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.

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.

The objective was to determine the impact of feeding MCE on ruminal and intestinal morphology and microbiota composition of calves. A total of 10 male and 10 female crossbred (dairy × beef) calves (6 d of age) were assigned randomly to control (CTL; n = 10) or MCE-supplemented (TRT; n = 10) groups. The MCE was fed in the milk replacer and top-dressed on the calf starter during pre-weaning (6 to 49 d) and post-weaning (50 to 95 d) periods, respectively. Calves were slaughtered at 95 d to collect rumen and intestinal samples to determine volatile fatty acid (VFA) profile, mucosal morphology, and microbiota composition. The effects of MCE were analyzed by accounting for the sex and breed effects. Feeding MCE increased rumen papillae length (p = 0.010) and intestinal villus height: crypt depth (p < 0.030) compared to CTL but did not affect rumen VFA profile. The TRT had a negligible impact on microbial community composition in both the rumen and the jejunum. In conclusion, feeding MCE from birth through weaning can improve ruminal and small intestinal mucosa development of calves despite the negligible microbiota composition changes observed post-weaning.

The products of rumen microbial fermentations are considered essential for animal growth and performance. Changes in these microbial communities can have major effects on animal growth and performance. Saccharin-based artificial sweeteners can be included in livestock diets to increase palatability and encourage feed intake. Despite the importance of the rumen microbial fermentation, little or no research is available regarding how saccharin-based artificial sweeteners affect rumen content and rumen epithelial microbial communities. The aim of this study was to identify changes in both the rumen content and rumen epithelial microbial communities in response to the supplementation of Sucram ^® , a sodium-saccharin-based sweetener (Pancosma S.A./ADM Groups, Rolle, Switzerland) during standard, non-stress conditions using 16SrRNA gene amplicon sequencing. The rumen epithelial and rumen content microbiota of five Holstein-Friesian milking dairy cattle were compared before (baseline, BL) and after a 28-day supplementation of Sucram ^® . Illumina MiSeq-based 16S rRNA gene sequencing was conducted, and community analysis revealed significant changes in the abundance of specific phylotypes when comparing BL to Sucram ^® experimental groups. Sucram ^® did not have a significant effect on overall rumen microbial community structure between experimental groups. Statistically significant changes in microbial community composition following Sucram ^® supplementation were observed most consistently across a number of bacterial taxa in the rumen epithelium, while fewer changes were seen in the rumen content. Predicted genomic potentials of several significantly different OTUs were mined for genes related to feed efficiency and saccharin degradation. Operational taxonomic units (OTUs) classified as Prevotella and Sharpea were significantly (p<0.05) increased in samples supplemented with Sucram ^® , whereas a reduction in abundance was seen for OTUs classified as Treponema , Leptospiraceae , Ruminococcus and methanogenic archaea. This is the first study to report an effect of Sucram ^® on ruminant microbial communities, suggesting possible beneficial impacts of Sucram ^® on animal health and performance that may extend beyond increasing feed palatability.

Strategies to counteract interleukin ( IL )- 10-mediated immune evasion by Eimeria spp. during coccidiosis- like anti-IL-10 antibodies- may protect broiler chicken health and reduce incidence of secondary necrotic enteritis ( Clostridium perfringens ) via undetermined mechanisms. Objectives were to use sequencing techniques to evaluate jejunal microbial community composition and function in anti-IL-10-fed broilers during coccidiosis and necrotic enteritis. On d0, Ross 308 chicks were placed in 32 cages (15 chicks/ cage) for a 25d study and randomly assigned to diets +/- 0.03% antiIL-10. Six chicks/ diet were euthanized for distal jejunum content and tissue collection on d 14 (baseline) before inoculating the remainder with saline or 15,000 E. maxima oocysts (M6 strain). Half the chicks challenged with E. maxima were challenged with C. perfringens (1 pound 10 8 colony forming units) on d 18 and 19. Follow-up samples (6 chicks/treatment) were collected at 7 and 11 d postinoculation ( pi ) for the E. maxima-only group, or 3 and 7 dpi for the E. maxima + C. perfringens group with 3/7 dpi being designated as peak and 7/11dpi as postpeak challenge. DNA was extracted from digesta for microbiota composition analysis (16S rRNA gene sequencing) while RNA was extracted from tissue to evaluate the metatranscriptome (RNA sequencing). Alpha diversity and genus relative abundances were analyzed using the diet or challenge main effects with associated interactions (SAS 9.4; P <= 0.05). No baseline microbial changes were associated with dietary anti-IL10. At peak challenge, a diet main effect reduced observed species 36.7% in chicks fed anti-IL-10 vs. control; however, the challenge effect reduced observed species and Shannon diversity 51.2-58.3% and 33.0 to 35.5%, respectively, in chicks challenged with E. maxima +/- C. perfringens compared to their unchallenged counterparts ( P <= 0.05). Low sequencing depth limited metatranscriptomic analysis of jejunal microbial function via RNA sequencing. This study demonstrates that challenge impacted the broiler distal jejunum microbiota more than anti-IL-10 while future research to characterize the microbial metatranscriptome may bene fit from investigating other intestinal compartments.

The aim of this pilot study was to identify changes in both the rumen content and rumen epithelial microbiota in response to the supplementation of Sucram ® , a sodium-saccharin-based sweetener (Pancosma S.A./ADM Groups, Rolle, Switzerland). Rumen microbial communities are essential for animal growth and performance, and changes in these communities can have major effects on these parameters. Little or no research is available regarding how saccharin-based artificial sweeteners, fed to cattle in attempts to increase palatability and encourage feed intake, affect rumen microbial communities. The rumen epithelium and rumen content microbiota of five lactating Holstein-Friesian dairy cattle were compared before (baseline, BL) and after a 28-day supplementation of Sucram ® using Illumina MiSeq-based 16S rRNA gene sequencing. After supplementation of Sucram ® , significant changes in the abundance of specific taxa were detected: an increase in Prevotella and Sharpea species, a decrease in Treponema , Leptospiraceae , Ruminococcus and methanogenic archaea (p<0.05), but Sucram® did not affect the overall rumen microbial community structure. This is the first study to report an effect of Sucram ® on ruminant microbial communities.