Papers by Roger Bumgarner
Journal of Clinical Microbiology, Jan 28, 2020
Cutibacterium acnes is the most common bacterium associated with periprosthetic shoulder infectio... more Cutibacterium acnes is the most common bacterium associated with periprosthetic shoulder infections. Sequencing of C. acnes has been proposed as a potential rapid diagnostic tool and a method of determining subtypes associated with pathogenicity and antibiotic resistance patterns. When multiple deep samples from the same surgery are culture positive for the same species and the isolates show the same culture phenotype, it is typically assumed that these isolates are clonal. However, it is well-known that C. acnes is not clonal on the skin of most individuals. We hypothesized that the C. acnes bacteria recovered at the time of revision shoulder arthroplasty would often represent more than one subtype, and we tested this hypothesis in this work. For patients undergoing revision shoulder arthroplasty, multiple samples from the surgical field were taken. For those patients with multiple samples that were culture positive for C. acnes, isolates from each sample were subjected to full genome sequencing. Of 11 patients, 5 (45%) had different subtypes of C. acnes within the deep tissues even though the colony morphology was similar. One patient had four subtypes in the deep tissues, while four patients had two different subtypes. Up to four different subtypes of C. acnes were observed in the deep tissues of a single patient. Clonality of C. acnes isolates from deep specimens from a potential periprosthetic shoulder infection cannot be assumed. Sequence-based characterization of virulence and antibiotic resistance may require testing of multiple deep specimens.
Pathogens, Dec 3, 2019
Aggregatibacter actinomycetemcomitans genome can be divided into an accessory gene pool (found in... more Aggregatibacter actinomycetemcomitans genome can be divided into an accessory gene pool (found in some but not all strains) and a core gene pool (found in all strains). The functions of the accessory genes (genomic islands and non-island accessory genes) are largely unknown. We hypothesize that accessory genes confer critical functions for A. actinomycetemcomitans in vivo. This study examined the expression patterns of accessory and core genes of A. actinomycetemcomitans in distinct growth conditions. We found similar expression patterns of island and non-island accessory genes, which were generally lower than the core genes in all growth conditions. The median expression levels of genomic islands were 29%-37% of the core genes in enriched medium but elevated to as high as 63% of the core genes in nutrient-limited media. Several putative virulence genes, including the cytolethal distending toxin operon, were found to be activated in nutrient-limited conditions. In conclusion, genomic islands and non-island accessory genes exhibited distinct patterns of expression from the core genes and may play a role in the survival of A. actinomycetemcomitans in nutrient-limited environments.
Genome Announcements, Feb 25, 2016
Here, we present the draft genome sequence of Actinomyces odontolyticus subsp. actinosynbacter st... more Here, we present the draft genome sequence of Actinomyces odontolyticus subsp. actinosynbacter strain XH001, isolated from the human oral cavity. Uniquely, it was discovered as a host bacterium to the ultrasmall epibiont TM7x, which is the first cultivated member of "Candidatus Saccharibacteria" (formerly candidate phylum TM7).
Current protocols in molecular biology, 2013
This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000'... more This chapter provides an overview of DNA microarrays. Microarrays are a technology in which 1000's of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. We first cover the history of microarrays and the antecedent technologies that led to their development. We then discuss the methods of manufacture of microarrays and the most common biological applications. The chapter ends with a brief discussion of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.
Pathogens, 2019
Aggregatibacter actinomycetemcomitans genome can be divided into an accessory gene pool (found in... more Aggregatibacter actinomycetemcomitans genome can be divided into an accessory gene pool (found in some but not all strains) and a core gene pool (found in all strains). The functions of the accessory genes (genomic islands and non-island accessory genes) are largely unknown. We hypothesize that accessory genes confer critical functions for A. actinomycetemcomitans in vivo. This study examined the expression patterns of accessory and core genes of A. actinomycetemcomitans in distinct growth conditions. We found similar expression patterns of island and non-island accessory genes, which were generally lower than the core genes in all growth conditions. The median expression levels of genomic islands were 29%–37% of the core genes in enriched medium but elevated to as high as 63% of the core genes in nutrient-limited media. Several putative virulence genes, including the cytolethal distending toxin operon, were found to be activated in nutrient-limited conditions. In conclusion, genomi...
Journal of Clinical Microbiology, 2019
Cutibacterium acnes is the most common bacterium associated with periprosthetic shoulder infectio... more Cutibacterium acnes is the most common bacterium associated with periprosthetic shoulder infections. Sequencing of C. acnes has been proposed as a potential rapid diagnostic tool and a method of determining subtypes associated with pathogenicity and antibiotic resistance patterns. When multiple deep samples from the same surgery are culture positive for the same species and the isolates show the same culture phenotype, it is typically assumed that these isolates are clonal.
Genome Research, 1998
Extremely halophilic archaea, which flourish in hypersaline environments, are known to contain a ... more Extremely halophilic archaea, which flourish in hypersaline environments, are known to contain a variety of large dynamic replicons. Previously, the analysis of one such replicon, pNRC100, inHalobacterium sp. strain NRC-1, showed that it undergoes high-frequency insertion sequence (IS) element-mediated insertions and deletions, as well as inversions via recombination between 39-kb-long inverted repeats (IRs). Now, the complete sequencing of pNRC100, a 191,346-bp circle, has shown the presence of 27 IS elements representing eight families. A total of 176 ORFs or likely genes of 850-bp average size were found, 39 of which were repeated within the large IRs. More than one-half of the ORFs are likely to represent novel genes that have no known homologs in the databases. Among ORFs with previously characterized homologs, three different copies of putative plasmid replication and four copies of partitioning genes were found, suggesting that pNRC100 evolved from IS element-mediated fusions...
Nature, 2001
Bacteria often adopt a sessile bio®lm lifestyle that is resistant to antimicrobial treatment 1±5 ... more Bacteria often adopt a sessile bio®lm lifestyle that is resistant to antimicrobial treatment 1±5 . Opportunistic pathogenic bacteria like Pseudomonas aeruginosa can develop persistent infections 1±3 . To gain insights into the differences between free-living P. aeruginosa cells and those in bio®lms, and into the mechanisms underlying the resistance of bio®lms to antibiotics, we used DNA microarrays. Here we show that, despite the striking differences in lifestyles, only about 1% of genes showed differential
PLOS ONE, 2016
The microbiome of plants is diverse, and like that of animals, is important for overall health an... more The microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. In legumes and actinorhizal plants, a portion of essential nitrogen (N) is obtained through symbiosis with nodule-inhabiting, N 2 -fixing microorganisms. However, a variety of non-nodulating plant species can also thrive in natural, low-N settings. Some of these species may rely on endophytes, microorganisms that live within plants, to fix N 2 gas into usable forms. Here we report the first direct evidence of N 2 fixation in the early successional wild tree, Populus trichocarpa, a non-leguminous tree, from its native riparian habitat. In order to measure N 2 fixation, surface-sterilized cuttings of wild poplar were assayed using both 15 N 2 incorporation and the commonly used acetylene reduction assay. The 15 N label was incorporated at high levels in a subset of cuttings, suggesting a high level of N-fixation. Similarly, acetylene was reduced to ethylene in some samples. The microbiota of the cuttings was highly variable, both in numbers of cultured bacteria and in genetic diversity. Our results indicated that associative N 2 -fixation occurred within wild poplar and that a non-uniformity in the distribution of endophytic bacteria may explain the variability in N-fixation activity. These results point to the need for molecular studies to decipher the required microbial consortia and conditions for effective endophytic N 2 -fixation in trees.
Genome Announcements, 2016
We present the draft genome of Porphyromonas gingivalis MP4-504, a low-passage clinical isolate o... more We present the draft genome of Porphyromonas gingivalis MP4-504, a low-passage clinical isolate obtained from a periodontitis patient. The genome is composed of 92 contigs for a length of 2,373,453 bp and a G+C of 48.3%. The traA-Q conjugative transfer locus is genetically distinct from W83 but highly similar to ATCC 33277.
Genome announcements, Jan 18, 2016
We announce here a draft genome sequence of Veillonella parvula strain SHI-1, obtained from healt... more We announce here a draft genome sequence of Veillonella parvula strain SHI-1, obtained from healthy human saliva, discovered to be active at low pH using metatranscriptomics within an in vitro oral biofilm model. The genome is composed of 7 contigs, for a total of 2,200,064 bp.
Genome announcements, Jan 4, 2016
Here, we present the draft genome sequence of Actinomyces odontolyticus subsp. actinosynbacter st... more Here, we present the draft genome sequence of Actinomyces odontolyticus subsp. actinosynbacter strain XH001, isolated from the human oral cavity. Uniquely, it was discovered as a host bacterium to the ultrasmall epibiont TM7x, which is the first cultivated member of "Candidatus Saccharibacteria" (formerly candidate phylum TM7).
Genome Announcements, 2015
Tannerella forsythia is an oral pathogen implicated in the development of periodontitis. Here, we... more Tannerella forsythia is an oral pathogen implicated in the development of periodontitis. Here, we report the draft genome sequence of the Tannerella forsythia strain ATCC 43037. The previously available genome of this designation (NCBI reference sequence NC_016610.1) was discovered to be derived from a different strain, FDC 92A2 (= ATCC BAA-2717).
PloS one, 2015
Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the ident... more Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the identification of variants in sequence populations at lower levels than consensus sequencing and most single-template Sanger sequencing experiments. We sought to determine if the greater depth of population sampling attainable using MPS technology would allow detection of minor variants in HIV founder virus populations very early in infection in instances where Sanger sequencing detects only a single variant. We compared single nucleotide polymorphisms (SNPs) during acute HIV-1 infection from 32 subjects using both single template Sanger and 454-pyrosequencing. Pyrosequences from a median of 2400 viral templates per subject and encompassing 40% of the HIV-1 genome, were compared to a median of five individually amplified near full-length viral genomes sequenced using Sanger technology. There was no difference in the consensus nucleotide sequences over the 3.6kb compared in 84% of the subjects...
Genome Announcements, 2014
Haemophilus parasuis is a normal commensal of the upper respiratory tract of healthy pigs. Howeve... more Haemophilus parasuis is a normal commensal of the upper respiratory tract of healthy pigs. However, in conjunction with stress and/or viral infections, or in immunocompromised animals, H. parasuis can transform into a pathogen causing Glasser's disease, which is typically characterized by fibrinous polyserositis, polyarthritis, meningitis, and sometimes acute pneumonia and septicemia. H. parasuis serotype 5 is highly virulent and more frequently isolated from respiratory and systemic infection in pigs. Recently Newport Laboratories isolated highly virulent H. parasuis serotype 4 strains from the tissues of diseased pigs. This study was undertaken to identify the genes responsible for H. parasuis serotype 4 virulence. To achieve this objective we performed genome-wide association studies (GWAS) across two virulent and three avirulent H. parasuis serotype 4 strains.
Current Protocols in Molecular Biology, 2013
This unit provides an overview of DNA microarrays. Microarrays are a technology in which thousand... more This unit provides an overview of DNA microarrays. Microarrays are a technology in which thousands of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. This overview first discusses the history of microarrays and the antecedent technologies that led to their development. This is followed by discussion of the methods of manufacture of microarrays and the most common biological applications. The unit ends with a brief description of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies. Curr. Protoc. Mol. Biol. 101:22.1.1–22.1.11. © 2013 by John Wiley & Sons, Inc.
The Open Dentistry Journal, 2012
This study tested the feasibility of a high throughput metagenomic approach to analyze the pre- a... more This study tested the feasibility of a high throughput metagenomic approach to analyze the pre- and posttreatment of subgingival plaque in two subjects with aggressive periodontitis. DNA was extracted from subgingival samples and subjected to PCR amplification of the c2-c4 regions of the 16S rDNA using primers with bar codes to identify individual samples. The PCR products were pooled and sequenced for the v4 region of the 16S rDNA using the 454 FLX standard platform. The results were analyzed for species/phylotypes in the Human Oral Microbiome Database (HOMD) and Ribosomal Database Project (RDP) database. The sequencing of the amplicons resulted in 24,673 reads and identified 208 species/phylotypes. Of those, 129 species/phylotypes were identified in both patients but their proportions varied. While >120 species/phylotypes were identified in all samples, 28-42 species/phylotypes cumulatively represent 90% of all subgingival bacteria in each sample. The remaining species/phylotyp...
Science, 2007
The rhesus macaque ( Macaca mulatta ) is an abundant primate species that diverged from the ances... more The rhesus macaque ( Macaca mulatta ) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
Science, 2001
We demonstrate an integrated approach to build, test, and refine a model of a cellular pathway, i... more We demonstrate an integrated approach to build, test, and refine a model of a cellular pathway, in which perturbations to critical pathway components are analyzed using DNA microarrays, quantitative proteomics, and databases of known physical interactions. Using this approach, we identify 997 messenger RNAs responding to 20 systematic perturbations of the yeast galactose-utilization pathway, provide evidence that approximately 15 of 289 detected proteins are regulated posttranscriptionally, and identify explicit physical interactions governing the cellular response to each perturbation. We refine the model through further iterations of perturbation and global measurements, suggesting hypotheses about the regulation of galactose utilization and physical interactions between this and a variety of other metabolic pathways.
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Papers by Roger Bumgarner