MR DNA Molecular Research LP

Shallowater, TX, United States

MR DNA Molecular Research LP

Shallowater, TX, United States
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Gupta R.W.,Louisiana State University Health Sciences Center | Tran L.,Baton Rouge General Hospital Medical Center | Norori J.,Childrens Hospital | Ferris M.J.,Louisiana State University Health Sciences Center | And 4 more authors.
Journal of Pediatric Gastroenterology and Nutrition | Year: 2013

OBJECTIVES: Bacterial colonization is considered a major risk factor for necrotizing enterocolitis (NEC). The objective of the present study was to test the hypothesis that histamine-2 receptor (H2-) blockers alter colonic bacterial colonization by analyzing and comparing the fecal microbiota in premature infants with and without H2-blocker therapy using sensitive molecular biological techniques. METHODS: Seventy-six premature infants ≤1500 g or <34 weeks gestation were enrolled in this case-controlled, cross-sectional study. Stool samples were collected from 25 infants receiving H2-blockers and 51 babies who had never received them. Following DNA extraction and PCR amplification of 16S rRNA, 454 pyrosequencing was undertaken and the resulting sequences were subjected to comparison with published sequence libraries. RESULTS: Proteobacteria and Firmicutes were the major phyla contributing to fecal microbial communities. Microbial diversity was lower, relative abundance of Proteobacteria (primarily of the family Enterobacteriaceae) was increased, whereas that of Firmicutes was decreased in the stools of infants receiving H2-blockers compared with those who had never received them. CONCLUSIONS: Although not designed to look specifically at the effect of H2-blockers on the incidence of NEC, our study suggests that their use lowers fecal microbial diversity and shifts the microfloral pattern toward Proteobacteria. These alterations in fecal microbiota may predispose the vulnerable immature gut to necrotizing enterocolitis and suggest prudence in the use of H2-blockers in the premature infant. Copyright © 2013 by European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition.

Slapeta J.,University of Sydney | Dowd S.E.,MR DNA Molecular Research LP | Alanazi A.D.,Shaqra University | Westman M.E.,University of Sydney | Brown G.K.,University of Sydney
International Journal for Parasitology | Year: 2015

The protozoan parasite Giardia duodenalis causes a waterborne diarrhoeal disease in animals and humans, yet many Giardia-infected hosts remain asymptomatic. Mixed parasite infections are common in both animals and humans with unknown consequences for Giardia or other parasites. We compared the composition and diversity of bacterial communities from 40 dogs, including free-roaming dogs, and 21 surrendered cats from Australia. The dog cohort included 17 (42.5%) dogs positive for Giardia and 13 (32.5%) dogs positive for dog hookworm (Ancylostoma caninum). The cat samples included eight positive for Giardia and eight positive for Cystoisospora. The V4 region of 16S rRNA was sequenced at an average of 36,383 high quality sequences (>200 bp) per sample using the Ion Torrent PGM™ platform. In dogs we found significant (P < 0.05, AnoSim) difference between the Giardia-positive and -negative groups when evaluating bacterial genera. No such difference was demonstrated between Ancylostoma-positive and -negative dogs. However, there was a modest but not significant separation of the Giardia-negative and -positive dogs (P = 0.09, UniFrac) using principal coordinate analysis. Removal of dogs with hookworms further separated Giardia-positive and -negative groupings (P = 0.06, UniFrac). In cats, the presence of Giardia was not associated with a significant difference based on bacterial genera (P > 0.05, AnoSim). Cystoisospora-positive cats, however, exhibited significantly different profiles from Cystoisospora-negative cats (P = 0.02, AnoSim) and UniFrac showed significant separation of Cystoisospora-positive and -negative samples (P < 0.01). The results suggest that in clinically heathy dogs and cats, helminths and protozoa are associated with different microbiomes and possibly variable gut microbiota functions. Understanding the association of parasites and microbiomes has important consequences for the administration of antiparasitic drugs in animals and humans. © 2015 Australian Society for Parasitology Inc.

Hooda S.,Urbana University | Vester Boler B.M.,Urbana University | Rossoni Serao M.C.,Urbana University | Brulc J.M.,General Mills Inc. | And 5 more authors.
Journal of Nutrition | Year: 2012

The relative contribution of novel fibers such as polydextrose and soluble corn fiber (SCF) to the human gut microbiome and its association with host physiology has not been well studied. This study was conducted to test the impact of polydextrose and SCF on the composition of the human gut microbiota using 454 pyrosequencing and to identify associations among fecal microbiota and fermentative end-products. Healthy adult men (n = 20) with a mean dietary fiber (DF) intake of 14 g/d were enrolled in a randomized, double-blind, placebo-controlled crossover study. Participants consumed 3 treatment snack bars/d during each 21-d period that contained no supplemental fiber (NFC), polydextrose (PDX; 21 g/d), or SCF (21 g/d) for 21 d. There were no washout periods. Fecal samples were collected on d 16-21 of each period; DNA was extracted, followed by amplification of the V4-V6 region of the 16S rRNA gene using barcoded primers. PDX and SCF significantly affected the relative abundance of bacteria at the class, genus, and species level. The consumption of PDX and SCF led to greater fecal Clostridiaceae and Veillonellaceae and lower Eubacteriaceae compared with a NFC. The abundance of Faecalibacterium, Phascolarctobacterium, and Dialister was greater (P< 0.05) in response to PDX and SCF intake, whereas Lactobacillus was greater (P< 0.05) only after SCF intake. Faecalibacterium prausnitzii, well known for its antiinflammatory properties, was greater (P< 0.05) after fiber consumption. Principal component analysis clearly indicated a distinct clustering of individuals consuming supplemental fibers. Our data demonstrate a beneficial shift in the gut microbiome of adults consuming PDX and SCF, with potential application as prebiotics. © 2012 American Society for Nutrition.

McLaughlin R.W.,Gateway Technical College | McLaughlin R.W.,Saint Mary's University of Minnesota | Cochran P.A.,Saint Mary's University of Minnesota | Dowd S.E.,MR DNA Molecular Research LP
Current Microbiology | Year: 2014

In certain species of fish, such as rainbow trout, infection by the Firmicutes Lactococcus garvieae is problematic. This organism is the causative agent of lactococcosis disease in fish, and it is also considered a potential zoonotic bacterium, since it can cause several opportunistic infections in humans. In this study, L. garvieae strain TRF1 was grown and isolated in pure culture from the fecal material of a Timber Rattlesnake (Crotalus horridus), living in the wild. The presence/absence of several putative virulence factors was identified using staining, PCR amplification, and the construction of a draft genome. Strain TRF1 shared several putative virulence factors with strain Lg2, a known fish pathogen. However, the capsule gene cluster, found in strain Lg2, was not found in strain TRF1. Since this gene cluster is absent in several non-pathogenic strains of L. garvieae, it suggests strain TRF1 may not be pathogenic. However, this hypothesis will have to be tested in an animal model. © 2014 Springer Science+Business Media.

Hooda S.,Urbana University | Vester Boler B.M.,Urbana University | Kerr K.R.,Urbana University | Dowd S.E.,MR DNA Molecular Research LP | Swanson K.S.,Urbana University
British Journal of Nutrition | Year: 2012

High-protein, low-carbohydrate (HPLC) diets are common in cats, but their effect on the gut microbiome has been ignored. The present study was conducted to test the effects of dietary protein:carbohydrate ratio on the gut microbiota of growing kittens. Male domestic shorthair kittens were raised by mothers fed moderate-protein, moderate-carbohydrate (MPMC; n 7) or HPLC (n 7) diets, and then weaned at 8 weeks onto the same diet. Fresh faeces were collected at 8, 12 and 16 weeks; DNA was extracted, followed by amplification of the V4-V6 region of the 16S rRNA gene using 454 pyrosequencing. A total of 384 588 sequences (average of 9374 per sample) were generated. Dual hierarchical clustering indicated distinct clustering based on the protein:carbohydrate ratio regardless of age. The protein:carbohydrate ratio affected faecal bacteria. Faecal Actinobacteria were greater (P < 0·05) and Fusobacteria were lower (P < 0·05) in MPMC-fed kittens. Faecal Clostridium, Faecalibacterium, Ruminococcus, Blautia and Eubacterium were greater (P < 0·05) in HPLC-fed kittens, while Dialister, Acidaminococcus, Bifidobacterium, Megasphaera and Mitsuokella were greater (P < 0·05) in MPMC-fed kittens. Principal component analysis of faecal bacteria and blood metabolites and hormones resulted in distinct clusters. Of particular interest was the clustering of blood TAG with faecal Clostridiaceae, Eubacteriaceae, Ruminococcaceae, Fusobacteriaceae and Lachnospiraceae; blood ghrelin with faecal Coriobacteriaceae, Bifidobacteriaceae and Veillonellaceae; and blood glucose, cholesterol and leptin with faecal Lactobacillaceae. The present results demonstrate that the protein:carbohydrate ratio affects the faecal microbiome, and highlight the associations between faecal microbes and circulating hormones and metabolites that may be important in terms of satiety and host metabolism.

Ramirez H.A.R.,University of Nebraska - Lincoln | Nestor K.,Mycogen Seed | Tedeschi L.O.,Texas A&M University | Callaway T.R.,U.S. Department of Agriculture | And 3 more authors.
Canadian Journal of Animal Science | Year: 2012

Thirty-six Holstein cows (24 multiparous and 12 primiparous), four multiparous were ruminally cannulated, (mean±SD, 111±35 days in milk; 664976.5 kg body weight) were used in replicated 4×4 Latin squares with a 2×2 factorial arrangement of treatments to investigate the effects of brown midrib (bm3) and conventional (DP) corn silages, and the inclusion of dried distillers' grains with solubles (DDGS) on milk production and N utilization. Experimental periods were 28 d in length. Treatments were DP corn silage and 0% DDGS; bm3 corn silage and 0% DDGS; DP corn silage and 30% DDGS; and bm3 corn silage and 30% DDGS. Compared with DP hybrid, total tract fiber digestibility was greater for cows consuming bm3 (32.5 vs. 38.1±1.79%) and DDGS (40.0 vs. 35.2±1.76%). Milk yield was not affected by treatment, and averaged 30.5±1.09 kg d-1. Milk protein yield was positively affected by bm3 corn silage and the inclusion of DDGS. An interaction between hybrid and DDGS on milk fat was also observed. The nature of the interaction was such that milk fat was only affected when DDGS were included in the diet and the lowest milk fat was observed when bm3 corn silage was fed (3.46, 3.59, 2.84 and 2.51±0.10% DP 0% DDGS, bm3 0% DDGS, DP 30% DDGS and bm3 30% DDGS, respectively). As a proportion of the total N consumed, manure N was significantly reduced by the inclusion of bm3 corn silage and DDGS (64.1, 57.1, 52.0, 51.2% for DP 0% DDGS, bm3 0% DDGS, DP 30% DDGS and bm3 30% DDGS, respectively). The Firmicutes:Bacteriodetes ratio in the rumen decreased when cattle consumed DDGS. When cows were fed bm3 corn silage, the population of Fibrobacter sp. tended to represent a larger proportion of the total bacterial population (1.8 vs. 2.3±0.28% for DP and bm3, respectively) and this shift may have been driven by the fact that bm3 corn silage has less lignin, therefore the cellulose digesting bacteria may have more access to the cellulose.

Tran L.,Louisiana State University Health Sciences Center | Ferris M.,Louisiana State University Health Sciences Center | Ferris M.,Research Institute for Children | Norori J.,Research Institute for Children | And 5 more authors.
Pediatrics | Year: 2013

Necrotizing enterocolitis is the most common gastrointestinal emergency in neonates. The etiology is considered multifactorial. Risk factors include prematurity, enteral feeding, hypoxia, and bacterial colonization. The etiologic role of viruses is unclear. We present a case of necrotizing enterocolitis associated with cytomegalovirus and Proteobacteria in a 48-day-old, ex-premature infant and discuss the effects of potential viral-bacterial interactions on host susceptibility to this disease. Pediatrics 2013;131:e318-e322. Copyright © 2013 by the American Academy of Pediatrics.

PubMed | MR DNA Molecular Research LP, Gateway Technical College and University of California at San Diego
Type: Journal Article | Journal: Antonie van Leeuwenhoek | Year: 2016

Using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing, the microbiota of the faecal material of two blue whales living in the wild off the coast of California was investigated. In both samples the most predominant bacterial phylum was the Firmicutes with Clostridium spp. being the most dominant bacteria. The most predominant fungi were members of the phylum Ascomycota with Metschnikowia spp. being the most dominant. In this study, we also preliminarily characterised the culturable anaerobic bacteria from the faecal material, using traditional culture and 16S rRNA gene sequencing approaches. In total, three bacterial species belonging to the phylum Firmicutes were identified.

PubMed | MR DNA Molecular Research LP, Urbana University, Roquette America Inc., Roquette Freres and Texas A&M University
Type: Journal Article | Journal: The British journal of nutrition | Year: 2016

Inclusion of fermentable fibres in the diet can have an impact on the hindgut microbiome and provide numerous health benefits to the host. Potato fibre (PF), a co-product of potato starch isolation, has a favourable chemical composition of pectins, resistant and digestible starch, cellulose, and hemicelluloses. The objective of the present study was to evaluate the effect of increasing dietary PF concentrations on the faecal microbiome of healthy adult dogs. Fresh faecal samples were collected from ten female dogs with hound bloodlines (613 (SEM 017) years; 220 (SEM 21) kg) fed five test diets containing graded concentrations of PF (0, 15, 3, 45 or 6% as-fed; Roquette Frres) in a replicated 5 5 Latin square design. Extraction of DNA was followed by amplification of the V4-V6 variable region of the 16S rRNA gene using barcoded primers. Sequences were classified into taxonomic levels using Basic Local Alignment Search Tool (BLASTn) against a curated GreenGenes database. Inclusion of PF increased (P< 005) the faecal proportions of Firmicutes, while those of Fusobacteria decreased (P< 005). Similar shifts were observed at the genus level and were confirmed by quantitative PCR (qPCR) analysis. With increasing concentrations of PF, faecal proportions of Faecalibacterium increased (P< 005). Post hoc Pearsons correlation analysis showed positive (P< 005) correlations with Bifidobacterium spp. and butyrate production and Lactobacillus spp. concentrations. Overall, increases in the proportion of Faecalibacterium (not Lactobacillus/Bifidobacterium, as confirmed by qPCR analysis) and faecal SCFA concentrations with increasing dietary PF concentrations suggest that PF is a possible prebiotic fibre.

PubMed | Indiana University and MR DNA Molecular Research LP
Type: Journal Article | Journal: PloS one | Year: 2016

Dysbiosis is a hallmark of inflammatory bowel disease (IBD), but it is unclear which specific intestinal bacteria predispose to and which protect from IBD and how they are regulated. Peptidoglycan recognition proteins (Pglyrps) are antibacterial, participate in maintaining intestinal microflora, and modulate inflammatory responses. Mice deficient in any one of the four Pglyrp genes are more sensitive to dextran sulfate sodium (DSS)-induced colitis, and stools from Pglyrp-deficient mice transferred to wild type (WT) germ-free mice predispose them to much more severe colitis than stools from WT mice. However, the identities of these Pglyrp-regulated bacteria that predispose Pglyrp-deficient mice to colitis or protect WT mice from colitis are not known. Here we identified significant changes in -diversity of stool bacteria in Pglyrp-deficient mice compared with WT mice. The most consistent changes in microbiome in all Pglyrp-deficient mice were in Bacteroidales, from which we selected four species, two with increased abundance (Prevotella falsenii and Parabacteroides distasonis) and two with decreased abundance (Bacteroides eggerthii and Alistipes finegoldii). We then gavaged WT mice with stock type strains of these species to test the hypothesis that they predispose to or protect from DSS-induced colitis. P. falsenii, P. distasonis, and B. eggerthii all enhanced DSS-induced colitis in both WT mice with otherwise undisturbed intestinal microflora and in WT mice with antibiotic-depleted intestinal microflora. By contrast, A. finegoldii (which is the most abundant species in WT mice) attenuated DSS-induced colitis both in WT mice with otherwise undisturbed intestinal microflora and in WT mice with antibiotic-depleted intestinal microflora, similar to the colitis protective effect of the entire normal microflora. These results identify P. falsenii, P. distasonis, and B. eggerthii as colitis-promoting species and A. finegoldii as colitis-protective species.

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