA metabolism may be more important during intracellular replication. Other studies indicate that the CDGC is utilized when L. monocytogenes is exposed to food and food production relevant stress conditions. Perhaps most noteworthy, L. monocytogenes exhibits attenuated growth at cold temperatures when a key EA utilization pathway gene was deleted. This review aims to summarize the current knowledge of these pathways in L. monocytogenes and their significance in virulence and stress tolerance, especially considering recent developments.

Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota

Tall fescue (Lolium arundinaceum) is a widely used forage grass which shares a symbiosis with the endophytic fungus Epichloë coenophiala. The endophyte produces an alkaloid toxin that provides herbivory, heat and drought resistance to the grass, but can cause fescue toxicosis in grazing livestock. Fescue toxicosis can lead to reduced weight gain and milk yields resulting in significant losses to the livestock industry. The objective of this study was to identify bacterial and fungal communities associated with fescue toxicosis tolerance. In this trial, 149 Angus cows across two farms were continuously exposed to toxic, endophyte-infected, fescue for a total of 13 weeks. Of those 149 cows, 40 were classified into either high (HT) or low (LT) tolerance groups according to their growth performance (weight gain). 20 HT and 20 LT cattle balanced by farm were selected for amplicon sequencing to compare the fecal microbiota of the two tolerance groups. This study reveals significantly (q<0.05) different bacterial and fungal microbiota between HT and LT cattle, and indicates that fungal phylotypes may be important for an animal’s response to fescue toxicosis: We found that fungal phylotypes affiliating to the Neocallimastigaceae, which are known to be important fiber-degrading fungi, were consistently more abundant in the HT cattle. Whereas fungal phylotypes related to the genus Thelebolus were more abundant in the LT cattle. This study also found more pronounced shifts in the microbiota in animals receiving higher amounts of the toxin. We identified fungal phylotypes which were consistently more abundant either in HT or LT cattle and may thus be associated with the respective animal’s response to fescue toxicosis. Our results thus suggest that some fungal phylotypes might be involved in mitigating fescue toxicosis.

Host immunity and the colon microbiota of mice infected with Citrobacter rodentium are beneficially modulated by lipid-soluble extract from late-cutting alfalfa in the early stages of infection

Alfalfa is a forage legume commonly associated with ruminant livestock production that may be a potential source of health-promoting phytochemicals. Anecdotal evidence from producers suggests that later cuttings of alfalfa may be more beneficial to non-ruminants; however, published literature varies greatly in measured outcomes, supplement form, and cutting. The objective of this study was to measure body weight, average daily feed intake, host immunity, and the colon microbiota composition in mice fed hay, aqueous, and chloroform extracts of early (1^st) and late (5^th) cutting alfalfa before and after challenge with Citrobacter rodentium. Prior to inoculation, alfalfa supplementation did not have a significant impact on body weight or feed intake, but 5^th cutting alfalfa was shown to improve body weight at 5- and 6-days post-infection compared to 1^st cutting alfalfa (P = 0.02 and 0.01). Combined with the observation that both chloroform extracts improved mouse body weight compared to control diets in later stages of C. rodentium infection led to detailed analyses of the immune system and colon microbiota in mice fed 1^st and 5^th cutting chloroform extracts. Immediately following inoculation, 5^th cutting chloroform extracts significantly reduced the relative abundance of C. rodentium (P = 0.02) and did not display the early lymphocyte recruitment observed in 1^st cutting extract. In later timepoints, both chloroform extracts maintained lower splenic B-cell and macrophage populations while increasing the relative abundance of potentially beneficially genera such as Turicibacter (P = 0.02). At 21dpi, only 5^th cutting chloroform extracts increased the relative abundance of beneficial Akkermansia compared to the control diet (P = 0.02). These results suggest that lipid soluble compounds enriched in late-cutting alfalfa modulate pathogen colonization and early immune responses to Citrobacter rodentium, contributing to protective effects on body weight.

Beginning to offer drinking water at birth increases the species richness and the abundance of Faecalibacterium and Bifidobacterium in the gut of preweaned dairy calves

We previously demonstrated that dairy calves having access to drinking water since birth (W0) achieved greater body weight, fiber digestibility, and feed efficiency than those that first received drinking water at 17 d of age (W17). Since gut microbiota composition could be linked to growth and development of animals, the objective of this study was to examine the effect of offering drinking water to newborn calves on composition of bacteria in the gut using a fecal microbiota analysis. Fresh feces were collected directly from the rectum of calves in W0 (n = 14) and W17 (n = 15) at 2, 6, and 10 wk of age. All of the calves were fed pasteurized waste milk, weaned at 7 wk of age, and offered tap water according to the treatment. The DNA was sequenced using 16S rRNA gene-amplicon sequencing on an Illumina MiSeq system (Illumina Inc., San Diego, CA). The sequences were clustered into operational taxonomic units (OTU) with a 99% similarity threshold. Treatment effects on α-diversity indices and relative abundance of the 10 most abundant genera were analyzed using GLIMMIX procedure of SAS (SAS Institute Inc., Cary, NC). Statistical significance (q-value) of treatment effects on the 50 most abundant OTU was determined with a false discovery rate analysis. At 2 wk of age, W0 had a greater number of observed OTU (5,908 vs. 4,698) and species richness (Chao 1 index) than W17. The number of OTU and richness indices increased from wk 2 to 6, but the increment of W17 was greater than that of W0. The Shannon and inverse-Simpson indices increased linearly with age, but no difference was observed between W0 and W17 at any time point. The Firmicutes to Bacteroidetes ratios were also similar at every time point but decreased markedly when calves were weaned. The relative abundance of genera Faecalibacterium and Bacteroides was greater in W0 than W17 at 2 wk of age. The genus Faecalibacterium continued to be more abundant in W0 than W17 at 6 wk of age but had similar abundance 3 wk after weaning (10 wk of age). The abundance of Faecalibacterium at wk 6 was positively correlated with apparent total-tract digestibility of acid detergent fiber at 10 wk of age. Calves receiving water since birth had greater abundance of OTU related to Faecalibacterium prausnitzii, and Bifidobacterium breve at 6 wk of age (q < 0.085). These species are known to improve growth in preweaned calves. The abundance of none of the genera and OTU was different between W0 at W17 at 10 wk of age (q > 0.100). Overall, beginning to offer drinking water at birth has a potential to modulate gut microbiota composition and thereby positively affect performance of young dairy heifer calves (≤10 wk of age).

Transcriptome Sequencing of Listeria monocytogenes Reveals Major Gene Expression Changes in Response to Lactic Acid Stress Exposure but a Less Pronounced Response to Oxidative Stress

Listeria monocytogenes is a well-characterized pathogen that represents a major threat to food safety. In this study, we examine the chromosomal and plasmid transcriptomes of two different L. monocytogenes strains, 6179 [belonging to sequence type (ST) 121] and R479a (ST8), in response to 30 min exposure to oxidative (0.01% hydrogen peroxide) and acid (1% lactic acid, pH 3.4) stress. The exposure to oxidative stress resulted in 102 and 9 differentially expressed (DE) genes in the chromosomal transcriptomes of 6179 and R479a, respectively. In contrast, 2280 and 2151 DE genes were observed in the respective chromosomal transcriptomes of 6179 and R479a in response to lactic acid stress. During lactic acid stress, we observed upregulation of numerous genes known to be involved in the L. monocytogenes stress response, including multiple members of the σ^B regulon, many of which have not been functionally characterized. Among these genes, homologs of lmo2230 were highly upregulated in both strains. Most notably, the σ^B-dependent non-coding RNA Rli47 was by far the most highly expressed gene in both 6179 and R479a, accounting for an average of 28 and 38% of all mapped reads in the respective chromosomal transcriptomes. In response to oxidative stress, one DE gene was identified in the 6179 plasmid transcriptome, and no DE genes were observed in the transcriptome of the R479a plasmid. However, lactic acid exposure resulted in upregulation of the stress response gene clpL, among others, on the 6179 plasmid. In R479a, a number of uncharacterized plasmid genes were upregulated, indicating a potential role in stress response. Furthermore, an average of 65% of all mapped transcriptome reads for the R479a plasmid following acid stress were mapped to an intergenic region bearing similarity to riboswitches involved in transition metal resistance. The results of this study support the conclusion that members of the σ^B regulon, particularly lmo2230 and the non-coding RNA Rli47, play an integral role in the response of L. monocytogenes to acid stress. Furthermore, we report the first global transcriptome sequencing analysis of L. monocytogenes plasmid gene expression and identify a putative, plasmid-encoded riboswitch with potential involvement in response to acid exposure.

69 The ability of an artificial sweetener (Sucram®) to influence microbial community structure in the rumen papillae and content through the production of microbial-based neurochemicals

The study of microorganisms to produce and utilize neurochemical signaling molecules that interact with the host is the emerging field known as microbial endocrinology. Production of these molecules can be regulated by several different environmental factors, including diet. The effect of artificial sweeteners on ruminant gastrointestinal tract microbiota and the ability of individual members to produce neurochemicals that may determine community composition and affect host physiology are unknown. To analyze whether an artificial sweetener (Sucram®, Pancosma, Switzerland) affects rumen content (RC) and rumen papillae (RP) microbiota, six fistulated, lactating Holstein cows were sampled before (baseline) and after exposure to Sucram®. 16S rRNA gene sequencing was conducted to identify Sucram®-induced microbial community changes. Additionally, ex vivo microbial cultures were used to identify neurochemical production in RP bacteria. Exposure to Sucram significantly increased the abundance of Operational Taxonomic Units (OTUs) belonging to Ruminobacter, Prevotella, Sharpea, Ruminococcus and Rikenella on the RP. These organisms have been reported to aid in digestion of feedstuffs and methane reduction, suggesting that Sucram® may induce beneficial shifts in rumen microbial communities. To gain preliminary insight into neurochemical production of RP microorganisms, we tested four different Lactobacillus isolates from RP for neurochemical production. We observed that the neurochemicals DOPAC (3,4-Dihydroxyphenylacetic acid) and L-DOPA (L-3,4-dihydroxyphenylalanine) were produced by three and four isolates, respectively. Ongoing experiments are evaluating the effects of Sucram® on neurochemical production in a larger number of rumen microbes. Overall, we observed significant differences in OTU abundance in response to the addition of Sucram®. Additionally, we confirmed that RP bacteria can produce neurochemicals. Both of these results are key to understanding how Sucram® modifies microbial communities within the rumen and possibly influences host physiology. Research into microbial endocrinology-based neurochemical signaling between rumen microbiota and their animal hosts may lead to advancement of livestock feed efficiency and welfare.

219 Relationship between host-genetics and the vaginal microbiome in commercial gilts

The objective of this study was to investigate host-genetic contributions to the vaginal microbiome of commercial gilts vaccinated for Porcine Reproductive and Respiratory Syndrome (PRRS). Vaginal swab samples (n = 576) from 308 F1 gilts (183±12 days old) were collected on day 4 (D4) and 52 (D52) post-vaccination with a commercial modified live virus PRRS vaccine. Samples were used to profile the vaginal microbiome by 16S rRNA gene sequencing, with sequences clustered into operational taxonomic units (OTUs) and taxonomically classified. All animals were genotyped for 45,536 SNPs. Arcsine of the square root-transformed OTUs abundance data were analyzed using a linear mixed animal model with age at vaccination as a covariate and animal (random) for estimation of genetic parameters. The same model was used for GWAS for the 100 most abundant OTUs but with addition of genotype of SNPs as a covariate, one at a time. For D4, heritability estimates ranged from &lt; 0.001±0.01(13 OTUs) to 0.60±0.13 (Fusobacterium), with OTUs corresponding to the genera Fusobacterium, Pasteurellaceae, Clostridiales, Prevotellaceae, and Lactobacillus having high estimates (0.41±0.13 to 0.60±0.13). For D52, heritability estimates ranged from &lt; 0.001±0.01 (10 OTUs) to 0.63±0.12 (Terrisporobacter), with OTUs corresponding to Clostridium, Terrisporobacter, Romboutsia, Turicibacter, Phascolarctobacterium, Muribaculaceae, and Ruminococcaceae having high estimates (0.42±0.14 to 0.63±0.12). Forty-six QTLs were significantly (P &lt; 0.00001) associated with OTU across days. Among these, one main QTL on chromosome 12 (20–23Mb), a gene-rich region with previously identified QTL for immune-related traits, was identified for 5 and 6 OTUs on D4 and D52, respectively. These OTUs were mainly of the phyla Proteobacteria and Firmicutes on D4 and D52, respectively. In conclusion, there is evidence of substantial host genetic variation for vaginal microbiome in commercial PRRS-vaccinated gilts, including the identification of many QTLs. Additional research is needed to investigate the genetic relationship between vaginal microbiome, health, and production in pigs.

Development of a multi-locus sequence typing system helps reveal the evolution of Cardinium hertigii, a reproductive manipulator symbiont of insects

Background

Cardinium is an intracellular bacterial symbiont in the phylum Bacteroidetes that is found in many different species of arthropods and some nematodes. This symbiont is known to be able to induce three reproductive manipulation phenotypes, including cytoplasmic incompatibility. Placing individual strains of Cardinium within a larger evolutionary context has been challenging because only two, relatively slowly evolving genes, 16S rRNA gene and Gyrase B, have been used to generate phylogenetic trees, and consequently, the relationship of different strains has been elucidated in only its roughest form.

Results

We developed a Multi Locus Sequence Typing (MLST) system that provides researchers with three new genes in addition to Gyrase B for inferring phylogenies and delineating Cardinium strains. From our Cardinium phylogeny, we confirmed the presence of a new group D, a Cardinium clade that resides in the arachnid order harvestmen (Opiliones). Many Cardinium clades appear to display a high degree of host affinity, while some show evidence of host shifts to phylogenetically distant hosts, likely associated with ecological opportunity. Like the unrelated reproductive manipulator Wolbachia, the Cardinium phylogeny also shows no clear phylogenetic signal associated with particular reproductive manipulations.

Conclusions

The Cardinium phylogeny shows evidence of diversification within particular host lineages, and also of host shifts among trophic levels within parasitoid-host communities. Like Wolbachia, the relatedness of Cardinium strains does not necessarily predict their reproductive phenotypes. Lastly, the genetic tools proposed in this study may help future authors to characterize new strains and add to our understanding of Cardinium evolution.

Investigating the relationship between vaginal microbiota and host genetics and their impact on immune response and farrowing traits in commercial gilts

Our objectives were to evaluate the interaction between host genetics and vaginal microbiota and their relationships with antibody (Ab) response to porcine reproductive and respiratory syndrome virus (PRRSV) vaccination and farrowing performance in commercial gilts. The farrowing performance traits were number born alive, number weaning (NW), total number born, number born dead, stillborn, mummies and preweaning mortality (PWM). The vaginal microbiota was collected on days 4 (D4) and 52 (D52) after vaccination for PRRSV. Blood samples were collected on D52 for Ab measurement. Actinobacteria, Bacterioidetes, Firmicutes, Proteobacteria and Tenericutes were the most abundant Phyla identified in the vaginal microbiota. Heritability ranged from ~0 to 0.60 (Fusobacterium) on D4 and from ~0 to 0.63 (Terrisporobacter) on D52, with 43 operational taxonomic units (OTUs) presenting moderate to high heritability. One major QTL on chromosome 12 was identified for 5 OTUs (Clostridiales, Acinetobacter, Ruminococcaceae, Campylobacter and Anaerococcus), among other 19 QTL. The microbiability for Ab response to PRRSV vaccination was low for both days (<0.07). For farrowing performance, microbiability varied from <0.001 to 0.15 (NW on D4). For NW and PWM, the microbiability was greater than the heritability estimates. Actinobacillus, Streptococcus, Campylobacter, Anaerococcus, Mollicutes, Peptostreptococcus, Treponema and Fusobacterium showed different abundance between low and high Ab responders. Finally, canonical discriminant analyses revealed that vaginal microbiota was able to classify gilts in high and low Ab responders to PRRSV vaccination with a misclassification rate of <0.02. Although the microbiota explained limited variation in Ab response and farrowing performance traits, there is still potential to explore the use of vaginal microbiota to explain variation in traits such as NW and PWM. In addition, these results revealed that there is a partial control of host genetic over vaginal microbiota, suggesting a possibility for genetic selection on the vaginal microbiota.

Microbiota of newborn calves and their mothers reveals possible transfer routes for newborn calves' gastrointestinal microbiota

The intestinal microbiota of newborns plays an important role in the development of immunity and metabolism. In livestock animals, knowledge of the intestinal microbiota is essential not only to prevent diseases but also to optimize weight gain and performance. The aim of our study was to examine faecal samples repeatedly within the first two days of life using 16S rRNA gene High Throughput Sequencing. Additionally, samples from the mouths of the calves and the vaginas, colostrum, and faeces of the dams were included to evaluate possible sources of the calf faecal microbiota. The calf faecal microbiota was highly variable during the first 48 hours post natum (p.n.). Significant changes were found in species diversity and richness, in copy numbers evaluated by qPCR and in predominant bacteria over time. The most pronounced changes occurred between 6 and 24 hours p.n. All calf faecal samples were dominated by Operational Taxonomic Units (OTUs) belonging to the family Enterobacteriaceae. Cow faecal samples showed significantly higher species richness, diversity, number of observed OTUs, and copy numbers compared to all other samples. OTUs belonging to the family Ruminococcaceae were most abundant in cow faecal and vaginal samples. Colostrum was dominated by Enhydrobacter affiliated OTUs. To identify possible inoculation routes for the calf microbiota, we analysed OTU sharing between samples. The calf microbiota during the first two days of life was clearly distinct from the dam's faecal microbiota. Furthermore, colostrum microbiota clearly differed from calf and cow faecal microbiota and thus most likely does not play an important role as inoculation source for calf microbiota during the first two days of life. In contrast, the cow vaginal and the calf faecal microbiota were more similar, suggesting that some of the calf faecal microbiota may derive from inoculation from the birth canal during birth.

130 Young Scholar Presentation: Can exogenous carbohydrase supplementation to higher-fiber diets improve gut function, microbiota, and growth performance of weaned pigs?

There is increasing interest in feeding higher-fiber coproducts to weaned pigs due to their potential benefits on gut function and microbiota. However, young pigs are not efficient at utilizing fibrous coproducts. Exogenous carbohydrases can be used to improve nutrient utilization and growth of pigs fed higher levels of coproducts. Previous results regarding the impact of carbohydrases on performance in pigs have been inconsistent, thus a better understanding of associated mechanisms is needed. Using 460 weaned pigs (6.4 ± 0.1 kg), our first study showed that a carbohydrase enzyme blend (EB) improved ADG of weaned pigs fed higher-fiber diets (with added DDGS and wheat middlings) over a 28-d experimental period (P < 0.05). Pigs fed EB-supplemented diets had lower urinary lactulose:mannitol ratio, decreased plasma IL-8 concentration, and greater ileal CLDN3 (claudin 3) mRNA abundance, compared with those fed diets without EB (P < 0.05). These changes may partly explain the improved growth, providing mode of action evidence for carbohydrase in improving performance of weaned pigs. Carbohydrases may also exert prebiotic effects through release of oligosaccharides from fiber degradation. Thus, carbohydrases and dietary fiber may improve disease resilience of young pigs against bacterial infections, for example, enterotoxigenic Escherichia coli (ETEC) induced post-weaning diarrhea. Our second study evaluated the impact of soluble versus insoluble fiber with or without carbohydrases in newly weaned pigs (n = 60; 6.9 ± 0.07 kg) challenged with F18 ETEC. A diet containing a soluble and highly fermentable fiber from sugar beet pulp with added carbohydrases improved (P < 0.05) ADG, tended to increase (P < 0.10) ileal OCLN (occludin) mRNA, increased (P < 0.05) colonic OCLN mRNA, and tended to decrease (P < 0.10) ileal Escherichia-Shigella compared with ETEC-challenged control. Collectively, appropriate use of exogenous carbohydrases in higher-fiber diets (with the right type and amount of enzyme substrate) is promising in improving gut health and growth performance in weaned pigs.

PSII-16 Evidence for stratification of rumen wall microbial communities revealed by 16S rRNA based amplicon sequencing

Rumen content (RC) stratifies based on particle size and density consisting of the less dense forage within the dorsal and the denser particles in the ventral portions of the rumen and is in constant contact with the microbial communities present on the rumen wall (RW) epithelium. Little is known about the nutrient requirements and functional processes of RW microbial communities. Our hypothesis is that the RW microbial communities stratify mirroring the stratification of RC due to different available nutrients. Five fistulated, milking Holstein cows of the same management conditions were sampled at four rumen layers corresponding to the RC stratification. Epithelial biopsies were taken through the fistula; the uppermost aligned with the dorsal portion of the RC (A), and three other sites, each 10 cm ventral to the previous (B, C and D). Each cow and stratification layer was sampled five times over four months to analyze temporal stability of the RW microbial communities. DNA was extracted using the Qiagen Powerlyzer Powersoil kit and used for 16S rRNA gene Illumina MiSeq sequencing. Sequences were clustered into operational taxonomic units (OTU) based on a 99% similarity cutoff using MOTHUR. After quality control, 2.0 million reads remained for 90 samples which were clustered into 5,016 OTUs with 10 or more reads. 99.2% of the reads were bacterial, whereas 0.8% affiliated to Archaea. Statistical analysis revealed that among the 20 most abundant OTUs, phylotypes classified as Desulfobulbus, unclassified_Cardiobacteraceae, Mogibacterium, Lachnospiraceae-UCG008 and Methanobrevibacter were significantly different in abundance between sites A compared to D. On a whole community level, analysis of molecular variance (AMOVA) revealed significant differences between groups A, C and D. Our data reveal first evidence that a stratification of RW microbiota is present in dairy cattle and also reveal high temporal stability of RW microbiota.

77 Responses to alfalfa supplementation in mice

Anecdotal evidence suggests health benefits from feeding late cutting alfalfa to non-ruminants, but there is a lack of published literature to support these claims. The objective was to compare early (1st) and late (5th) cutting alfalfa as ground hay, aqueous, or chloroform-extracted hay in combination with a gastrointestinal challenge to understand the effect of supplementation form and cutting on the overall health, microbiome, and immune system of mice. 163 C57BL/6J mice were housed for 35 d (Innovive system; 2–4 mice/cage) and fed treatments that consisted of an 18% protein rodent diet (alfalfa-free control), or control supplemented with 1st or 5th cutting 9% ground alfalfa hay, 0.25% aqueous extract (AAE), or 0.25% chloroform extract (CAE). After a 14 d enrichment period, 6 mice/treatment were euthanized for baseline tissue and digesta sampling, and remaining mice were orally gavaged with 2x1010 CFU Citrobacter rodentium. On d18, 22, 28, and 35, 4 mice/treatment were euthanized for sampling. Body weight (BW) and feed intake (FI) were recorded, 13 serum cytokines were measured, and changes in the microbial communities were analyzed using 16S rRNA amplicon sequencing. Data were analyzed using PROC MIXED and linear discrimination analysis effect size (LEfSe), with significance at P ≤ 0.05. No BW differences were observed between treatments at the key timepoints (P > 0.05). Mice fed hay diets ate 16% more per day during the enrichment period (P = 0.03), 19% more from d14–18 (P = 0.001), and 17% more from d18–22 (P = 0.03) versus mice fed AAE. Citrobacter rodentium infection was confirmed via MiSeq in colon digesta. Significant shifts in microbial taxa were observed in mice fed alfalfa hay regardless of cutting (P < 0.05). Cytokine analysis, flow cytometry, and microbiome analysis is ongoing. Preliminary results show that alfalfa form significantly impacts FI and microbiome while cutting impacts weight (P < 0.05).

Brevibacterium from Austrian hard cheese harbor a putative histamine catabolism pathway and a plasmid for adaptation to the cheese environment

The genus Brevibacterium harbors many members important for cheese ripening. We performed real-time quantitative PCR (qPCR) to determine the abundance of Brevibacterium on rinds of Vorarlberger Bergkäse, an Austrian artisanal washed-rind hard cheese, over 160 days of ripening. Our results show that Brevibacterium are abundant on Vorarlberger Bergkäse rinds throughout the ripening time. To elucidate the impact of Brevibacterium on cheese production, we analysed the genomes of three cheese rind isolates, L261, S111, and S22. L261 belongs to Brevibacterium aurantiacum, whereas S111 and S22 represent novel species within the genus Brevibacterium based on 16S rRNA gene similarity and average nucleotide identity. Our comparative genomic analysis showed that important cheese ripening enzymes are conserved among the genus Brevibacterium. Strain S22 harbors a 22 kb circular plasmid which encodes putative iron and hydroxymethylpyrimidine/thiamine transporters. Histamine formation in fermented foods can cause histamine intoxication. We revealed the presence of a putative metabolic pathway for histamine degradation. Growth experiments showed that the three Brevibacterium strains can utilize histamine as the sole carbon source. The capability to utilize histamine, possibly encoded by the putative histamine degradation pathway, highlights the importance of Brevibacterium as key cheese ripening cultures beyond their contribution to cheese flavor production.

Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs

Microorganisms are translocated from the gut to lymphatic tissues via immune cells, thereby challenging and training the mammalian immune system. Antibiotics alter the gut microbiome and consecutively might also affect the corresponding translocation processes, resulting in an imbalanced state between the intestinal microbiota and the host. Hence, understanding the variant effects of antibiotics on the microbiome of gut-associated tissues is of vital importance for maintaining metabolic homeostasis and animal health. In the present study, we analyzed the microbiome of (i) pig feces, ileum, and ileocecal lymph nodes under the influence of antibiotics (Linco-Spectin and Colistin sulfate) using 16S rRNA gene sequencing for high-resolution community profiling and (ii) ileocecal lymph nodes in more detail with two additional methodological approaches, i.e., cultivation of ileocecal lymph node samples and (iii) metatranscriptome sequencing of a single lymph node sample. Supplementation of medicated feed showed a local effect on feces and ileal mucosa-associated microbiomes. Pigs that received antibiotics harbored significantly reduced amounts of segmented filamentous bacteria (SFB) along the ileal mucosa (p = 0.048; 199.17-fold change) and increased amounts of Methanobrevibacter, a methanogenic Euryarchaeote in fecal samples (p = 0.005; 20.17-fold change) compared to the control group. Analysis of the porcine ileocecal lymph node microbiome exposed large differences between the viable and the dead fraction of microorganisms and the microbiome was altered to a lesser extent by antibiotics compared with feces and ileum. The core microbiome of lymph nodes was constituted mainly of Proteobacteria. RNA-sequencing of a single lymph node sample unveiled transcripts responsible for amino acid and carbohydrate metabolism as well as protein turnover, DNA replication and signal transduction. The study presented here is the first comparative study of microbial communities in feces, ileum, and its associated ileocecal lymph nodes. In each analyzed site, we identified specific phylotypes susceptible to antibiotic treatment that can have profound impacts on the host physiological and immunological state, or even on global biogeochemical cycles. Our results indicate that pathogenic bacteria, e.g., enteropathogenic Escherichia coli, could escape antibiotic treatment by translocating to lymph nodes. In general ileocecal lymph nodes harbor a more diverse and active community of microorganisms than previously assumed.