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The goal of this study was to evaluate the variation in spoilage microbiota associated with sliced, prepackaged deli-style ham from varying processing environments available in the retail market in the United States. Three different brands of presliced ham, water added were purchased at local markets and evaluated every 2 wk beginning 4 wk prior to the sell-by date until 4 wk beyond the sell-by date. Analysis of 16S ribosomal RNA genes using operational taxonomic units showed that Brand A had a different bacterial community structure compared with Brands B and C, according to unweighted (P=0.006) and weighted (P

A feline papillomavirus genome was assembled from metagenomic sequencing data collected from the skin of a house cat owner. The circular genome of strain P20 is 8,069 bp in length, has a GC content of 54.38%, and displays genome organization typical of feline papillomaviruses. The genome exhibits approximately 75% sequence similarity to other feline papillomavirus genomes.

Aims Our objective was to determine how injectable antimicrobials affected populations of Salmonella enterica, Escherichia coli and Enterococcus spp. in feedlot cattle. Methods and Results Two arrival date blocks of high-risk crossbred beef cattle (n = 249; mean BW = 244 kg) were randomly assigned one of four antimicrobial treatments administered on day 0: sterile saline control (CON), tulathromycin (TUL), ceftiofur (CEF) or florfenicol (FLR). Faecal samples were collected on days 0, 28, 56, 112, 182 and study end (day 252 for block 1 and day 242 for block 2). Hide swabs and subiliac lymph nodes were collected the day before and the day of harvest. Samples were cultured for antimicrobial-resistant Salmonella, Escherichia coli and Enterococcus spp. The effect of treatment varied by day across all targeted bacterial populations (p ≤ 0.01) except total E. coli. Total E. coli counts were greatest on days 112, 182 and study end (p ≤ 0.01). Tulathromycin resulted in greater counts and prevalence of Salmonella from faeces than CON at study end (p ≤ 0.01). Tulathromycin and CEF yielded greater Salmonella hide prevalence and greater counts of 128ERYR E. coli at study end than CON (p ≤ 0.01). No faecal Salmonella resistant to tetracyclines or third-generation cephalosporins were detected. Ceftiofur was associated with greater counts of 8ERYR Enterococcus spp. at study end (p ≤ 0.03). By the day before harvest, antimicrobial use did not increase prevalence or counts for all other bacterial populations compared with CON (p ≥ 0.13). Conclusions Antimicrobial resistance (AMR) in feedlot cattle is not caused solely by using a metaphylactic antimicrobial on arrival, but more likely a multitude of environmental and management factors.

The human skin is our point of contact with the microbial world, yet little is known about the diversity of the skin virome. Studies of the human skin virome have focused on bacteriophage and double-stranded DNA viral genomes, however, there have been few efforts to characterize circular single-stranded DNA viruses that populate human skin. Here, we evaluate the diversity of the circular single-stranded DNA virome collected across three anatomical skin locations from 60 human individuals with five time-point collections spanning six-months. Our analyses resulted in the identification of 272 novel and unique Rep-encoded single-stranded DNA viruses associated with human skin. Sequence similarity networks and maximum likelihood estimations of the Rep and Capsid protein amino acid sequences from our sequencing and public database references, reveal family level stability of the Cressdnaviricota across the study participants and a larger host-range than previously thought for these putative multi-host pathogens.

Bovine respiratory disease (BRD) is the primary animal health concern facing feedlot producers. Many antimicrobial mitigation strategies are available, but few studies have compared feedlot performance during both the receiving and finishing periods following application of different antimicrobials used as metaphylaxis at arrival. The objective of this study was to compare antimicrobial metaphylaxis methods on clinical health and growth performance across both the receiving and finishing periods. A total of 238 multiple-sourced steers in two source blocks were used in a generalized complete block design. The four treatments included: 1) a negative control, 5 mL of sterile saline injected subcutaneously (CON); 2) subcutaneous administration of florfenicol at 40 mg/kg of BW (NUF); 3) subcutaneous administration of ceftiofur in the posterior aspect of the ear at 6.6 mg/kg of BW (EXC); and 4) subcutaneous administration of tulathromycin at 2.5 mg/kg of BW (DRA). The morbidity rate for the first treatment of BRD was decreased for the DRA and EXC treatments compared to CON and NUF (P

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.

Addition of pre- and probiotics may confer growth and health benefits when added to the diet of pigs. To determine the effects of feeding mannan oligosaccharide (MOS) and Lactobacillus mucosae (LM) as prebiotic and probiotic sources in weanling pigs under immune challenge, 96 weaned pigs were randomly allotted to 16 experimental pens within a 2 × 2 factorial arrangement of treatments. Control diets with or without 0.1% yeast-derived MOS were randomly assigned to pens and 109 cfu/pig LM broth or a control broth were top-dressed daily. Pigs were fed one of four dietary treatments (control, MOS, LM, and MOS+LM) in Phases I and II (days 0 to 7 and days 7 to 21 postweaning, respectively) and a common diet during Phase III (days 21 to 35 postweaning). On day 14, all pigs were challenged with 100 µg/kg body weight (BW) Escherichia coli lipopolysaccharide (LPS) via intraperitonial injection. Feed disappearance and pig BW were measured weekly. Blood and fecal samples were collected weekly, and additional blood samples were collected on days 1 and 3 post-LPS challenge. On days 15 and 21, one pig per pen was euthanized for collection of ileal mucosa and duodenal and ileal tissue samples. From days 0 to 14, feeding LM decreased gain-to-feed ratio (G:F; P < 0.05). An interaction between LM and MOS was observed for G:F on days 14 to 21 (P < 0.05); G:F in LM (715 g/kg) was greater compared with MOS+LM (P < 0.05; 600 g/kg) and control (P < 0.10; 615 g/kg), but was not different (P > 0.10) from MOS (674 g/kg). After pigs were fed a common diet (days 21 to 35), G:F was decreased (P < 0.05) in the LM treatment groups. Pigs fed diets that included MOS had increased serum immunoglobulin (Ig) G on days 1 and 3 post-LPS challenge and 2 wk after removal of treatments (P < 0.05) and on days 14 and 21 postweaning (P < 0.10) compared with pigs fed diets without MOS. On day 15, mucosal immunoglobulin G was increased (P < 0.05) in control vs. MOS and LM groups. Circulating IL-1β in control and MOS+LM pigs increased (P < 0.05) on day 1 post-LPS challenge but did not change (P > 0.10) in MOS and LM groups. On day 15, pigs fed LM had decreased (P < 0.05) ileal crypt depth compared with pigs fed the control diet. On day 21, fecal propionate and butyrate tended to be lower (P < 0.10) in pigs fed MOS vs. control and MOS+LM diet. These preliminary findings suggest that feeding LM alone improved feed efficiency and ileal morphological structure during the first week of LPS challenge; additionally, feeding LM and MOS may have beneficial effects relative to immune biomarkers.

Reduction in dietary crude protein and addition of fiber could mitigate the incidence and severity of post-weaning diarrhea, a common gastrointestinal condition in newly weaned pigs. Therefore, 360 weanling pigs, initially 5.0 ± 0.10 kg, were used to evaluate the effects of crude protein (CP) level and fiber source on growth performance and fecal microbial communities. At weaning, pigs were randomly assigned to pens and allotted to 1 of 8 dietary treatments in a 2 × 4 factorial with main effects of CP (21 or 18%) and fiber source (none, coarse wheat bran, oat hulls, or cellulose). There were 5 pigs per pen and 9 pens per treatment. Experimental diets were formulated in two dietary phases from d 0 to 10 and 10 to 24, with a common post-treatment diet fed from 24 to 45. The 21% CP diets contained 1.40% standardized ileal digestible (SID) Lys in phase 1 and 1.35% SID Lys in phase 2. By using a maximum SID Lys:digestible CP ratio of 6.35%, the 18% CP diets contained 1.25% SID Lys in both phases. Diets containing a fiber source were formulated to the level of insoluble fiber provided by 4% coarse wheat bran, resulting in the addition of 1.85% oat hulls and 1.55% cellulose. No fiber source × CP level interactions (P > 0.05) were observed. Decreasing CP (and subsequently SID lysine) decreased (P = 0.05) ADG and G:F during the experimental period. From d 0 to 45, ADG decreased (P = 0.05) for pigs fed 18% CP diets compared to pigs fed 21% CP. No effect of fiber source was observed for growth performance. Fecal DM on d 17 increased (P < 0.001) for pigs fed 18% CP diets compared to pigs fed 21% CP diets. Pigs fed diets with added cellulose had increased (P < 0.05) fecal dry matter during the experimental period compared to pigs fed no fiber source or wheat bran. Bacterial community structure was investigated by sequencing the V4 region of the 16S rRNA gene. Analysis indicated a significant difference between CP content at d 24 (P = 0.023) using a Weighted UniFrac distance matrix. Further investigation identified five differential Amplicon Sequence Variants associated with CP content at d 24. In conclusion, reducing crude protein (and subsequently SID Lys) decreased growth performance but increased fecal dry matter content. The source of dietary fiber in nursery diets had no impact on growth performance; but pigs fed added cellulose had increased fecal DM compared with other treatments. Microbial analysis identified differential taxa associated with CP content.

A feline papillomavirus was assembled from metagenomic sequencing data collected from the human skin of a house cat owner. This circular papillomavirus strain P20 is 8069 bp in length, has a GC content of 54.38%, and displays genome organization typical of feline papillomaviruses with six annotated protein coding regions. The genome exhibits approximately 75% sequence similarity to other feline papillomavirus genomes.

The use of skin virome for human identification purposes offers a unique approach to instances where a viable and statistically relevant human DNA profile is unavailable. The human skin virome may act as an alternative DNA profile and/or an additional form of probative genetic material. To date, no study has attempted to investigate the human virome over a time series across various physical locations of the body to identify its potential as a tool for human identification. For this study, we set out to evaluate the stability, diversity, and individualization of the human skin virome. An additional goal was to identify viral signatures that can be used in conjunction with traditional forensic STR loci. In order to accomplish this, human virome metagenomes were collected and sequenced from 42 individuals at three anatomical locations (left hand, right hand, and scalp) across multiple collections periods over a 6-month window of time. Assembly dependent and independent bioinformatic approaches were employed, along with a database-based assessment, which resulted in three sets of stable putative viral markers. In total, with the three sets combined, 59 viral species and uncharacterized viral genome assemblies were identified as being significantly stable (P=5.3×10-15). Viral diversity, based on presence or absence, is significantly different across subjects (PHighlightsHere we provide the largest human skin virome study, to date. Our study revealed novel diversity findings of high abundance for certain viral taxa, for example, the Cress-like DNA phages, that have not previously been characterized in human skin viral ecology studies.There were 59 putative human skin viral biomarkers suitable for human identification from the core stable human skin virome of 42 subjects.The putative markers we identified were significantly stable over a 6-month period of time within individuals and across three autosomal locations of left hand, right hand, and scalp.Diversity of profiles, based on the presence and absence of our putative marker data set, were significantly different across test subjects.

Mitigating the spread of antimicrobial resistance (AMR) has become a top priority globally over the last decade. Thus, understanding how bacterial communities acquire and transfer antibiotic resistance is of upmost importance in identifying intervention points for maintaining antibiotic efficacy. It is well documented that horizontal gene transfer (HGT) via bacteriophage transduction has the potential to shift metabolic flux in bacterial communities, yet phage mediated HGT in feedlot cattle with regard to AMR remains poorly characterized. Here we characterize the viral community of 72 beef cattle, where 36 animals received antibiotic exposure and 36 control animals received no antibiotic exposure throughout the duration of the study. Treatment groups were divided into 9 pens with 4 animals per pen. Fecal samples were collected at 3 timepoints and pooled by pen for viral enrichments. Viral particle enrichment was performed using tangential flow filtration and ultracentrifugation. Viral DNA/RNA was extracted with Zymo Quick-DNA/RNA Viral Magbead extraction kit, and shotgun metagenomic libraries were prepared using NEBNext Ultra II library prep kit for Illumina. Libraries were sequenced on the Illumina HiSeq platform (150bp paired-end reads). Sequencing reads were assembled using MEGAHIT, viral genomes were predicted using Virsorter2 and CheckV, and annotated using VIBRANT. In total, 5,875 viral genomes were predicted from the dataset. 635 of those viral genomes were > 60% complete, and 45 were complete circular genomes. 544 auxiliary metabolic genes (AMGs) were detected across all genomes, spanning 49 metabolic pathways with most genes falling under energy, amino acid, and vitamin/cofactor metabolism. Notably, 25 genes involved in secondary metabolite biosynthesis of vancomycin, validamycin, streptomycin, and monobactams were detected. Results indicate that fecal bacteriophages harbor a wide array of AMGs with diverse metabolic potential, including secondary metabolites potentially involved with AMR. The USDA is an equal opportunity provider and employer.

Although the inclusion of fat has reduced methane production in ruminants, relatively little research has been conducted comparing the effects of source and profile of fatty acids on methane production in lactating dairy cows. A study using 8 multiparous (325 ± 17 DIM; mean ± SD) lactating Jersey cows was conducted to determine effects of feeding canola meal and lard versus extruded byproduct containing flaxseed as a high-C18:3 fat source on methane production and diet digestibility in late-lactation dairy cows. A crossover design with 32-d periods (28-d adaptation and 4-d collections) was used to compare 2 different fat sources. Diets contained approximately 50% forage mixture of corn silage, alfalfa hay, and brome hay; the concentrate mixture changed between diets to include either (1) a conventional diet of corn, soybean meal, and canola meal with lard (control) or (2) a conventional diet of corn and soybean meal with an extruded byproduct containing flaxseed (EXF) as the fat source. Diets were balanced to decrease corn, lard, and canola meal and replace them with soybean mean and EXF to increase the concentration of C18:3 (0.14 vs. 1.20% of DM). Methane production was measured using headbox-style indirect calorimeters. Cattle were restricted to 95% ad libitum feed intake during collections. Milk production (17.4 ± 1.04 kg/d) and dry matter intake (15.4 ± 0.71 kg/d) were similar among treatments. Milk fat (5.88 ± 0.25%) and protein (4.08 ± 0.14%) were not affected by treatment. For methane production, no difference was observed for total production (352.0 vs. 349.8 ± 16.43 L/d for control vs. EXF, respectively). Methane production per unit of dry matter intake was not affected and averaged 23.1 ± 0.57 L/kg. Similarly, methane production per unit of energy-corrected milk was not affected by fat source and averaged 15.5 ± 0.68 L/kg. Heat production was similar, averaging 21.1 ± 1.02 Mcal/d. Digestibility of organic matter, neutral detergent fiber, and crude protein was not affected by diet and averaged 69.9, 53.6, and 73.3%, respectively. Results indicated that increasing C18:3 may not affect methane production or digestibility of the diet in lactating dairy cows.

The addition of fat and calcium sulfate to diets fed to ruminants has resulted in a reduction in methane production, but the effects on energy balance have not been studied. A study using indirect calorimetry and 16 multiparous (8 Holstein and 8 Jersey; 78 ± 15 d in milk; mean ± standard deviation) lactating dairy cows was conducted to determine how mitigating methane production by adding corn oil or calcium sulfate to diets containing reduced-fat distillers grains affects energy and nitrogen balance. A replicated 4 × 4 Latin square design with 35-d periods (28 d of adaption and 4 d of collections) was used to compare 4 different dietary treatments. Treatments were composed of a control (CON) diet, which did not contain reduced-fat distillers grain and solubles (DDGS), and treatment diets containing 20% (dry matter basis) DDGS (DG), 20% DDGS with 1.38% (dry matter basis) added corn oil (CO), and 20% DDGS with 0.93% (dry matter basis) added calcium sulfate (CaS). Compared with CON, dry matter intake was not affected by treatment, averaging 29.6 ± 0.67 kg/d. Milk production was increased for diets containing DDGS compared with CON (26.3 vs. 27.8 ± 0.47 kg/d for CON vs. DDGS, respectively), likely supported by increased energy intake. Compared with CON, energy-corrected milk was greater in DG and CO (30.1 vs. 31.4, 31.7, and 31.0 ± 0.67 kg/d for CON, DG, CO, and CaS, respectively). Compared with CON, the addition of calcium sulfate and corn oil to diets containing DDGS reduced methane production per kg of dry matter intake (22.3, 19.9, and 19.6 ± 0.75 L/kg per d for CON, CO, and CaS, respectively). Similarly, methane production per kilogram of energy-corrected milk was reduced with the addition of calcium sulfate and corn oil to diets containing DDGS (14.2, 12.5, and 12.4 ± 0.50 L/kg per d for CON, CO, and CaS, respectively). Compared with CON and CaS, the intake of digestible energy was greater for DG and CO treatments (57.7, 62.1, 62.0, and 59.0 ± 1.38 Mcal/d for CON, DG, CO, and CaS, respectively). Intake of metabolizable energy was greater in all treatments containing DDGS compared with CON (50.5 vs. 54.0 ± 1.08 Mcal/d for CON vs. DDGS, respectively). Net balance (milk plus tissue energy) per unit of dry matter was greater in CO (containing DDGS and oil) than CON (1.55 vs. 1.35 ± 0.06 Mcal/kg for CO vs. CON, respectively). Tissue energy was greater in DG and CO compared with CON (6.08, 7.04, and 3.16 ± 0.99 Mcal/d for DG, CO, and CON, respectively. Results of this study suggest that the addition of oil and calcium sulfate to diets containing DDGS may be a viable option to reduce methane production and in the case of oil also improve net energy balance in lactating dairy cows.

Atomic force microscopy (AFM) is a device that is used for not only high-resolution imaging but also used for measuring forces. It is possible to quantify the surface density change for both colloid and nano probe as well as silica surface. By changing the quantity of ions within a potassium chloride solution, it then becomes possible to evaluate the quantity of ions that attach themselves to AFM colloid probe, nano probe and silica samples. In this study, the force was measured between AFM probes and silica surface in different ionic concentrations. Two different types of AFM probe were used: a colloid probe with a radius of 500 nano-meters and a nano probe with a radius of 10 nano-meters. This study is focused on measuring how the force magnitude, especially electrical double layer force, varied between the two types of probes by changing ionic concentrations. For all test trials, the results agreed with the electrical double layer theory. Although the micron probe was almost an exact match for all ranges, the nano probe was closest within its short-range forces. This is attributed to the formula use when analyzing the electrical double layer force. Because the formula was originally calculated for the micron probe, the shape and size of the nano probe created too many variables for an exact match. Along with quantifying the forces, this experiment allowed for an observation of Van der Waals force making it possible to calculate the Hamaker constant. Conclusively, all results show that the obtained surface charge density increases as the ionic concentration increases. In addition, through the comparison of the results obtained from the nano-sized probe and the micron-sized probe, it was concluded that nano size probe mapped higher surface charge density above the silica surface than the micron-sized probe under the same conditions.

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 LfQi6 (LF) on sow and litter performance. First parity, gestating sows (UNL Resource Population Rep x DNA Genetics Duroc; n = 28) were allotted one of two treatment groups. Treatment groups consisted of a control group (CTL) fed a standard gestation and lactation diet for the duration of the study, while the experimental group was fed CTL supplemented with 10^10 CFU LF per day from d 80 of gestation through lactation. Individual piglet body weights (BW) were recorded weekly. LF sows tended to enter the farrowing crates lighter than the control sows (209.93 vs 200.91kg; P = 0.0794). LF sows had a smaller loin eye area when compared to CTL sows (6.24 vs 5.86 cm2; P = 0.0374) when entering the farrowing crates. However, LF sows tended to lose less loin area per day when in the crate (0.025 vs 0.012 cm2/d; P = 0.078); resulting with there being no difference in loin area when the sows left the farrowing crates. Piglet BW tended to be greater at weaning for the sows fed the LF (5.37 vs 5.66 kg, P = 0.0528). The mean piglet BW were 1.25,1.33; 2.37,2.44; 4.08,4.22; and 5.37,5.66 at d 0, 7, 14, 21; respectively for CTL and LF. Sows fed the LF had fewer pigs born alive per litter (16.09 vs 14.12; P < 0.05) when compared to the sows fed the control diet. However, piglet mortality tended to be decreased for LF compared to CTL (3 vs 1.76; P = 0.0645). Results suggest that supplementation with Lactobacillus fermentum LfQi6 may provide some benefits with respect to sow and litter performance.

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 > 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.

A moderately acidophilic Geobacter sp. strain, strain FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp, with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling., A moderately acidophilic Geobacter sp. strain, FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.

Liver abscesses in feedlot cattle are polymicrobial infections. Culture-based studies have identified Fusobacterium necrophorum as the primary causative agent, but a number of other bacterial species are frequently isolated. The incidence of liver abscesses is highly variable and is affected by a number of factors, including cattle type. Holstein steers raised for beef production have a higher incidence than crossbred feedlot cattle. Tylosin is the commonly used antimicrobial feed additive to reduce the incidence of liver abscesses. The objective of this study was to utilize 16S ribosomal RNA amplicon sequence analyses to analyze the bacterial community composition of purulent material of liver abscesses of crossbred cattle (n = 24) and Holstein steers (n = 24), each fed finishing diet with or without tylosin. DNA was extracted and the V3 and V4 regions of the 16S rRNA gene were amplified, sequenced, and analyzed. The minimum, mean, and maximum sequence reads per sample were 996, 177,070, and 877,770, respectively, across all the liver abscess samples. Sequence analyses identified 5 phyla, 14 families, 98 genera, and 102 amplicon sequence variants (ASV) in the 4 treatment groups. The dominant phyla identified were Fusobacteria (52% of total reads) and Proteobacteria (33%). Of the top 25 genera identified, 17 genera were Gram negative and 8 were Gram positive. The top 3 genera, which accounted for 75% of the total reads, in the order of abundance, were Fusobacterium, Pseudomonas, and Bacteroides. The relative abundance, expressed as percent of total reads, of phyla, family, and genera did not differ (P > 0.05) between the 4 treatment groups. Generic richness and evenness, determined by Shannon–Weiner and Simpson’s diversity indices, respectively, did not differ between the groups. The UniFrac distance matrices data revealed no clustering of the ASV indicating variance between the samples within each treatment group. Co-occurrence network analysis at the genus level indicated a strong association of Fusobacterium with 15 other genera, and not all of them have been previously isolated from liver abscesses. In conclusion, the culture-independent method identified the bacterial composition of liver abscesses as predominantly Gram negative and Fusobacterium as the dominant genus, followed by Pseudomonas. The bacterial community composition did not differ between crossbred and Holstein steers fed finishing diets with or without tylosin.

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., Aluthge et al. evaluated the establishment of human fecal bacterial communities in human microbiota-associated (HMA) piglet and mouse models under identical dietary conditions. They find that human fecal bacterial communities from mature microbiotas establish more successfully in the HMA porcine model than mice, suggesting the broader applicability of the piglet model for human microbiome studies.

Weaning stress and the negative health effects that occur with it cause serious concerns for pork producers. The abrupt environmental and dietary transitions that occur at weaning often take place before the gut microbiome is stabilized in the piglet. This leaves weanling piglets vulnerable to gut dysbiosis and increases susceptibility to enteric pathogens. The infections by opportunistic pathogens can be prevented with antibiotics, but due to growing concerns surrounding antimicrobial resistance in bacterial populations, direct-fed microbial (DFM) formulations have emerged as an alternative prevention method. In the current study, we isolated Lactobacillus spp. and Bifidobacterium spp. from fecal samples collected from neonatal pigs and sows that are capable of inhibiting colonization of Salmonella spp. and Escherichia coli isolated from sick pigs. Diluted fecal samples were plated on Bifidus selective medium (BSM) and deMan, Rogosa Sharpe (MRS) medium to isolate Bifidobacterium and Lactobacillus, respectively. Bacterial isolates were screened against Salmonella and E. coli isolates of porcine origin using a medium consisting of 50% MRS and 50% brain, heart, lung infusion (BHI) using disk diffusion assays. The resulting isolates that demonstrated the greaest degree of pathogen inhibition were characterized using 16s rRNA sequencing. Sequence analysis identified the top isolates as L. mucosae, L. reuteri, and B. thermacidophilum subsp. porcinum. Currently, genome sequencing of the selected isolates is underway to identify the mechanisms of inhibition.

Infectious Bovine Keratoconjuctivitis (IBK), or more commonly known as pinkeye, impacts the beef cattle industry with expenses reaching close to 150 million dollars annually. Thus far, successful prevention of infectious outbreaks of IBK have been limited. Partly, this may be due to our limited understanding of the establishment and composition of the ocular microbiome. However, understanding of the establishment and composition of the ocular microbiome, may provide indicators species for early detection of IBK and to identify a window of opportunity to treat IBK before outbreaks occur. As an attempt to characterize the establishment and colonization patterns of the ocular microbiome in beef calves, we conducted a longitudinal study utilizing 239 calves. The calves were placed on three different preventative treatments which included an initial vaccination followed by a booster 3 weeks later (Autogenous, Commercial, and Placebo). Ocular swabs were collected at four different time points during summer and fall months. The V4 region of the 16S rDNA gene was sequenced from the 889 samples collected using the Illumina Miseq™ platform. The resulting sequences were analyzed using the Dada2 pipeline. The analysis demonstrated a significant difference in community composition (p< 0.001) across time periods sampled, where the microbiome reverted back to the original composition within three months of ocular microbiome perturbation and vaccination, demonstrating the resilience of the ocular microbiome to perturbation. This suggests the ocular microbiome is stable at 30 days of age. We also identified Mycoplasma sp. and Moraxella sp. which are candidate organisms known to predispose animals to IBK. Moraxella was prevalent during initial sampling, while Mycoplasma demonstrated greater abundance at all time points. This study demonstrates the diversity and the resilience of the ocular microbiome in calves and the potential to develop probiotic interventions to reduce IBK outbreaks.

This objective of this study was to evaluate the effects of a swine feed additive (GREEN GRASS, GG Sunseo Omega 3, Seoul, South Korea) on pork meat quality attributes. Thirty-six individually fed barrows were assigned one of four dietary treatments: moderately complex diet devoid of GG (CTRL;NRC 2012); CTRL with 10% GG (GG10) , CTRL with 20% GG (GG20), or CTRL with 17% dried-distillers grains with solubles (DDGS). Following slaughter, carcass and primal weights, LM area, 10th and last-rib backfat, and belly flop distance were measured. Physicochemical measures on the LM were instrumental color (L*, a*, b*), pH, proximate composition, drip loss, and shear force. Consumer panelists (n=112) evaluated loin samples for juiciness, pork flavor, off-flavor, tenderness, and overall liking. Belly and LM sample fatty acid composition was evaluated. Data were analyzed via PROC GLIMMIX of SAS with animal as the experimental unit. Panelist was considered a random effect. Diet treatment had no effect (P > 0.05) on weights, physicochemical measures, or panelist off-flavor rating. The GG20 treatment had less 10th rib backfat (P = 0.0178) than CTRL and GG10. DDGS and GG20 had the smallest (P = 0.026) belly flop values; CTRL and GG10 diets had the greatest. Belly and loin GG samples had greater (P < 0.001) total ω3, C18:3ω3, and C22:5 compared to CTRL and DDGS samples. Bellies from barrows fed DDGS had the greatest (P = 0.001) amount of C18:2 (linoleic acid), and bellies from the DDGS and GG treatments had greater (P = 0.001) overall PUFA than CTRL. Pork chops from the CTRL group were among the highest rated for all sensory attributes, and the GG20 treatment was more similar (P > 0.05) to the CTRL than GG10. These data suggest that feeding GG preferentially alters fatty acid composition without compromising quality attributes.

Different dietary and feed additive strategies have been developed to reduce the liver abscess in feedlot cattle, but liver abscesses are still a major problem in beef production. We have limited knowledge about how rumen microbial communities interact with host epithelial gene expression in healthy and liver-abscessed animals. The objective of this study was to investigate the associations between the rumen content associated and rumen epimural microbiome and epithelial gene expression in liver-abscessed and healthy animals. To this end, we collected the ruminal contents and tissue samples from healthy (N=30; score=0, steers n=19 and heifers n=11) and liver-abscessed (N=30; score=A+, steers n=21 and heifers n=9) feedlot cattle at harvest. The bacterial community compositions in the ruminal contents and papillae were evaluated via 16S rDNA sequencing of the V4 region using the Illumina MiSeq platform. Additionally, total RNA was extracted from rumen epithelial tissues and sequenced using the Illumina NextSeq platform. The permutational analysis (PERMANOVA) on Bray Curtis distances matrices showed the microbial community in the ruminal contents was significantly different (P< 0.001) from the bacterial community observed in rumen papillae. The ruminal contents contained a higher abundance of Bacteroidetes and Proteobacteria while papillae contained higher abundance of Firmicutes. The epimural microbiota was different (P< 0.01) between healthy and liver abscessed animals while ruminal contents microbiome was not different between the two groups. The DeSeq2 algorithm identified differentially expressed genes (221) related to MAPK, NF-kappa B signaling pathway, immune and inflammatory response in liver-abscessed animals. Additionally, a wide range of epimural bacterial taxa were correlated (-0.52 to 0.67) with differentially expressed genes. These data demonstrate the interaction between epimural microbiota and the host and its effect on liver abscesses, and indicate the need to study the epimural microbiome for its impact on liver abscesses in feedlot cattle. USDA is an equal opportunity provider and employer.

Global meat and milk demands are projected to increase by 50% by the year 2050, making a highly efficient cattle industry a top priority. Widespread use of antibiotics over the last 70 years has led to increases in antibiotic resistance genes (ARGs) in microbial populations, posing health risks to animal and human populations. Thus, a thorough understanding of where antibiotic resistance genes reside in microbial ecosystems surrounding livestock is paramount in developing strategies to mitigate transfer of antibiotic resistance. Recent advances in metagenome sequencing have made it possible to predict microbial genomes from shotgun metagenome datasets. However, genomes binned from metagenome data are often smaller than genomes from pure cultures, omitting genetic information that is not part of the core genome e.g. antibiotic resistance. This study uses a new linked-read metagenome sequencing approach, partitioning long fragments of DNA (>40Kbp) into millions of droplets which are individually barcoded giving each strand a unique index, improving metagenome assembly and increasing access to genetic information pertaining to antibiotic resistance. Rumen samples from four animals which received daily antibiotics in feed as well as antibiotic injections were pooled for linked-read metagenome sequencing. Additionally, soil samples from the animal pen were collected from three locations and pooled for analysis. Linked-read sequencing reads were assembled using MEGAHIT and ATHENA assemblers (N50 > 2702bp, 578,838 contigs >1000bp). Metagenome assembled genomes (MAGs) were binned using MetaBAT2, yielding 341 genome bins. Of these, 144 bins were of intermediate to high quality (>70% completeness, < 10% contamination), 79 genomes from rumen and 65 from soil samples, respectively. Genomes were scanned for ARGs (ABRicate), revealing 12 genomes containing ARGs, 5 from rumen, 7 from soil. MAGs possessed genes conferring resistance to penicillin, macrolide, nitroimidazole, aminoglycoside, and tetracycline class antibiotics, helping uncover information about where ARGs are sequestered in their respective environments. USDA is an equal opportunity provider and employer.

Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F. necrophorum to invade the bloodstream and colonize the liver. The objective of this study was to determine the changes in gene expression in the rumen epithelium and microbial populations adherent to the rumen epithelium and in the rumen contents of beef cattle with liver abscesses compared with those with no liver abscesses. Rumen epithelial tissue and rumen content were collected from 31 steers and heifers with liver abscesses and 30 animals with no liver abscesses. Ribonucleic acid (RNA) sequencing was performed on the rumen epithelium, and a total of 221 genes were identified as differentially expressed in the animals with liver abscesses compared with animals with no abscesses, after removal of genes that were identified as a result of interaction with sex. The nuclear factor kappa-light-chain enhancer of activated B cells signaling and interferon signaling pathways were significantly enriched in the differentially expressed gene (DEG) set. The majority of the genes in these pathways were downregulated in animals with liver abscesses. In addition, RNA translation and protein processing genes were also downregulated, suggesting that protein synthesis may be compromised in animals with liver abscesses. The rumen content bacterial communities were significantly different from the rumen wall epimural bacterial communities. Permutational multivariate analysis of variance (PERMANOVA) analysis did not identify global differences in the microbiome of the rumen contents but did identify differences in the epimural bacterial communities on the rumen wall of animals without and with liver abscesses. In addition, associations between DEG and specific bacterial amplicon sequence variants of epimural bacteria were observed. The DEG and bacterial profile on the rumen papillae identified in this study may serve as a method to monitor animals with existing liver abscesses or to predict those that are more likely to develop liver abscesses.

Growing crossbred steers [n = 80, initial body weight (BW) = 274 kg, SD = 21] were used to evaluate the effect of ad libitum and limit-fed intakes on methane (CH4) production. Two treatments with four pens per treatment (10 steers per pen) were evaluated in a randomized block designed experiment, with BW as a blocking factor. Treatments included feeding the same diet at ad libitum intake or limit fed at 75% of ad libitum intakes. Diet consisted of 45% alfalfa, 30% sorghum silage, 22% modified distillers grains plus solubles, and supplement at 3% on a dry matter (DM) basis. This trial was followed by a finishing trial (n = 80; initial BW = 369 kg; SD = 25) to evaluate the effects of dietary corn oil on CH4 production. Two treatments with four pens per treatment (10 steers per pen) were used in a randomized complete block designed experiment. Cattle were rerandomized and blocked by BW within the previous treatment. Treatments consisted of a control diet (CON) containing 66% corn, 15% wet distillers grains plus solubles, 15% corn silage, and 4% supplement (DM basis). Corn oil treatment (OIL) displaced 3% corn by adding corn oil. Methane was collected in two pen-scale chambers by collecting air samples continuously from pens by rotating every 6 min with an ambient sample taken between pen measurements. Steers fed ad libitum had greater DM intake (DMI) by design and greater average daily gain (ADG; P < 0.01) compared to limit-fed cattle; however, feed efficiency was not different between treatments (P = 0.40). Cattle fed ad libitum produced 156 g/d of CH4, which was greater (P < 0.01) than limit-fed cattle (126 g per steer daily). In the finishing trial, BW, gains, and carcass traits were not impacted by treatment (P ≥ 0.14). Feed efficiency (P = 0.02) improved because intakes decreased (P = 0.02) by feeding OIL compared to CON. Daily CH4 production was less (P = 0.03) for OIL-fed cattle (115 g per steer daily) compared to CON-fed cattle (132 g per steer daily). Methane was reduced (P < 0.01) by 17% for OIL-fed cattle compared to CON-fed cattle when expressed as grams of CH4 per kilogram of ADG. Feeding corn oil at 3% of diet DM reduced enteric CH4 production (grams per day) by 15%, which was only partially explained by a 3% decrease in DMI. Overall, a decrease in CH4 was observed when intake is limited in growing cattle and when corn oil is added in finishing diets.

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 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.

Ruminants are critical to global food security as they transform lignocellulosic biomass into high-quality protein products. The rumen microbes ferment feed to provide necessary energy and nutrients for the ruminant host. However, we still lack insight into the metabolic processes encoded by most rumen microbial populations. In this study, we implemented metagenomic binning approaches to recover 2,809 microbial genomes from cattle, sheep, moose, deer, and bison. By clustering genomes based on average nucleotide identity, we demonstrate approximately one-third of the metagenome-assembled genomes (MAGs) to represent species not present in current reference databases and rumen microbial genome collections. Combining these MAGs with other rumen genomic datasets permitted a phylogenomic characterization of the biosynthetic gene clusters (BGCs) from 8,160 rumen microbial genomes, including the identification of 195 lanthipeptides and 5,346 diverse gene clusters for nonribosomal peptide biosynthesis. A subset of Prevotella and Selenomonas BGCs had higher expression in steers with lower feed efficiency. Moreover, the microdiversity of BGCs was fairly constant across types of BGCs and cattle breeds. The reconstructed genomes expand the genomic representation of rumen microbial lineages, improve the annotation of multi-omics data, and link microbial populations to the production of secondary metabolites that may constitute a source of natural products for manipulating rumen fermentation., Anderson and Fernando use metagenomic binning approaches to reconstruct 2,809 microbial metagenome-assembled genomes from ruminants, and perform phylogenomic analyses on the biosynthetic gene clusters from over 8,000 total rumen microbial genomes. These genomes provide insight into the relationship between microbial populations and the production of secondary metabolites that may be important for manipulating rumen fermentation.

In light of recent host-microbial association studies, a consensus is evolving that species composition of the gastrointestinal microbiota is a polygenic trait governed by interactions between host genetic factors and the environment. Here, we investigated the effect of host genetic factors in shaping the bacterial species composition in the rumen by performing a genome-wide association study. Using a common set of 61,974 single-nucleotide polymorphisms found in cattle genomes (n = 586) and corresponding rumen bacterial community composition, we identified operational taxonomic units (OTUs), Families and Phyla with high heritability. The top associations (1-Mb windows) were located on 7 chromosomes. These regions were associated with the rumen microbiota in multiple ways; some (chromosome 19; position 3.0–4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae, and RF16), some (chromosome 27; position 3.0–4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae, RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0–1.0) associated with both related and unrelated taxa. The annotated genes associated with identified genomic regions suggest the associations observed are directed toward selective absorption of volatile fatty acids from the rumen to increase energy availability to the host. This study demonstrates that host genetics affects rumen bacterial community composition.

Feeding fat to lactating dairy cows may reduce methane production. Relative to cellulose, fermentation of hemicellulose is believed to result in less methane; however, these factors have not been studied simultaneously. Eight multiparous, lactating Jersey cows averaging (±SD) 98 ± 30.8 d in milk and body weight of 439.3 ± 56.7 kg were used in a twice-replicated 4 × 4 Latin square to determine the effects of fat and hemicellulose on energy utilization and methane production using a headbox-type indirect calorimetry method. To manipulate the concentration of fat, porcine tallow was included at either 0 or 2% of the diet dry matter. The concentration of hemicellulose was adjusted by manipulating the inclusion rate of corn silage, alfalfa hay, and soybean hulls resulting in either 11.3 or 12.7% hemicellulose (dry matter basis). The resulting factorial arrangement of treatments were low fat low hemicellulose (LFLH), low fat high hemicellulose (LFHH), high fat low hemicellulose (HFLH), and high fat high hemicellulose (HFHH). Neither fat nor hemicellulose affected dry matter intake, averaging 16.2 ± 1.18 kg/d across treatments. Likewise, treatments did not affect milk production, averaging 23.0 ± 1.72 kg/d, or energy-corrected milk, averaging 30.1 ± 2.41 kg/d. The inclusion of fat tended to reduce methane produced per kilogram of dry matter intake from 24.9 to 23.1 ± 1.59 L/kg, whereas hemicellulose had no effect. Increasing hemicellulose increased neutral detergent fiber (NDF) digestibility from 43.0 to 51.1 ± 2.35%. Similarly, increasing hemicellulose concentration increased total intake of digestible NDF from 6.62 to 8.42 ± 0.89 kg/d, whereas fat had no effect. Methane per unit of digested NDF tended to decrease from 64.8 to 49.2 ± 9.60 L/kg with increasing hemicellulose, whereas fat had no effect. An interaction between hemicellulose and fat content on net energy balance (milk plus tissue energy) was observed. Specifically, increasing hemicellulose in low-fat diets tended to increase net energy balance, but this was not observed in high-fat diets. These results confirm that methane production may be reduced with the inclusion of fat, whereas energy utilization of lactating dairy cows is improved by increasing hemicellulose in low-fat diets.

Sectioned and formed turkey breast and roast beef were manufactured with four salt concentrations (1.0%, 1.5%, 2.0%, and 2.5%, meat block basis). After cooking, chilling, and slicing, samples were evaluated throughout 18 weeks of storage for various quality parameters, and microbial community changes. Microbial community changes were analyzed using 16S rRNA gene sequencing for the V4 region. Bacterial richness decreased over storage time (P = .040) and as salt concentration increased (P = .021). Microbial communities were dominated by bacteria from family Pseudomonadaceae, regardless of treatment or storage time. Salt reduction had greater negative effects on cooking yield (P

The importance of the rumen microbiota on nutrient cycling to the animal is well recognized; however, our understanding of the influence of the rumen microbiome composition on feed efficiency is limited. The rumen microbiomes of two large animal cohorts (125 heifers and 122 steers) were characterized to identify specific bacterial members (operational taxonomic units [OTUs]) associated with feed efficiency traits (ADFI, ADG, and G:F) in beef cattle. The heifer and steer cohorts were fed a forage-based diet and a concentrate-based diet, respectively. A rumen sample was obtained from each animal via esophageal tubing and bacterial community composition was determined through 16S rRNA gene sequencing of the V4 region. Based on a regression approach that used individual performance measures, animals were classified into divergent feed efficiency groups. Within cohort, an extreme set of 16 animals from these divergent groups was selected as a discovery population to identify differentially abundant OTUs across the rumen bacterial communities. The remaining samples from each cohort were selected to perform forward stepwise regressions using the differentially abundant OTUs as explanatory variables to distinguish predictive OTUs for the feed efficiency traits and to quantify the OTUs collective impact on feed efficiency phenotypes. OTUs belonging to the families Prevotellaceae and Victivallaceae were present across models for heifers, whereas OTUs belonging to the families Prevotellaceae and Lachnospiraceae were present across models for steers. Within the heifer cohort, models explained 19.3%, 25.3%, and 19.8% of the variation for ADFI, ADG, and G:F, respectively. Within the steer cohort, models explained 27.7%, 32.5%, and 26.9% of the variation for ADFI, ADG, and G:F, respectively. Overall, this study suggests a substantial role of the rumen microbiome on feed efficiency responses.

Aims The effects of partial replacement of a barley-based concentrate with flaxseed-based products on the rumen bacterial population of lactating Holstein dairy cows were evaluated. Methods and Results Treatments fed were CONT, a normal diet that included barley silage, alfalfa hay, and a barley-based concentrate that contained no flaxseed or faba beans; FLAX, inclusion of a non-extruded flaxseed-based product containing 55.0% flaxseed, 37.8% field peas and 6.9% alfalfa; EXT, similar to FLAX, but the product was extruded; and EXTT, similar to FLAX, but product was extruded and field peas were replaced by high-tannin faba beans. The rumen bacterial population was evaluated by utilizing 16S rRNA gene sequencing. Most abundant phyla, families and genera were unaffected. However, some taxa were affected; for example, unsaturated fatty acid content was negatively correlated with Clostridiaceae, tannin content was negatively correlated with BS11 and Paraprevotellaceae. Conclusions Predominant rumen bacterial taxa were not affected, but the abundance of some taxa found in lower proportions shifted, possibly due to sensitivity to unsaturated fatty acids or tannins. Significance and impact of the study Flaxseed-based products were effective for partially replacing barley-based concentrate in rations of lactating dairy cows. No negative effects of these products were observed on the abundance of predominant rumen bacterial taxa, with only minor shifts in less abundant bacteria. This article is protected by copyright. All rights reserved.

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 < 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.

A study was conducted to determine the effect of nitrate and sulfate supplementation on cattle performance and methane emissions in finishing diets and to identify the effect of nitrate and sulfate addition on rumen microbiota composition and function. One hundred and thirty one day feeding trial was conducted using 24 head of cattle (initial BW = 918 lb; SD = 79 lb) where the cattle received one of four treatments no supplementation (CON), 2.0% dietary nitrate (NT), 0.54% dietary sulfate (SF) or both (COMBO), with 6 steers per treatment. Performance, volatile fatty acid (VFAs) profile and CH4:CO2 emissions data were analyzed using MIXED procedure of SAS. Rumen samples were collected and analyzed through amplicon sequencing targeting the 16S rDNA gene V4 region. Microbiome richness and composition were analyzed using Qiime2. Microbial genes involved in pathways linked to methanogenesis, nitrate, and sulfate metabolism were identified with metagenomic sequencing. Gene prediction, functional profile and pathway mapping were conducted using KEGG database. In diets with only sulfate or nitrate, diet had no impact on CH4:CO2 emissions, but nitrate and sulfate in combination decreased CH4:CO2. However, a reduction in dry matter intake (DMI) (P < 0.01), average daily gain (ADG) (P = 0.07) and gain:feed (G:F) (P = 0.09) was also recorded. Significant increase in bacterial genera with H2 utilization capability e.g. propionate, lactate forming bacteria e.g. Prevotella, Bacteroides, Megasphaera, Selenomonas, Lactobacillus; nitrate and sulfate reducing bacteria e.g. Selenomonas, Desulfovibrio was observed in COMBO diet. Differential gene abundance in metabolic pathways illustrated decrease of enzymes linked to methanogenesis in COMBO diet. This study provides evidence that methane yield is linked to diet type and differential gene abundance in the cattle rumen microbiome.

Bacterial and archaeal genomes can contain 30% or more hypothetical genes with no predicted function. Phylogenetically deep-branching microbes, such as methane-producing archaea (methanogens), contain up to 50% genes with unknown function. In order to formulate hypotheses about the function of hypothetical gene functions in the strict anaerobe, Methanosarcina acetivorans, we have developed high-throughput anaerobic techniques to UV mutagenize, screen, and select for mutant strains in 96-well plates. Using these approaches we have isolated 10 mutant strains that exhibit a variety of physiological changes including increased or decreased growth rate relative to the parent strain when cells use methanol and/or acetate as carbon and energy sources. This method provides an avenue for the first step in identifying new gene functions: associating a genetic mutation with a reproducible phenotype. Mutations in bona fide methanogenesis genes such as corrinoid methyltransferases and proton-translocating F420H2:methanophenazine oxidoreductase (Fpo) were also generated, opening the door to in vivo functional complementation experiments. Irradiation-based mutagenesis such as from ultraviolet (UV) light, combined with modern genome sequencing, is a useful procedure to discern systems-level gene function in prokaryote taxa that can be axenically cultured but which may be resistant to chemical mutagens.

An experiment was conducted to evaluate the effect of dietary medium-chain fatty acid (MCFA) addition on nursery pig growth performance, fecal microbial composition, and mitigation of porcine epidemic diarrhea virus (PEDV) following storage. A total of 360 pigs (DNA 400 × 200, Columbus, NE; initially 6.7 ± 0.07 kg) were randomized to pens (5 pigs per pen) on the day of weaning (approximately 20 d of age), allowed a 6-d acclimation, blocked by BW, and randomized to dietary treatment (9 pens per treatment). All MCFA (Sigma–Aldrich, St. Louis, MO) were guaranteed ≥98% purity, including hexanoic (C6:0), octanoic (C8:0), and decanoic (C10:0) acids. Treatment diets were formulated in 2 phases (7 to 11 and 11 to 23 kg BW) and formulated to meet or exceed NRC requirement estimates. Treatments (n = 8) were a dose response including 0%, 0.25%, 0.5%, 1.0%, and 1.5% added MCFA blend (1:1:1 ratio C6:0, C8:0, and C10:0), as well as treatments with individual additions of 0.5% C6:0, C8:0, or C10:0. Fecal samples were collected from pigs fed control and 1.5% MCFA blend diets on days 0 and 14 and analyzed using 16s rDNA sequencing. Following feed manufacture, feed was stored in bags at barn temperature and humidity for 40 d before laboratory inoculation with PEDV. Subsamples of retained feed were inoculated with PEDV to achieve a titer of 104 TCID50/g and separate sample bottles were analyzed on 0 and 3 d post-inoculation (dpi). Overall, ADG and ADFI were increased (linear, P ≤ 0.010) and feed efficiency (G:F) improved (linear, P = 0.004) with increasing MCFA blend. Pigs fed 0.5% C8:0 had greater (P = 0.038) ADG compared with pigs fed the control diet, and G:F was improved (P ≤ 0.024) when pigs were fed 0.5% C6:0, 0.5% C8:0, or 0.5% C10:0 compared with control. An inclusion level × day interaction was observed (quadratic, P = 0.023), where PEDV Ct values increased (quadratic, P = 0.001) on 0 dpi with increasing levels of MCFA blend inclusion and also increased on 3 dpi (linear, P < 0.001). Fecal microbial diversity and composition were similar between control and 1.5% MCFA blend. In summary, the use of MCFA in nursery pig diets improves growth performance, provides residual mitigation activity against PEDV, and does not significantly alter fecal microbial composition.