Background Infectious Bovine Keratoconjunctivitis (IBK), commonly known as pinkeye, is one of the most significant diseases of beef cattle. As such, IBK costs the US beef industry at least 150 million annually. However, strategies to prevent IBK are limited, with most cases resulting in treatment with antibiotics once the disease has developed. Longitudinal studies evaluating establishment of the ocular microbiota may identify critical risk periods for IBK outbreaks or changes in the microbiota that may predispose animals to IBK. Results In an attempt to characterize the establishment and colonization patterns of the bovine ocular microbiota, we conducted a longitudinal study consisting of 227 calves and evaluated the microbiota composition over time using amplicon sequence variants (ASVs) based on 16S rRNA sequencing data and culture-based approaches. Beef calves on trial consisted of both male (intact) and females. Breeds were composed of purebred Angus and composites with varying percentages of Simmental, Angus, and Red Angus breeds. Average age at the start of the trial was 65 days ±15.02 and all calves remained nursing on their dam until weaning (day 139 of the study). The trial consisted of 139 days with four sampling time points on day 0, 21, 41, and 139. The experimental population received three different vaccination treatments (autogenous, commercial (both inactivated bacteria), and adjuvant placebo), to assess the effectiveness of different vaccines for IBK prevention. A significant change in bacterial community composition was observed across time periods sampled compared to the baseline (p < 0.001). However, no treatment effect of vaccine was detected within the ocular bacterial community. The bacterial community composition with the greatest time span between sampling time periods (98d span) was most similar to the baseline sample collected, suggesting re-establishment of the ocular microbiota to baseline levels over time after perturbation. The effect of IgA levels on the microbial community was investigated in a subset of cattle within the study. However, no significant effect of IgA was observed. Significant changes in the ocular microbiota were identified when comparing communities pre- and post-clinical signs of IBK. Additionally, dynamic changes in opportunistic pathogens Moraxella spp. were observed and confirmed using culture based methods. Conclusions Our results indicate that the bovine ocular microbiota is well represented by opportunistic pathogens such as Moraxella and Mycoplasma. Furthermore, this study characterizes the diversity of the ocular microbiota in calves and demonstrates the plasticity of the ocular microbiota to change. Additionally, we demonstrate the ocular microbiome in calves is similar between the eyes and the perturbation of one eye results in similar changes in the other eye. We also demonstrate the bovine ocular microbiota is slow to recover post perturbation and as a result provide opportunistic pathogens a chance to establish within the eye leading to IBK and other diseases. Characterizing the dynamic nature of the ocular microbiota provides novel opportunities to develop potential probiotic intervention to reduce IBK outbreaks in cattle.

The majority of microbiome studies focused on understanding mechanistic relationships between the host and the microbiota have used mice and other rodents as the model of choice. However, the domestic pig is a relevant model that is currently underutilized for human microbiome investigations. In this study, we performed a direct comparison of the engraftment of fecal bacterial communities from human donors between human microbiota-associated (HMA) piglet and mouse models under identical dietary conditions. Analysis of 16S rRNA genes using amplicon sequence variants (ASVs) revealed that with the exception of early microbiota from infants, the more mature microbiotas tested established better in the HMA piglets compared to HMA mice. Of interest was the greater transplantation success of members belonging to phylum Firmicutes in the HMA piglets compared to the HMA mice. Together, these results provide evidence for the HMA piglet model potentially being more broadly applicable for donors with more mature microbiotas while the HMA mouse model might be more relevant for developing microbiotas such as those of infants. This study also emphasizes the necessity to exercise caution in extrapolating findings from HMA animals to humans, since up to 28% of taxa from some donors failed to colonize either model.

Multiple sclerosis (MS) is the most common autoimmune disorder affecting the central nervous system. Epstein‐Barr virus (EBV) is a causative agent for infectious mononucleosis (IM) that is associated with MS pathogenesis. However, the exact mechanism by which EBV, specifically in IM, increases the risk for MS remains unknown. EBV immortalizes primary B lymphocytes in vitro and causes excessive B lymphocyte proliferation in IM in vivo. In asymptomatic carriers, EBV‐infected B lymphocytes still proliferate to certain degrees, the process of which is tightly controlled by the host immune systems. Experimental autoimmune encephalomyelitis (EAE) mimics key features of MS in humans and is a well‐established rodent model for human MS. We have found that xenografts of EBV‐immortalized B lymphocytes, which partially resemble the hyperproliferation of EBV‐infected cells in IM, exacerbate autoimmune responses in myelin oligodendrocyte glycoprotein‐induced EAE in C57BL/6 mice. After remission, an additional challenge with EBV‐immortalized cells induces a relapse in EAE. Moreover, xenografts with EBV‐immortalized cells tighten the integrity of the blood‐brain barrier (BBB) in the thalamus and hypothalamus areas of the mouse brains. Genomic sequences of prokaryotic 16S ribosomal RNA presented in the feces reveal that EBV‐immortalized cells significantly change the diversities of microbial populations. Our data collectively suggest that EBV‐mediated proliferation of B lymphocytes may be a risk factor for the exacerbation of MS, which are associated with gut microbiome changes and BBB modulations. Furthermore, multiple xenografts of EBV‐immortalized cells into C57BL/6 mice could serve as a useful model for human relapsing‐remitting MS with predictable severity and timing.

The use of probiotics may be an effective strategy in sustainable pig production. The objective of this experiment was to examine the effects of Lactobacillus fermentum (LF) on nursery pig performance. Weaned pigs (n = 70; average initial BW 6.464 kg) were randomly allotted to 1 of 3 treatments, forming 6 replicates per treatment. Treatments included: 1) pigs fed a standard nursery diet (NRC 2012); CTL; 2) pigs fed CTL with the addition of 10^10 CFU LF per day for phase 1 (wk 2 and 3; LF1); and 3) pigs fed CTL with the addition of 10^10 CFU LF per day for phase 1 and phase 2 (wk 2 thru 5). A common diet was fed during adaptation (wk 1) and during a wash out phase (wk 6). Individual piglet BW were recorded weekly along with pen feed disappearance. No differences were observed in BW by the end of phase 1; at the end of phase 2 the pigs fed LF had a lower BW than the others (19.38, 19.22, 17.3 kg; P = 0.031). This was associated with a reduced feed efficiency seen in week 5 (0.679, 0.656, 0.445; P = 0.0404). However, no differences (P &gt; 0.10) were observed in BW of the pigs throughout the trial and final BW were 24.15, 24.45, 24.3 kg. No differences were observed in ADFI between treatments (ADFI Phase 1: 0.359, 0.366, 0.353 kg/d;P = 0.965; Phase 2: 0.906, 0.896, 0.843 kg/d; P = 0.578; Phase 3: 1.183, 1.227, 1.196 kg; P = 0.920). Results suggest that pigs fed diets supplemented with Lactobacillus fermentum performed similar to pigs fed a conventional diet.

The rumen microbial community is responsible for producing a majority of the energetic needs for the animal, yet our understanding of the rumen microbiome is in its infancy. To better understand the effect of corn-ethanol coproducts on rumen microbial communities, a replicated 4 × 4 Latin square design study utilizing 12 cows in three squares was conducted to evaluate the replacement of alfalfa hay with a mixture (CoP) containing straw and dried distillers grains plus solubles (DDGS) in lactating Jersey cows. The experimental treatments were (proportions on a dry matter basis): a control diet (CON) containing 18.2% of alfalfa hay with no straw or DDGS. A low coproduct diet (LCoP) containing 12.1% alfalfa, 2.1% straw, and 6.0% DDGS. A medium coproduct diet (MCoP) containing 6.1% alfalfa, 4.2% straw, and 12.1% DDGS. A high coproduct diet (HCoP) containing 6.2% straw, 18.1% DDGS with no alfalfa. Rumen digesta samples were collected via an esophageal tube. No differences were observed for milk production and dry matter intake (P ≥ 0.307) (mean ± SEM) 19.5 kg ± 0.60, 29.6 kg ± 0.91, across treatments, while a decrease in methane was observed (P &lt; 0.01) for the HCoP treatment. The bacterial community was assessed by sequencing the V4 region of the 16S rRNA gene. Additionally, the archaeal community was assessed by sequencing the V4-V5 region of the 16S rRNA gene on the Illumina MiSeq platform. Amplicon Sequence Variants were identified using the DADA2 pipeline. No significant differences were observed for the bacterial (P = 0.334) and archaeal (P = 0.593) communities. Although global effects in microbial community dynamics were not observed, differential taxa were observed with Lachnospiraceae being the major differentially abundant Family. The archaeal community composition demonstrated that Methanobacteriales to be the differentially abundant Order across treatments, and may contribute to methane production.