Garth D. Ehrlich
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View article: Development of a long-read high-throughput chromatin conformation capture method for evaluating both <i>cis</i> and <i>trans</i> interactions between integrated Hepatitis B Virus and host genomes
Development of a long-read high-throughput chromatin conformation capture method for evaluating both <i>cis</i> and <i>trans</i> interactions between integrated Hepatitis B Virus and host genomes Open
High-throughput chromatin conformation capture (Hi-C) has been utilized for characterizing the 3-dimensional (3D) interactome of the genome. However, short-read sequencing approaches have limited the information it provides, especially for…
View article: Outer Membrane Vesicles From <i>Bacteroides fragilis</i> Contain Coding and Non‐Coding Small RNA Species That Modulate Inflammatory Signalling in Intestinal Epithelial Cells
Outer Membrane Vesicles From <i>Bacteroides fragilis</i> Contain Coding and Non‐Coding Small RNA Species That Modulate Inflammatory Signalling in Intestinal Epithelial Cells Open
Alterations to the community structure and function of the microbiome are associated with changes to host physiology, including immune responses. However, the contribution of microbe‐derived RNAs carried by outer membrane vesicles (OMVs) t…
View article: Outer membrane vesicles from<i>Bacteroides fragilis</i>contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells
Outer membrane vesicles from<i>Bacteroides fragilis</i>contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells Open
Alterations to the community structure and function of the microbiome are associated with changes to host physiology, including immune responses. However, the contribution of microbe-derived RNAs carried by outer membrane vesicles (OMVs) t…
View article: Characterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol
Characterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol Open
Background The Borreliaceae family includes many obligate parasitic bacterial species which are etiologically associated with a myriad of zoonotic borrelioses including Lyme disease and vector-borne relapsing fevers. Infections by the Borr…
View article: <i>Borreliella burgdorferi</i> factor H-binding proteins are not required for serum resistance and infection in mammals
<i>Borreliella burgdorferi</i> factor H-binding proteins are not required for serum resistance and infection in mammals Open
The causative agent of Lyme disease (LD), Borreliella burgdorferi , binds factor H (FH) and other complement regulatory proteins to its surface. B. burgdorferi B31 (type strain) encodes five FH-binding proteins (FHBPs): CspZ, CspA, and the…
View article: Characterization of integrated hepatitis B virus DNA harboring pre‐S mutations in hepatocellular carcinoma patients with ground glass hepatocytes
Characterization of integrated hepatitis B virus DNA harboring pre‐S mutations in hepatocellular carcinoma patients with ground glass hepatocytes Open
Ground glass hepatocytes (GGHs) have been associated with hepatocellular carcinoma (HCC) recurrence and poor prognosis. We previously demonstrated that pre‐S expression in some GGHs is resistant to current hepatitis B virus (HBV) antiviral…
View article: Otitis media: Interactions between host and environment, immune and inflammatory responses
Otitis media: Interactions between host and environment, immune and inflammatory responses Open
View article: Establishment of a consensus protocol to explore the brain pathobiome in patients with mild cognitive impairment and Alzheimer's disease: Research outline and call for collaboration
Establishment of a consensus protocol to explore the brain pathobiome in patients with mild cognitive impairment and Alzheimer's disease: Research outline and call for collaboration Open
Microbial infections of the brain can lead to dementia, and for many decades microbial infections have been implicated in Alzheimer's disease (AD) pathology. However, a causal role for infection in AD remains contentious, and the lack of s…
View article: Tick Microbiome and Borreliaceae Pan-genome Characterization
Tick Microbiome and Borreliaceae Pan-genome Characterization Open
Tick-borne diseases (TBD) have been a blight on human health worldwide despite numerous efforts to advance proper treatment and prevention for this group of maladies. The lack of improvement primarily stems from the paucity of available in…
View article: Evidence for the Existence of a Bacterial Etiology for Alzheimer’s Disease and for a Temporal-Spatial Development of a Pathogenic Microbiome in the Brain
Evidence for the Existence of a Bacterial Etiology for Alzheimer’s Disease and for a Temporal-Spatial Development of a Pathogenic Microbiome in the Brain Open
Background Over the last few decades, a growing body of evidence suggests a role for various infectious agents in Alzheimer’s Disease (AD) pathogenesis. Despite diverse pathogens (virus, bacteria, or fungi) being detected in AD subjects’ b…
View article: Bacterial persistence and biofilms
Bacterial persistence and biofilms Open
Bacterial persistence is a transient state of dormancy exhibited by a small subset of cells that allow them to survive antibiotic treatment. This is a ubiquitous phenomenon exhibited by all bacteria to all known classes of antibiotics whic…
View article: Transition of Serotype 35B Pneumococci From Commensal to Prevalent Virulent Strain in Children
Transition of Serotype 35B Pneumococci From Commensal to Prevalent Virulent Strain in Children Open
In our community-based prospective cohort study in young children, we observed a significant increase in pneumococcal serotype 35B nasopharyngeal (NP) commensal colonization during the 2011–2014 timeframe, but these strains were not associ…
View article: Editorial: Otitis Media Genomics and the Middle Ear Microbiome
Editorial: Otitis Media Genomics and the Middle Ear Microbiome Open
EDITORIAL article Front. Genet., 12 October 2021Sec.Genetics of Common and Rare Diseases https://doi.org/10.3389/fgene.2021.763688
View article: Phase Variation in HMW1A Controls a Phenotypic Switch in Haemophilus influenzae Associated with Pathoadaptation during Persistent Infection
Phase Variation in HMW1A Controls a Phenotypic Switch in Haemophilus influenzae Associated with Pathoadaptation during Persistent Infection Open
Human-adapted bacterial pathogens have evolved specific mechanisms to colonize their host niche. Phase variation is a contingency strategy to allow adaptation to changing conditions, as phase-variable bacterial loci rapidly and reversibly …
View article: Bacterial Biofilm Growth on 3D-Printed Materials
Bacterial Biofilm Growth on 3D-Printed Materials Open
Recent advances in 3D printing have led to a rise in the use of 3D printed materials in prosthetics and external medical devices. These devices, while inexpensive, have not been adequately studied for their ability to resist biofouling and…
View article: Whole genome sequencing of Streptomyces actuosus ISP-5337, Streptomyces sioyaensis B-5408, and Actinospica acidiphila B-2296 reveals secondary metabolomes with antibiotic potential
Whole genome sequencing of Streptomyces actuosus ISP-5337, Streptomyces sioyaensis B-5408, and Actinospica acidiphila B-2296 reveals secondary metabolomes with antibiotic potential Open
View article: Genome-wide analysis of DNA uptake across the outer membrane of naturally competent Haemophilus influenzae
Genome-wide analysis of DNA uptake across the outer membrane of naturally competent Haemophilus influenzae Open
View article: The Development of a Pipeline for the Identification and Validation of Small-Molecule RelA Inhibitors for Use as Anti-Biofilm Drugs
The Development of a Pipeline for the Identification and Validation of Small-Molecule RelA Inhibitors for Use as Anti-Biofilm Drugs Open
Biofilm infections have no approved effective medical treatments and can only be disrupted via physical means. This means that any biofilm infection that is not addressable surgically can never be eliminated and can only be managed as a ch…
View article: The Development of a Pipeline for the Identification and Validation of Small-Molecule RelA Inhibitors for Use as Anti-biofilm Drugs
The Development of a Pipeline for the Identification and Validation of Small-Molecule RelA Inhibitors for Use as Anti-biofilm Drugs Open
Biofilm infections have no effective medical treatments and can only be disrupted via physical means. This means that any biofilm infection that is not addressable surgically can never be eliminated and can only be managed as a chronic dis…
View article: Rapid Genomic Change and Intraclonal Variation in the Bacterial Opportunistic Pathogens Haemophilus influenzae and Acinetobacter baumannii
Rapid Genomic Change and Intraclonal Variation in the Bacterial Opportunistic Pathogens Haemophilus influenzae and Acinetobacter baumannii Open
The immense genetic diversity observed within many human-associated bacterial species is an important consideration when studying pathogenesis. The studies described here explore the phenotypic impact of genetic diversity across natural po…
View article: Genome-wide analysis of DNA uptake by naturally competent Haemophilus influenzae
Genome-wide analysis of DNA uptake by naturally competent Haemophilus influenzae Open
This is the data associated with our paper "Genome-wide analysis of DNA uptake by naturally competent Haemophilus influenzae". The paper used an innovative application of deep sequencing to measure how Haemophilus influenzae takes up genom…
View article: The Bacterial Guide to Designing a Diversified Gene Portfolio
The Bacterial Guide to Designing a Diversified Gene Portfolio Open
The stunning ability of bacteria to evolve and adapt has contributed to the success of these single cells, which have inhabited the Earth for billions of years and play vital roles in the environment and in human health. The goal of this c…
View article: Additional file of Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates
Additional file of Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates Open
Additional file of Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates
View article: Additional file 1 of Author Correction: Interaction between the microbiome and TP53 in human lung cancer
Additional file 1 of Author Correction: Interaction between the microbiome and TP53 in human lung cancer Open
Additional file 5. Clinical metadata and OTUs for NCI-MD samples.
View article: Additional file 1 of Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates
Additional file 1 of Comparative analysis and supragenome modeling of twelve Moraxella catarrhalis clinical isolates Open
Additional file 1: Table S1: Reconstruction of M. catarrhalis Central Metabolic Pathways. Highlighted cells denote differences between strains; n.p. = ORFs not present in one or more strains. * denotes inclusion of RH4 gene annotation data…
View article: Panel 3: Genomics, precision medicine and targeted therapies
Panel 3: Genomics, precision medicine and targeted therapies Open
View article: Genome-wide analysis of DNA uptake across the outer membrane of naturally competent<i>Haemophilus influenzae</i>
Genome-wide analysis of DNA uptake across the outer membrane of naturally competent<i>Haemophilus influenzae</i> Open
SUMMARY The genomes of naturally competent Pasteurellaceae and Neisseriaceae have many short uptake sequences (USS), which allow them to distinguish self-DNA from foreign DNA. To fully characterize this preference we developed genome-wide …
View article: Genome rearrangements induce biofilm formation in Escherichia coli C – an old model organism with a new application in biofilm research
Genome rearrangements induce biofilm formation in Escherichia coli C – an old model organism with a new application in biofilm research Open
View article: A Culture-Independent Analysis of the Microbiota of Female Interstitial Cystitis/Bladder Pain Syndrome Participants in the MAPP Research Network
A Culture-Independent Analysis of the Microbiota of Female Interstitial Cystitis/Bladder Pain Syndrome Participants in the MAPP Research Network Open
We surveyed urine microbiota of females diagnosed with interstitial cystitis/bladder pain syndrome (IC/BPS) and matched control participants enrolled in the National Institutes of Health (NIH) Multidisciplinary Approach to the Study of Chr…
View article: Deletion of genes involved in the ketogluconate metabolism, Entner-Doudoroff pathway, and glucose dehydrogenase increase local and invasive virulence phenotypes in Streptococcus pneumoniae
Deletion of genes involved in the ketogluconate metabolism, Entner-Doudoroff pathway, and glucose dehydrogenase increase local and invasive virulence phenotypes in Streptococcus pneumoniae Open
Streptococcus pneumoniae displays increased resistance to antibiotic therapy following biofilm formation. A genome-wide search revealed that SP 0320 and SP 0675 (respectively annotated as 5-keto-D-gluconate-5-reductase and glucose dehydrog…