Thomas S. Edrington

Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

BackgroundThe microbiota of an animals intestinal tract plays important roles in the animals overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP) approach that is able to perform diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows.ResultsUbiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the cattle, a total of 4 cows were found to be positive for Salmonella spp (tentative enterica) and 6 cows were positive for Campylobacter spp. (tentative lanienae).ConclusionUsing bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing.

Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing.

Dietary components and changes cause shifts in the gastrointestinal microbial ecology that can play a role in animal health and productivity. However, most information about the microbial populations in the gut of livestock species has not been quantitative. In the present study, we utilized a new molecular method, bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) that can perform diversity analyses of gastrointestinal bacterial populations. In the present study, cattle (n = 6) were fed a basal feedlot diet and were subsequently randomly assigned to 1 of 3 diets (n = 2 cows per diet). In each diet, 0, 25, or 50% of the concentrate portion of the ration was replaced with dried distillers grain (DDGS). Ruminal and fecal bacterial populations were different when animals were fed DDGS compared with controls; ruminal and fecal Firmicute:Bacteroidetes ratios were smaller (P = 0.07) in the 25 and 50% DDG diets compared with controls. Ruminal pH was decreased (P < 0.05) in ruminal fluid from cattle fed diets containing 50% compared with 0% DDGS. Using bTEFAP, the normal microbiota of cattle were examined using modern molecular methods to understand how diets affect gastrointestinal ecology and the gastrointestinal contribution of the microbiome to animal health and production.

Evaluation of the bacterial diversity in cecal contents of laying hens fed various molting diets by using bacterial tag-encoded FLX amplicon pyrosequencing

Laying hens are typically induced to molt to begin a new egg-laying cycle by withdrawing feed for up to 12 to 14 d. Fasted hens are more susceptible to colonization and tissue invasion by Salmonella enterica serovar Enteritidis. Much of this increased incidence in fasted hens is thought to be due to changes in the native intestinal microflora. An alternative to feed withdrawal involves feeding alfalfa meal crumble to hens, which is indigestible by poultry but provides fermentable substrate to the intestinal microbial population and reduces Salmonella colonization of hens compared with feed withdrawal. The present study was designed to quantify differences in the cecal microbial population of hens (n=12) fed a typical layer ration, undergoing feed withdrawal, or being fed alfalfa crumble by using a novel tag bacterial diversity amplification method. Bacteroides, Prevotella, and Clostridium were the most common genera isolated from all treatment groups. Only the ceca of hens undergoing feed withdrawal (n=4) contained Salmonella. The number of genera present was greatest in the alfalfa crumble-fed group and least in the feed withdrawal group (78 vs. 54 genera, respectively). Overall, the microbial diversity was least and Lactobacillius populations were not found in the hens undergoing feed withdrawal, which could explain much of these hens sensitivity to colonization by Salmonella.

Variation in the faecal shedding of Salmonella and E. coli O157:H7 in lactating dairy cattle and examination of Salmonella genotypes using pulsed‐field gel electrophoresis

Aims:u2002 To examine the variability in faecal shedding of Salmonella and Escherichia coli O157:H7 in healthy lactating dairy cattle and to evaluate the genetic relatedness of Salmonella isolates.

Antimicrobial susceptibility and factors affecting the shedding of E. coli O157:H7 and Salmonella in dairy cattle.

Aims: To examine factors affecting faecal shedding of the foodborne pathogens Escherichia coli O157:H7 and Salmonella in dairy cattle and evaluate antimicrobial susceptibility of these isolates.

Reduction of E. coli O157:H7 populations in sheep by supplementation of an experimental sodium chlorate product

Ruminant animals are naturally infected with the pathogen Escherichia coli O157:H7, annually responsible for numerous meat recalls, foodborne illnesses and deaths. E. coli are equipped with the enzyme nitrate reductase, which not only enables this bacteria to respire anaerobically, but also converts chlorate to the toxic metabolite chlorite. This enzyme system is particular to only a few intestinal bacteria, therefore the vast majority are not affected by chlorate. Sodium chlorate has been shown to effectively decrease foodborne pathogens in several livestock species, including ruminants. However, because infection and proliferation of E. coli occurs primarily in the lower intestine, there is interest in “by-passing” the rumen, thereby, delivering chlorate directly to the largest population of pathogens. The objective of the current study was to evaluate the ability of an experimental sodium chlorate product (ECP II), designed to by-pass the rumen, in reducing fecal shedding and gut concentrations of E. coli O157:H7. Twenty crossbred mature ewes were adapted to a high grain ration and experimentally inoculated with E. coli O157:H7. Thirty-six hours following inoculation, sheep received in their feed one of the following ECP treatments: (1) control (CON), no chlorate; (2) 1X (LOW); (3) 2X (MED); and (4) 4X (HIGH) where X=1.1 g chlorate ion equivalents/kg BW (five sheep per treatment). Fecal samples were collected every 12 h following inoculation and 24 h following the feeding of chlorate, all animals were euthanized and tissue samples and their respective contents collected from the rumen, cecum and rectum. The MED and HIGH chlorate treatments significantly reduced fecal shedding of E. coli O157:H7 compared to the CON treatment [1.53, 1.11, and 3.89 CFU/g feces (log10), respectively]. Ruminal contents were similar among treatments, while chlorate tended to decrease (P=0.08) and reduced (P<0.05) E. coli O157:H7 populations in the cecum and rectum, respectively. Populations of generic E. coli in the cecal contents were numerically lower (P=0.11) in the LOW treatment and tended to decrease (P=0.06) in the MED and HIGH chlorate treatments, respectively. Fermentation profiles through the gastrointestinal tract were unaffected as indicated by slight, but not significant, changes in volatile fatty acids (VFA) profiles in sheep fed chlorate. Results from this study indicate that this experimental chlorate product, administered in the feed, was effective in reducing E. coli O157:H7 from the lower gut of sheep as evidenced by the lower cecal and rectal but not ruminal concentrations. Feeding chlorate may be an effective method to decrease E. coli O157:H7 populations in ruminant animals prior to slaughter.

Cross-sectional Study Examining Salmonella enterica Carriage in Subiliac Lymph Nodes of Cull and Feedlot Cattle at Harvest

Bovine peripheral lymph nodes (LNs), including subiliac LNs, have been identified as a potential source of human exposure to Salmonella enterica, when adipose trim containing these nodes is incorporated into ground beef. In order to gain a better understanding of the burden of S. enterica in peripheral LNs of feedlot and cull cattle, a cross-sectional study was undertaken in which 3327 subiliac LNs were collected from cattle at harvest in seven plants, located in three geographically distinct regions of the United States. Samples were collected in three seasons: Fall 2010, Winter/Spring 2011, and Summer/Fall 2011. A convenience sample of 76 LNs per day, 2 days per season (approximately 1 month apart), was collected per plant, from carcasses held in the cooler for no less than 24u2009h. Every 10(th) carcass half on a rail was sampled, in an attempt to avoid oversampling any single cohort of cattle. Median point estimates of S. enterica contamination were generally low (1.3%); however, median Salmonella prevalence was found to be greater in subiliac LNs of feedlot cattle (11.8%) compared to those of cull cattle (0.65%). Enumeration analysis of a subset of 618 feedlot cattle LNs showed that 67% of those harboring S. enterica (97 of 144) did so at concentrations ranging from <0.1 to 1.8 log10 CFU/g, while 33% carried a higher burden of S. enterica, with levels ranging from 1.9 to >3.8 log10 CFU/g. Serotyping of S. enterica isolated identified 24 serotypes, with the majority being Montevideo (44.0%) and Anatum (24.8%). Antimicrobial susceptibility phenotypes were determined for all isolates, and the majority (86.1%) were pansusceptible; however, multidrug-resistant isolates (8.3%) were also occasionally observed. As Salmonella contained within LNs are protected from carcass interventions, research is needed to define opportunities for mitigating the risk of Salmonella contamination in LNs of apparently healthy cattle.

Reduction of Salmonella Typhimurium in experimentally challenged broilers by nitrate adaptation and chlorate supplementation in drinking water.

The effects of two feed supplements on Salmonella Typhimurium in the ceca of market-age broilers were determined. Broilers orally challenged 6 days before slaughter with a novobiocin- and nalidixic acid-resistant strain of Salmonella Typhimurium were divided into one of four groups (20 birds each). The first group (the control group) received no treatment, the second group received sodium nitrate (SN) treatment (574 mg of NaNO3 per kg of feed), the third group received experimental chlorate product (ECP) treatment (15 mM NaClO3 equivalents), and the fourth group received ECP treatment in combination with SN treatment. The SN treatment was administered via feed for 5 days immediately before slaughter, and ECP was provided via ad libitum access to drinking water for the last 2 days before slaughter. Cecal contents were subjected to bacterial analysis. Significant (P < 0.05) Salmonella Typhimurium reductions (ca. 2 log units) relative to levels for untreated control broilers were observed for broilers receiving ECP in combination with SN. The ECP-only treatment resulted in significant (P < 0.05) reductions (ca. 0.8 log) of Salmonella Typhimurium in trial 2. We hypothesize that increasing Salmonella Typhimurium nitrate reductase activity resulted in increased enzymatic reduction of chlorate to chlorite, with a concomitant decrease in cecal Salmonella Typhimurium levels. On the basis of these results, preadaptation with SN followed by ECP supplementation immediately preharvest could be a potential strategy for the reduction of Salmonella Typhimurium in broilers.

Salmonella prevalence in bovine lymph nodes differs among feedyards.

Lymphatic tissue, specifically lymph nodes, is commonly incorporated into ground beef products as a component of lean trimmings. Salmonella and other pathogenic bacteria have been identified in bovine lymph nodes, which may impact compliance with the Salmonella performance standards for ground beef established by the U.S. Department of Agriculture. Although Salmonella prevalence has been examined among lymph nodes between animals, no data are currently available regarding feedyard origin of the cattle and Salmonella prevalence. Bovine lymph nodes (279 superficial cervical plus 28 iliofemoral = 307) were collected from beef carcasses at a commercial beef harvest and processing plant over a 3-month period and examined for the prevalence of Salmonella. Cattle processed were from seven feedyards (A through G). Salmonella prevalence was exceptionally low (0% of samples were positive ) in cattle from feedyard A and high (88.2%) in cattle from feedyard B. Prevalence in the remaining feedyards ranged widely: 40.0% in feedyard C, 4.0% in feedyard D, 24.0% in feedyard E, 42.9% in feedyard F, and 40.0% in feedyard G. These data indicate the range of differences in Salmonella prevalence among feedyards. Such information may be useful for developing interventions to reduce or eliminate Salmonella from bovine lymph nodes, which would assist in the reduction of Salmonella in ground beef.

Experimental use of 2-nitropropanol for reduction of Salmonella Typhimurium in the ceca of broiler chicks

The effect of 2-nitropropanol (2NPOH) administration on Salmonella enterica serovar Typhimurium in experimentally infected chicks was determined. Chicks orally challenged with 10(6) CFU/ml of a novobiocin- and naladixic acid-resistant Salmonella Typhimurium at 6 days of age were divided into three groups receiving 0 (control), 6.5, and 13 mg 2NPOH per bird (experiment 1) or four groups receiving 0 (control), 13, 65, and 130 mg 2NPOH per bird (experiment 2). Treatments were administered orally 1 day post-Salmonella challenge. Cecal contents collected at necropsy 24 and 48 h after treatment were subjected to bacterial and volatile fatty acid (VFA) analysis. In experiment 1, concentrations (mean+/-SD log CFU per g) of Salmonella were reduced (P < 0.05) in the group administered 13 mg 2NPOH per bird at both the 24- and 48-h samplings compared with the controls (2.58+/-2.10 versus 4.64+/-1.79 and 2.88+/-2.78 versus 5.03+/-2.42 at 24 and 48 h, respectively). In experiment 2, mean+/-SD populations of Salmonella were reduced (P < 0.05) in all groups receiving 2NPOH compared with untreated controls (3.65+/-2.01, 3.39+/-2.42, and 3.47+/-1.55 at 13, 65, and 130 mg, respectively, versus 6.09+/-1.02). Propionate concentrations were reduced (P < 0.05) by the 13-mg 2NPOH per bird treatment. Total VFA concentrations from the group treated with 13 mg 2NPOH per bird were lower (P < 0.05) by 48, but not 24, hours posttreatment than those from the group treated with 6.5 mg 2NPOH per bird. These results demonstrate the inhibitory activity of 2NPOH against Salmonella Typhimurium in vivo.