Cindy H. Nakatsu

Purdue University West Lafayette

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Allan Konopka

Charité - Universitätsmedizin Berlin

Connie M. Weaver

San Diego State University

Yava Jones‐Hall

Texas A&M University

Mário G. Ferruzzi

David H. Murdock Research Institute

George P. McCabe

Purdue University West Lafayette

Linda D McCabe

Purdue University West Lafayette

Hang Lu

University of Michigan–Ann Arbor

Kolapo M. Ajuwon

Purdue University West Lafayette

Connie J. Rogers

Pennsylvania State University

Mary Jane De Souza

Pennsylvania State University

Cooperative Institutions

Purdue University West Lafayette

132

State Street (United States)

Michigan State University

Agricultural Research Service

National Institute of Advanced Industrial Science and Technology

University of Wisconsin–Madison

Indiana University – Purdue University Indianapolis

United States Department of Agriculture

United States Geological Survey

University of Illinois Urbana-Champaign

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Distribution of the tfdA Gene in Soil Bacteria That Do Not Degrade 2,4-Dichlorophenoxyacetic Acid (2,4-D)

Microbial Ecology (1997)

Deborah A. Hogan Daniel H. Buckley Cindy H. Nakatsu Thomas M. Schmidt

Soil microbiology

10.1007/s002489900038

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Citations (44)

Investigation of carryover effect of prior fibre consumption on growth, serum and tissue metabolic markers in Ossabaw pigs fed a high‐fat diet

Journal of Animal Physiology and Animal Nutrition (2018)

Vivian Vezzoni de Almeida Hui Yan Cindy H. Nakatsu Kolapo M. Ajuwon

Carryover effect of prior fibre consumption on metabolic markers was investigated. Treatments were arranged in 2 × 2 factorial with 2 fibre sources, 4% inulin or cellulose (Solka-Floc®) and fat levels (5 or 15%) for the low-fat diet (LFD) and high-fat diet (HFD) respectively. Pigs were fed the two fibre diets for the first 56d (nursery phase), and thereafter fed either the LFD or HFD containing no added fibre source from d56 to 140 (growing phase). Pigs on the HFD were heavier (p = .05) than those on LF (64.61 vs. 68.38 kg), regardless of prior fibre type consumed. Pigs that were fed cellulose during the nursery and later fed the HFD had the highest ADG (p < .05). Feeding the HFD resulted in higher back fat (BF) (13.41 and 18.18 ± 0.12 mm for LFD and HFD, respectively; p < .01). The HFD resulted in higher (p < .01) insulin (0.014 and 0.016 ± 0.001 mg/L for LF and HF respectively) and glucose (100.89 and 125.03 ± 4.39 mg/dl for LF and HF respectively) concentrations in the serum. Inulin increased (p ≤ .02) jejunal expression of SREBP-1c and CL-4, but reduced (p < .05) TNFɑ and IL-6 expression in the ileum. Alpha-diversity was significantly different (p < .05) between the inulin and cellulose fed pigs at the end of the nursery and finishing phases. Therefore, inulin feeding before a HFD may lead to reduction in ADG and inflammatory markers in the small intestine of pigs, and thus prevent future metabolic disorders.

10.1111/jpn.12900

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Citations (1)

Complete genome sequence of Arthrobacter sp. strain FB24

Standards in Genomic Sciences (2013)

Cindy H. Nakatsu Ravi D. Barabote Sue Thompson David Bruce Chris Detter

Arthrobacter

Strain (injury)

Genome size

10.4056/sigs.4438185

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Citations (19)

STATISTICAL ISSUES IN THE ANALYSIS OF MICROBIAL COMMUNITIES IN SOIL

Conference on Applied Statistics in Agriculture (2001)

Jayson D. Wilbur Cindy H. Nakatsu Sylvie M. Brouder Jayant Kumar Ghosh R. W. Doerge

Corn and soybean production dominates the agricultural systems of the mid-western United States. Studies have found that when a single crop species is grown continually, without the rotation of other crops, yield decline occurs. At present, this phenomenon, remains poorly understood, but there are possible links to microbial community dynamics in the associated rhizosphere soil. In this study, corn plants were grown in disturbed and undisturbed soils with a 24 year history of growth as a mono culture crop or two crops grown in annual rotation. Characteristic profiles of the microbial communities were obtained by denaturing gradient gel electrophoresis of polymerase chain reaction amplified 16S rDNA from soil extracted DNA. This problem is approached as the statistical analysis of high-dimensional multivariate binary data with an emphasis on modeling and variable selection.

Crop Rotation

10.4148/2475-7772.1221

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Dietary Fat Content and Fiber Type Modulate Hind Gut Microbial Community and Metabolic Markers in the Pig

PLoS ONE (2013)

Hui Yan Ramesh Babu Potu Hang Lu Vivian Vezzoni de Almeida T. S. Stewart

Obesity leads to changes in the gut microbial community which contribute to the metabolic dysregulation in obesity. Dietary fat and fiber affect the caloric density of foods. The impact of dietary fat content and fiber type on the microbial community in the hind gut is unknown. Effect of dietary fat level and fiber type on hindgut microbiota and volatile fatty acid (VFA) profiles was investigated. Expression of metabolic marker genes in the gut, adipose tissue and liver was determined. A 2 × 2 experiment was conducted in pigs fed at two dietary fat levels (5% or 17.5% swine grease) and two fiber types (4% inulin, fermentable fructo-oligosaccharide or 4% solka floc, non-fermentable cellulose). High fat diets (HFD) resulted in a higher (P<0.05) total body weight gain, feed efficiency and back fat accumulation than the low fat diet. Feeding of inulin, but not solka floc, attenuated (P<0.05) the HFD-induced higher body weight gain and fat mass accumulation. Inulin feeding tended to lead to higher total VFA production in the cecum and resulted in a higher (P<0.05) expression of acyl coA oxidase (ACO), a marker of peroxisomal β-oxidation. Inulin feeding also resulted in lower expression of sterol regulatory element binding protein 1c (SREBP-1c), a marker of lipid anabolism. Bacteria community structure characterized by DGGE analysis of PCR amplified 16S rRNA gene fragments showed that inulin feeding resulted in greater bacterial population richness than solka floc feeding. Cluster analysis of pairwise Dice similarity comparisons of the DGGE profiles showed grouping by fiber type but not the level of dietary fat. Canonical correspondence analysis (CCA) of PCR- DGGE profiles showed that inulin feeding negatively correlated with back fat thickness. This study suggests a strong interplay between dietary fat level and fiber type in determining susceptibility to obesity.

10.1371/journal.pone.0059581

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Citations (89)

Blueberry polyphenols alter gut microbiota & phenolic metabolism in rats

Food & Function (2021)

Dennis P. Cladis Abigayle M. R. Simpson Kaitlyn J. Cooper Cindy H. Nakatsu Mário G. Ferruzzi

Metabolism of orally dosed blueberry polyphenols is dependent upon both dose and food matrix, resulting in different compositions of phenolic metabolites and the gut microbiota.

Microbial Metabolism

10.1039/d0fo03457f

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Citations (28)

Parallel and Divergent Genotypic Evolution in Experimental Populations of Ralstonia sp

Journal of Bacteriology (1998)

Cindy H. Nakatsu Ryszard Korona Richard E. Lenski Frans J. de Bruijn Terence L. Marsh

ABSTRACT Genetic rearrangements within a population of bacteria were analyzed to understand the degree of divergence occurring after experimental evolution. We used 18 replicate populations founded from Ralstonia sp. strain TFD41 that had been propagated for 1,000 generations with 2,4-dichlorophenoxyacetic acid (2,4-D) as the carbon source. Genetic divergence was examined by restriction fragment length polymorphism analysis of the incumbent plasmid that carries the 2,4-D catabolic genes and by amplification of random regions of the genome via PCR. In 18 evolved clones examined, we observed duplication within the plasmid, including the tfdA gene, which encodes a 2,4-D dioxygenase that catalyzes the first step in the 2,4-D catabolic pathway. In 71 of 72 evolved clones, a common 2.4-kb PCR product was lost when genomic fingerprints produced by PCR amplification using degenerate primers based on repetitive extragenic palindromic (REP) sequences (REP-PCR) were compared. The nucleotide sequence of the 2.4-kb PCR product has homology to the TRAP (tripartite ATP-independent periplasmic) solute transporter gene family. Hybridization of the 2.4-kb REP-PCR product from the ancestor to genomic DNA from the evolved populations showed that the loss of the PCR product resulted from deletions in the genome. Deletions in the plasmid and presence and/or absence of other REP-PCR products were also found in these clones but at much lower frequencies. The common and uncommon genetic changes observed show that both parallel and divergent genotypic evolution occurred in replicate populations of this bacterium.

Ralstonia solanacearum

Ralstonia

10.1128/jb.180.17.4325-4331.1998

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Citations (58)

Selection of Binary Variables and Classification by Boosting

Communications in Statistics - Simulation and Computation (2007)

Junyong Park Jayson D. Wilbur Jayanta Kumar Ghosh Cindy H. Nakatsu Corinne Ackerman

We adopt boosting for classification and selection of high-dimensional binary variables for which classical methods based on normality and non singular sample dispersion are inapplicable. Boosting seems particularly well suited for binary variables. We present three methods of which two combine boosting with the relatively classical variable selection methods developed in Wilbur et al. (2002 Wilbur , J. D. , Ghosh , J. K. , Nakatsu , C. H. , Brouder , S. M. , Doerge , R. W. ( 2002 ). Variable selection in high-dimensional multivariate binary data with application to the analysis of microbial community DNA fingerprints . Biometrics 58 : 378 – 386 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]). Our primary interest is variable selection in classification with small misclassification error being used as validation of proposed method for variable selection. Two of the new methods perform uniformly better than Wilbur et al. (2002 Wilbur , J. D. , Ghosh , J. K. , Nakatsu , C. H. , Brouder , S. M. , Doerge , R. W. ( 2002 ). Variable selection in high-dimensional multivariate binary data with application to the analysis of microbial community DNA fingerprints . Biometrics 58 : 378 – 386 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]) in one set of simulated and three real life examples.

Boosting

Binary classification

Gradient boosting

10.1080/03610910701419729

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Citations (2)

Optimization of PCR‐DGGE technique to compare variations in human intestinal microflora community

The FASEB Journal (2006)

Merlin Ariefdjohan Dennis A. Savaiano Cindy H. Nakatsu

Advances in molecular techniques provide an advantage over conventional microbiological methods to study the diversity of human intestinal microflora. Variability in endogenous and dietary components makes extraction of bacterial DNA from feces a challenging task. The purity of DNA extracted from such a heterogeneous sample is crucial since it affects downstream analyses. In addition, both PCR and Denaturing Gradient Gel Electrophoresis (DGGE) methods must be optimized to perform meaningful comparative analyses. In this study, the relative efficacy of extracting bacterial DNA from feces was evaluated using: Mobio® DNA Stool Kit, QIAamp® DNA Mini Stool Kit, FastDNA® SPIN Kit for Soil, and FastDNA® SPIN Kit. These kits were found to yield 1.0 x 102, 1.1 x 102, 2.5 x 102, and 1.9 x 102 mg DNA per g feces, respectively. Optimum extraction yield was obtained using 10 to 25 mg of fecal sample (wet weight). Regardless of method, 16S rRNA gene of all samples was successfully amplified. Intestinal microflora community of four human subjects was evaluated using DGGE separation of the PCR products. Bacterial banding profiles showed similarity within each subject but high subject-to-subject variations. Bacterial DNA extracted using the Soil Kit produced the best profile in terms of clarity and number of bands. We conclude that using optimized conditions variations in human intestinal microflora community from fecal samples could be effectively compared using PCR-DGGE technique. Funded by Solae, LLC

Human feces

10.1096/fasebj.20.5.a1054

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Microbial Biomass and Activity in Lead-Contaminated Soil

Applied and Environmental Microbiology (1999)

Allan Konopka T Zakharova M. Bischoff L Oliver Cindy H. Nakatsu

Lead (geology)

Soil microbiology

10.1128/aem.65.10.4708-4708.1999

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Citations (16)