Robin C. Anderson

Bio: Robin C. Anderson is an academic researcher from United States Department of Agriculture. The author has contributed to research in topics: Salmonella & Chlorate. The author has an hindex of 48, co-authored 293 publications receiving 7939 citations. Previous affiliations of Robin C. Anderson include Texas A&M University & Agricultural Research Service.

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.

Abstract: 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 = 007) in the 25 and 50% DDG diets compared with controls Ruminal pH was decreased (P < 005) 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

Diet, Escherichia coli O157:H7, and cattle: a review after 10 years.

Abstract: Escherichia coli are commensal bacteria that can account for up to 1% of the bacterial population of the gut. Ruminant animals are reservoirs of the pathogenic bacteria E. colil strain O157:H7, and approximately 30% of feedlot cattle shed E. coli O157:H7. Feedlot and high-producing dairy cattle are fed high grain rations in order to increase feed efficiency. When cattle are fed high grain rations, some starch escapes ruminal microbial degradation and passes to the hindgut where it undergoes fermentation. Ten years ago researchers demonstrated that populations of total E. coli were higher in grain-fed than in forage-fed cattle, and when cattle were abruptly switched from a high grain diet to an all hay diet, total E. coli populations declined 1000-fold within 5 days and reduced the ability of the surviving E. coli to survive an acid shock mimicking passage through the human gastric stomach. This research provoked many questions about the effects of diet or E. coli O157:H7 populations that have not been conclusively answered to date. Subsequent research has shown that diet does affect E. coli O157:H7 populations, but the effects have varied in magnitude and impact. Further studies have demonstrated that the effects of forage feeding on E. coli O157:H7 populations may be due to concentrations of tannins and phenolic acids in forages. Other ration components such as rapidly ruminally fermented grains (e.g., barley) increase the shedding of E. coli O157:H7, and in some situations, feeding distillers grains can increase fecal shedding of E. coli O157:H7 due to VFA concentrations. Data from researchers across North America indicate that diet does impact STEC/EHEC populations in cattle prior to slaughter; however the economic, logistic and practical impacts of dietary changes must be examined and accounted for.

Probiotics, prebiotics and competitive exclusion for prophylaxis against bacterial disease.

Abstract: The microbial population of the intestinal tract is a complex natural resource that can be utilized in an effort to reduce the impact of pathogenic bacteria that affect animal production and efficiency, as well as the safety of food products. Strategies have been devised to reduce the populations of food-borne pathogenic bacteria in animals at the on-farm stage. Many of these techniques rely on harnessing the natural competitive nature of bacteria to eliminate pathogens that negatively impact animal production or food safety. Thus feed products that are classified as probiotics, prebiotics and competitive exclusion cultures have been utilized as pathogen reduction strategies in food animals with varying degrees of success. The efficacy of these products is often due to specific microbial ecological factors that alter the competitive pressures experienced by the microbial population of the gut. A few products have been shown to be effective under field conditions and many have shown indications of effectiveness under experimental conditions and as a result probiotic products are widely used in all animal species and nearly all production systems. This review explores the ecology behind the efficacy of these products against pathogens found in food animals, including those that enter the food chain and impact human consumers.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Anti-virulence strategies to combat bacteria-mediated disease

Abstract: Antibiotic resistance is one of the greatest challenges of the twenty-first century. However, the increasing understanding of bacterial pathogenesis and intercellular communication has revealed many potential strategies to develop novel drugs to treat bacteria-mediated disease. Interference with bacterial virulence and/or cell-to-cell signalling pathways is an especially compelling approach, as it is thought to apply less selective pressure for the development of bacterial resistance than traditional strategies, which are aimed at killing bacteria or preventing their growth. Here, we discuss the mechanisms of bacterial virulence and present promising anti-virulence strategies and compounds for the future treatment of bacterial infections.

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

Abstract: The microbiota of an animal's intestinal tract plays important roles in the animal's 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. Ubiquitous 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). Using 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.