R I Mackie

Summary

Affiliation: University of Illinois
Country: USA

Publications

  1. pmc Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches
    Roderick I Mackie
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Appl Environ Microbiol 69:6808-15. 2003
  2. ncbi request reprint Biochemical identification and biological origin of key odor components in livestock waste
    R I Mackie
    Department of Animal Sciences, University of Illinois, Urbana 61801, USA
    J Anim Sci 76:1331-42. 1998
  3. ncbi request reprint Tetracycline residues and tetracycline resistance genes in groundwater impacted by swine production facilities
    Roderick 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
  4. ncbi request reprint Developmental microbial ecology of the neonatal gastrointestinal tract
    R I Mackie
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana 61801, USA
    Am J Clin Nutr 69:1035S-1045S. 1999
  5. ncbi request reprint Biochemical and microbiological evidence for fermentative digestion in free-living land iguanas (Conolophus pallidus) and marine iguanas (Amblyrhynchus cristatus) on the Galápagos archipelago
    Roderick I Mackie
    Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
    Physiol Biochem Zool 77:127-38. 2004
  6. pmc Molecular ecology of tetracycline resistance: development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteins
    R I Aminov
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Appl Environ Microbiol 67:22-32. 2001
  7. pmc Occurrence and diversity of tetracycline resistance genes in lagoons and groundwater underlying two swine production facilities
    J C Chee-Sanford
    Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
    Appl Environ Microbiol 67:1494-502. 2001
  8. pmc Development, validation, and application of PCR primers for detection of tetracycline efflux genes of gram-negative bacteria
    R 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
  9. pmc Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year period
    S Koike
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Appl Environ Microbiol 73:4813-23. 2007
  10. ncbi request reprint Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiota
    V J McCracken
    Department of Animal Sciences, The University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
    J Nutr 131:1862-70. 2001

Collaborators

Detail Information

Publications47

  1. pmc Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches
    Roderick I Mackie
    Department of Animal Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Appl Environ Microbiol 69:6808-15. 2003
    ....
  2. ncbi request reprint Biochemical identification and biological origin of key odor components in livestock waste
    R 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...
  3. ncbi request reprint Tetracycline residues and tetracycline resistance genes in groundwater impacted by swine production facilities
    Roderick 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
    ....
  4. ncbi request reprint Developmental microbial ecology of the neonatal gastrointestinal tract
    R 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...
  5. ncbi request reprint Biochemical and microbiological evidence for fermentative digestion in free-living land iguanas (Conolophus pallidus) and marine iguanas (Amblyrhynchus cristatus) on the Galápagos archipelago
    Roderick I Mackie
    Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
    Physiol Biochem Zool 77:127-38. 2004
    ....
  6. pmc Molecular ecology of tetracycline resistance: development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteins
    R 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...
  7. pmc Occurrence and diversity of tetracycline resistance genes in lagoons and groundwater underlying two swine production facilities
    J 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...
  8. pmc Development, validation, and application of PCR primers for detection of tetracycline efflux genes of gram-negative bacteria
    R 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
    ....
  9. pmc Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year period
    S 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...
  10. ncbi request reprint Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiota
    V 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...
  11. doi request reprint Molecular ecology of macrolide-lincosamide-streptogramin B methylases in waste lagoons and subsurface waters associated with swine production
    Satoshi 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...
  12. ncbi request reprint Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions--II: Microbial population dynamics
    K 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...
  13. ncbi request reprint Characterization of fecal bacterial populations in canines: effects of age, breed and dietary fiber
    J 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...
  14. doi request reprint Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste
    Joanne C Chee-Sanford
    USDA ARS, 1102 S Goodwin Ave, Urbana, IL 61801, USA
    J Environ Qual 38:1086-108. 2009
    ....
  15. pmc Molecular ecological analysis of fecal bacterial populations from term infants fed formula supplemented with selected blends of prebiotics
    Noriko 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
    ....
  16. ncbi request reprint Characterization of two novel saccharolytic, anaerobic thermophiles, Thermoanaerobacterium polysaccharolyticum sp. nov. and Thermoanaerobacterium zeae sp. nov., and emendation of the genus Thermoanaerobacterium
    I 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...
  17. ncbi request reprint Bacterial diversity and distribution in the holocene sediments of a northern temperate lake
    David 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...
  18. pmc Antimicrobial use and resistance in swine waste treatment systems
    Archana 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
    ....
  19. ncbi request reprint Continuous culture selection of bifidobacteria and lactobacilli from human faecal samples using fructooligosaccharide as selective substrate
    A 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...
  20. ncbi request reprint Anaerobic codigestion of municipal solid waste and biosolids under various mixing conditions--I. Digester performance
    P 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...
  21. ncbi request reprint Characterization of the gene encoding glutamate dehydrogenase ( gdhA) from the ruminal bacterium Ruminococcus flavefaciens FD-1
    Dionysios 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...
  22. pmc Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes
    Dylan 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...
  23. pmc Comparative analyses of two thermophilic enzymes exhibiting both beta-1,4 mannosidic and beta-1,4 glucosidic cleavage activities from Caldanaerobius polysaccharolyticus
    Yejun 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...
  24. ncbi request reprint Selective growth of mucolytic bacteria including Clostridium perfringens in a neonatal piglet model of total parenteral nutrition
    Bart Deplancke
    Division of Nutritional Sciences, University of Illinois at Urbana Champaign, 61801, USA
    Am J Clin Nutr 76:1117-25. 2002
    ..Compromised barrier function and intestinal inflammation are common complications of total parenteral nutrition (TPN)...
  25. ncbi request reprint Paenibacillus tundrae sp. nov. and Paenibacillus xylanexedens sp. nov., psychrotolerant, xylan-degrading bacteria from Alaskan tundra
    David 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))...
  26. ncbi request reprint Coccidia-induced mucogenesis promotes the onset of necrotic enteritis by supporting Clostridium perfringens growth
    C 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...
  27. ncbi request reprint Complete nucleotide sequence of a cryptic plasmid, pBAW301, from the ruminal anaerobe Ruminococcus flavefaciens R13e2
    T 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...
  28. doi request reprint Microbial community analysis of rectal methanogens and sulfate reducing bacteria in two non-human primate species
    Noriko 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...
  29. pmc Functional diversity of four glycoside hydrolase family 3 enzymes from the rumen bacterium Prevotella bryantii B14
    Dylan Dodd
    Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
    J Bacteriol 192:2335-45. 2010
    ....
  30. pmc Biochemical and domain analyses of FSUAxe6B, a modular acetyl xylan esterase, identify a unique carbohydrate binding module in Fibrobacter succinogenes S85
    Shosuke Yoshida
    Energy Biosciences Institute, University of Illinois, Urbana, IL 61801, USA
    J Bacteriol 192:483-93. 2010
    ....
  31. pmc Domain analysis of a modular alpha-L-Arabinofuranosidase with a unique carbohydrate binding strategy from the fiber-degrading bacterium Fibrobacter succinogenes S85
    Shosuke 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...
  32. pmc Mutational insights into the roles of amino acid residues in ligand binding for two closely related family 16 carbohydrate binding modules
    Xiaoyun 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...
  33. pmc The BaeSR two-component regulatory system mediates resistance to condensed tannins in Escherichia coli
    Erwin 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...
  34. ncbi request reprint Molecular basis for the selectivity and specificity of ligand recognition by the family 16 carbohydrate-binding modules from Thermoanaerobacterium polysaccharolyticum ManA
    Brian 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...
  35. ncbi request reprint Molecular ecological analysis of the gastrointestinal microbiota: a review
    Erwin 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...
  36. pmc Effect of condensed tannins on bacterial diversity and metabolic activity in the rat gastrointestinal tract
    Alexandra H Smith
    Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801, USA
    Appl Environ Microbiol 70:1104-15. 2004
    ....
  37. ncbi request reprint Purification and characterization of a thermostable alpha-galactosidase from Thermoanaerobacterium polysaccharolyticum
    Michael 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...
  38. pmc Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23
    Dylan 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...
  39. pmc Biochemical and mutational analysis of glutamine synthetase type III from the rumen anaerobe Ruminococcus albus 8
    Kensey 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...
  40. ncbi request reprint Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function
    Erwin G Zoetendal
    Dept of Animal Sciences, University of Illinois at Urbana Champaign, IL, USA
    Curr Issues Intest Microbiol 5:31-47. 2004
    ....
  41. ncbi request reprint Novel rumen bacterial diversity in two geographically separated sub-species of reindeer
    Monica 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...
  42. ncbi request reprint Bacterial mechanisms to overcome inhibitory effects of dietary tannins
    Alexandra H Smith
    Department of Microbiology, University of Texas, Southwestern Medical Center, Dallas, TX 75390, USA
    Microb Ecol 50:197-205. 2005
    ....
  43. doi request reprint 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 zeae
    Yong 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))...
  44. ncbi request reprint Flow cytometric sorting, phylogenetic analysis and in situ detection of Oscillospira guillermondii, a large, morphologically conspicuous but uncultured ruminal bacterium
    Kazuhiro 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...
  45. ncbi request reprint Detection of tetracycline resistance genes by PCR methods
    Rustam 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...
  46. ncbi request reprint Evolution and ecology of antibiotic resistance genes
    Rustam 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...
  47. ncbi request reprint Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics
    Denis 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...