Research Topics
Genomes and GenesSpecies | R I MackieSummaryAffiliation: University of Illinois Country: USA Publications
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Publications
Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approachesRoderick I Mackie
Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
Appl Environ Microbiol 69:6808-15. 2003....
Biochemical identification and biological origin of key odor components in livestock wasteR I Mackie
Department of Animal Sciences, University of Illinois, Urbana 61801, USA
J Anim Sci 76:1331-42. 1998..Multiple combinations of nutritional management, housing systems, treatment options as well as storage and disposal of animal wastes will be required to reduce environmental pollution and provide for long-term sustainable growth...- Tetracycline residues and tetracycline resistance genes in groundwater impacted by swine production facilitiesRoderick I Mackie
Department of Animal Sciences, Division of Nutritional Sciences, Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
Anim Biotechnol 17:157-76. 2006.... - Developmental microbial ecology of the neonatal gastrointestinal tractR I Mackie
Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana 61801, USA
Am J Clin Nutr 69:1035S-1045S. 1999..Further advances in our understanding of developmental microbial ecology in the neonatal gastrointestinal tract are dependent on the application of these modern molecular techniques... - Biochemical and microbiological evidence for fermentative digestion in free-living land iguanas (Conolophus pallidus) and marine iguanas (Amblyrhynchus cristatus) on the Galápagos archipelagoRoderick I Mackie
Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
Physiol Biochem Zool 77:127-38. 2004.... - Molecular ecology of tetracycline resistance: development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteinsR I Aminov
Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
Appl Environ Microbiol 67:22-32. 2001..This is the first demonstration of the applicability of molecular ecology techniques to estimation of the gene pool and the flux of antibiotic resistance genes in production animals... - Occurrence and diversity of tetracycline resistance genes in lagoons and groundwater underlying two swine production facilitiesJ C Chee-Sanford
Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Appl Environ Microbiol 67:1494-502. 2001..This study demonstrated that tet genes occur in the environment as a direct result of agriculture and suggested that groundwater may be a potential source of antibiotic resistance in the food chain... - Development, validation, and application of PCR primers for detection of tetracycline efflux genes of gram-negative bacteriaR I Aminov
Department of Animal Sciences, University of Illinois at Urbana Champaign USDA Agricultural Research Service, Urbana, Illinois 61801, USA
Appl Environ Microbiol 68:1786-93. 2002.... - Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year periodS Koike
Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
Appl Environ Microbiol 73:4813-23. 2007..Novel sequence clusters and unique indigenous resistance gene pools were also found in the groundwater. Thus, antibiotic resistance genes in groundwater are affected by swine manure, but they are also part of the indigenous gene pool... - Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiotaV J McCracken
Department of Animal Sciences, The University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
J Nutr 131:1862-70. 2001..These results demonstrate the utility of cultivation-independent PCR-DGGE analysis combined with measurements of ecological diversity for monitoring diet- and antibiotic-induced alterations of the complex intestinal microbial ecosystem... 
Molecular ecology of macrolide-lincosamide-streptogramin B methylases in waste lagoons and subsurface waters associated with swine productionSatoshi Koike
Department of Animal Sciences, University of Illinois at Urbana Champaign, 1207 W Gregory Dr, Urbana, IL 61801, USA
Microb Ecol 59:487-98. 2010..Considerations of gene origins in history (i.e., phylogeny) and gene distributions in the landscape provide a useful "molecular ecology" framework for studying environmental spread of antibiotic resistance...- Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions--II: Microbial population dynamicsK D McMahon
Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3221 Newmark Civil Eng. Lab, 205 North Mathews Avenue, Urbana, IL 61801, USA
Water Res 35:1817-27. 2001..Based on the results presented here, mixing appears to inhibit the syntrophic oxidation of volatile fatty acids, possibly by disrupting the spatial juxtaposition of syntrophic bacteria and their methanogenic partners... - Characterization of fecal bacterial populations in canines: effects of age, breed and dietary fiberJ M Simpson
Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
Microb Ecol 44:186-97. 2002..The relative stability and individuality of the patterns indicates that each individual harbored a characteristic fecal bacterial community which was independent of diet... - Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure wasteJoanne C Chee-Sanford
USDA ARS, 1102 S Goodwin Ave, Urbana, IL 61801, USA
J Environ Qual 38:1086-108. 2009.... - Molecular ecological analysis of fecal bacterial populations from term infants fed formula supplemented with selected blends of prebioticsNoriko Nakamura
Division of Nutritional Sciences, Institute for Genomic Biology, University of Illinois at Urbana Champaign, 1207 W Gregory Drive, Urbana, IL 61801, USA
Appl Environ Microbiol 75:1121-8. 2009.... - Characterization of two novel saccharolytic, anaerobic thermophiles, Thermoanaerobacterium polysaccharolyticum sp. nov. and Thermoanaerobacterium zeae sp. nov., and emendation of the genus ThermoanaerobacteriumI K Cann
Department of Animal Sciences, University of Illinois at Urbana Champaign, 61801, USA
Int J Syst Evol Microbiol 51:293-302. 2001..nov. and Thermoanaerobacterium zeae sp. nov. are 46 and 42 mol%, respectively. The type strains are KMTHCJT (= ATCC BAA-17T = DSM 13641T) and mel2T (= ATCC BAA-16T = DSM 13642T), respectively... - Bacterial diversity and distribution in the holocene sediments of a northern temperate lakeDavid M Nelson
Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
Microb Ecol 54:252-63. 2007..The observed patterns of diversity may be caused by increased bacterial niche-partitioning in younger sediments that contain a greater abundance of labile organic matter than older sediments... - Antimicrobial use and resistance in swine waste treatment systemsArchana Jindal
Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 3204 Newmark Civil Engineering Laboratory, MC250, 205 North Mathews Avenue, Urbana, IL 61801, USA
Appl Environ Microbiol 72:7813-20. 2006.... - Continuous culture selection of bifidobacteria and lactobacilli from human faecal samples using fructooligosaccharide as selective substrateA Sghir
Department of Animal Sciences, University of IL at Urbana Champaign, USA
J Appl Microbiol 85:769-77. 1998..2-5.4 when FOS is the primary carbon and energy source, and (3) bifidobacteria can grow faster on FOS than lactobacilli under controlled conditions... - Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions--I. Digester performanceP G Stroot
Department of Civil and Environmental Engineering, University of Ilinois at Urbana-Champaign, 3221 Newmark Civil Eng. Lab, 205 North Mathews Avenue, Urbana, IL 61801, USA
Water Res 35:1804-16. 2001..In addition, reduction of mixing levels may be used as an operational tool to stabilize unstable digesters... - Characterization of the gene encoding glutamate dehydrogenase ( gdhA) from the ruminal bacterium Ruminococcus flavefaciens FD-1Dionysios A Antonopoulos
Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Dr, 61801, USA
Arch Microbiol 179:184-90. 2003..This is in agreement with the enzyme activity data obtained under ammonia- and carbon-limited growth conditions... - Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetesDylan Dodd
Department of Microbiology, University of Illinois, Urbana, Illinois 61801, USA
J Biol Chem 285:30261-73. 2010..This study therefore provides insights into capture of energy by xylanolytic Bacteroidetes and the application of their enzymes as a resource in the biofuel industry... - Comparative analyses of two thermophilic enzymes exhibiting both beta-1,4 mannosidic and beta-1,4 glucosidic cleavage activities from Caldanaerobius polysaccharolyticusYejun Han
Energy Biosciences Institute, University of Illinois, Urbana, IL 61801, USA
J Bacteriol 192:4111-21. 2010..Furthermore, on the basis of the biochemical and genomic data, a molecular mechanism for utilization of mannan-containing nutrients by C. polysaccharolyticus is proposed... - Selective growth of mucolytic bacteria including Clostridium perfringens in a neonatal piglet model of total parenteral nutritionBart Deplancke
Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 61801, USA
Am J Clin Nutr 76:1117-25. 2002..perfringens in particular were selected when enteral nutrients were withheld in this TPN piglet model. Similar enrichment processes may occur in humans nourished by TPN and may thereby contribute to intestinal dysfunction... - Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundraDavid M Nelson
Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
Int J Syst Evol Microbiol 59:1708-14. 2009..nov. are proposed, respectively. The type strain of Paenibacillus tundrae sp. nov. is A10b(T) (=NRRL B-51094(T)=DSM 21291(T)). The type strain of Paenibacillus xylanexedens sp. nov. is B22a(T) (=NRRL B-51090(T)=DSM 21292(T))... - Coccidia-induced mucogenesis promotes the onset of necrotic enteritis by supporting Clostridium perfringens growthC T Collier
Department of Animal Sciences, University of Illinois at Urbana Champaign, IL 61801, USA
Vet Immunol Immunopathol 122:104-15. 2008..perfringens. Collectively the data support the hypothesis that coccidial infection induces a host mucogenic response providing a growth advantage to C. perfringens, the causative agent of NE... - Complete nucleotide sequence of a cryptic plasmid, pBAW301, from the ruminal anaerobe Ruminococcus flavefaciens R13e2T May
Department of Animal Sciences, University of Illinois at Urbana Champaign 61801, USA
FEMS Microbiol Lett 144:221-7. 1996..These data suggest that this plasmid either replicates by an as yet undescribed mechanism, or represents a new class of theta replicating plasmids... - Microbial community analysis of rectal methanogens and sulfate reducing bacteria in two non-human primate speciesNoriko Nakamura
Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
J Med Primatol 38:360-70. 2009..Methanogenic status of mammals is suggested to be under evolutionary rather than dietary control. However, information is lacking regarding the dynamics of hydrogenotrophic microbial communities among different primate species... - Functional diversity of four glycoside hydrolase family 3 enzymes from the rumen bacterium Prevotella bryantii B14Dylan Dodd
Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
J Bacteriol 192:2335-45. 2010.... - Biochemical and domain analyses of FSUAxe6B, a modular acetyl xylan esterase, identify a unique carbohydrate binding module in Fibrobacter succinogenes S85Shosuke Yoshida
Energy Biosciences Institute, University of Illinois, Urbana, IL 61801, USA
J Bacteriol 192:483-93. 2010.... - Domain analysis of a modular alpha-L-Arabinofuranosidase with a unique carbohydrate binding strategy from the fiber-degrading bacterium Fibrobacter succinogenes S85Shosuke Yoshida
Energy Biosciences Institute, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
J Bacteriol 192:5424-36. 2010..These analyses showed that in GH43 members with a XX domain, the two modules have coevolved and that the length of a loop within the XX domain may serve as an important determinant of substrate specificity... - Mutational insights into the roles of amino acid residues in ligand binding for two closely related family 16 carbohydrate binding modulesXiaoyun Su
Energy Biosciences Institute, Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, USA
J Biol Chem 285:34665-76. 2010..Man5A is dependent on its CBMs for robust activity, and insights from this study should serve to enhance our understanding of the interdependence of its catalytic and substrate binding modules... - The BaeSR two-component regulatory system mediates resistance to condensed tannins in Escherichia coliErwin G Zoetendal
Department of Animal Sciences and Division of Nutritional Sciences, Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
Appl Environ Microbiol 74:535-9. 2008..BaeSR mutants were more tannin sensitive than their wild-type counterparts... - Molecular basis for the selectivity and specificity of ligand recognition by the family 16 carbohydrate-binding modules from Thermoanaerobacterium polysaccharolyticum ManABrian Bae
Department of Biochemistry, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
J Biol Chem 283:12415-25. 2008..These results provide detailed molecular insights into ligand recognition and yield a framework for rational engineering experiments designed to expand the natural repertoire of these targeting modules... - Molecular ecological analysis of the gastrointestinal microbiota: a reviewErwin G Zoetendal
Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, IL 61801, USA
J Nutr 134:465-72. 2004..Here, a critical summary is provided of current molecular ecological approaches for studying the GI microbiota... - Effect of condensed tannins on bacterial diversity and metabolic activity in the rat gastrointestinal tractAlexandra H Smith
Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801, USA
Appl Environ Microbiol 70:1104-15. 2004.... - Purification and characterization of a thermostable alpha-galactosidase from Thermoanaerobacterium polysaccharolyticumMichael R King
Department of Food Science and Human Nutrition and Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana 61801, USA
J Agric Food Chem 50:5676-82. 2002..Importantly, enzyme activity was only slightly inhibited by 75-100 mM galactose, an end product of hydrolysis. Enzyme activity was specific for the alpha-1,6-galactosyl bond, and activity was demonstrated on melibiose and soy molasses... - Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23Dylan Dodd
Department of Microbiology, University of Illinois, 1207 W Gregory Drive, Urbana, IL 61801, USA
J Bacteriol 191:3328-38. 2009..Directed mutagenesis of conserved residues for Xyl3A resulted in attenuation of activity, which supports the assignment of Xyl3A as a GH family 3 beta-D-xylosidase... - Biochemical and mutational analysis of glutamine synthetase type III from the rumen anaerobe Ruminococcus albus 8Kensey R Amaya
Department of Animal Sciences, 1207 W. Gregory Dr, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
J Bacteriol 187:7481-91. 2005..albus 8. Furthermore, the mutational studies on the conserved GSIII motifs demonstrated, for the first time, their importance in the structure and/or function of a GSIII protein... - Molecular microbial ecology of the gastrointestinal tract: from phylogeny to functionErwin G Zoetendal
Dept. of Animal Sciences, University of Illinois at Urbana-Champaign, IL, USA
Curr Issues Intest Microbiol 5:31-47. 2004.... - Novel rumen bacterial diversity in two geographically separated sub-species of reindeerMonica A Sundset
Department of Arctic Biology and Institute of Medical Biology, University of Tromsø, 9037, Tromsø, Norway
Microb Ecol 54:424-38. 2007..5%. Also, six of the isolates were putatively novel strains, possibly representing new species in the Clostridium subphylum (cluster XIVa), Actinomyces and Butyrivibrio... - Bacterial mechanisms to overcome inhibitory effects of dietary tanninsAlexandra H Smith
Department of Microbiology, University of Texas, Southwestern Medical Center, Dallas, TX 75390, USA
Microb Ecol 50:197-205. 2005.... - Description of Caldanaerobius fijiensis gen. nov., sp. nov., an inulin-degrading, ethanol-producing, thermophilic bacterium from a Fijian hot spring sediment, and reclassification of Thermoanaerobacterium polysaccharolyticum and Thermoanaerobacterium zeaeYong Jin Lee
Department of Microbiology, University of Georgia, Athens, GA 30602, USA
Int J Syst Evol Microbiol 58:666-70. 2008..nov., sp. nov. (the type species), Caldanaerobius polysaccharolyticus comb. nov. and Caldanaerobius zeae comb. nov., respectively. The type strain of Caldanaerobius fijiensis is JW/YJL-F3(T) (=ATCC BAA-1278(T) =DSM 17918(T))... - Flow cytometric sorting, phylogenetic analysis and in situ detection of Oscillospira guillermondii, a large, morphologically conspicuous but uncultured ruminal bacteriumKazuhiro Yanagita
Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science, Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
Int J Syst Evol Microbiol 53:1609-14. 2003..The probes hybridized specifically with the large, morphologically conspicuous Oscillospira cells... - Detection of tetracycline resistance genes by PCR methodsRustam I Aminov
Rowett Research Institute, Aberdeen, UK
Methods Mol Biol 268:3-13. 2004..Despite this shortcoming, antibiotics of this class still remain in the active arsenal for dermatologists to treat skin infections such as acne and rosacea... - Evolution and ecology of antibiotic resistance genesRustam I Aminov
Rowett Research Institute, Greenburn Road, Aberdeen, UK
FEMS Microbiol Lett 271:147-61. 2007..Besides direct selection by antibiotics, there is a number of other factors that may contribute to dissemination and maintenance of antibiotic resistance genes in bacterial populations... - Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomicsDenis O Krause
CSIRO Australia, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia
FEMS Microbiol Rev 27:663-93. 2003..Lastly, we will discuss how newer technologies such as genomic and metagenomic approaches can be used to improve our knowledge of the functional genomic framework of plant cell wall degradation in the rumen...