A5033333203- Genomics and Phylogenetic Studies
- Urinary Tract Infections Management
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Bacterial Identification and Susceptibility Testing
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Enterobacteriaceae and Cronobacter Research
- RNA and protein synthesis mechanisms
- Reproductive tract infections research
- Antimicrobial Resistance in Staphylococcus
- Streptococcal Infections and Treatments
- Plant Virus Research Studies
- Infective Endocarditis Diagnosis and Management
- Bladder and Urothelial Cancer Treatments
- Escherichia coli research studies
- Microbial infections and disease research
- Antibiotic Resistance in Bacteria
- Mycobacterium research and diagnosis
- Bacterial Genetics and Biotechnology
- Diphtheria, Corynebacterium, and Tetanus
- Environmental DNA in Biodiversity Studies
- Gene expression and cancer classification
- Mosquito-borne diseases and control
- Pelvic floor disorders treatments
Loyola University Chicago
2015-2024
University of Chicago
2017-2022
University of Houston
2004-2010
Lawrence Livermore National Laboratory
2007
Universidad de Guadalajara
2007
Rice University
2007
Loyola University New Orleans
2000
This paper presents standards and best practices for reporting genome sequences of uncultivated viruses. We present an extension the Minimum Information about any (x) Sequence (MIxS) standard virus genomes. Uncultivated Virus Genome (MIUViG) were developed within Genomic Standards Consortium framework include origin, quality, annotation, taxonomic classification, biogeographic distribution in silico host prediction. Community-wide adoption MIUViG standards, which complement a Single...
Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and experimental analyses. Here we isolate genome-sequence 149 bacterial from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds diversity within sampled bladders, including Proteobacteria, Actinobacteria, Firmicutes. Detailed genomic...
ABSTRACT Bacterial viruses (bacteriophages) play a significant role in microbial community dynamics. Within the human gastrointestinal tract, for instance, associations among bacteriophages (phages), microbiota stability, and health have been discovered. In contrast to phages associated with urinary are largely unknown. Preliminary metagenomic surveys of virome indicate rich diversity novel lytic phage sequences at an abundance far outnumbering that eukaryotic viruses. These surveys,...
Urobiome research has the potential to advance understanding of a wide range diseases, including lower urinary tract symptoms and kidney disease. Many scientific areas have benefited from early method consensus facilitate greater, common good. This document, developed by group expert investigators currently engaged in urobiome (UROBIOME 2020 conference participants), aims promote standardization advances this field adoption core practices. We propose standardized nomenclature as well...
Although the human bladder is reported to harbor unique microbiota, our understanding of how these microbial communities interact with their hosts limited, mostly owing lack isolates test mechanistic hypotheses. Niche-specific bacterial collections and associated reference genome databases have been instrumental in expanding knowledge microbiota other anatomical sites, such as gut oral cavity.
The Cuatro Ciénegas Basin (CCB) in the central part of Chihuahan desert (Coahuila, Mexico) hosts a wide diversity microorganisms contained within springs thought to be geomorphological relics an ancient sea. A major question remaining answered is whether bacteria from CCB are marine that adapted oligotrophic system poor NaCl, rich sulfates, and with extremely low phosphorus levels (<0.3 microM). Here, we report complete genome sequence Bacillus coahuilensis, sporulating bacterium isolated...
The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics cannot be examined by sequencing alone, further highlighting necessity for isolation and examination phages from environmental samples. While much our current knowledge base has been generated marine phages, freshwater viruses are understudied comparison. Our group previously conducted metagenomics-based studies samples collected Lake Michigan -...
Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs commonly associated with colonization by Escherichia coli, members this species also have been found within bladder individuals no lower urinary symptoms (no LUTS), known as asymptomatic bacteriuria. Prior studies that both uropathogenic E. coli (UPEC) strains and isolates not encode for virulence factors. Thus, reason(s) why sometimes causes UTI-like remain(s) elusive. In study, genomes 66 from...
ABSTRACT Bacteriophages are the most abundant and diverse biological entities on planet, new phage genomes being discovered at a rapid pace. As more published, methods needed for placing these in an ecological evolutionary context. Phages difficult to study by phylogenetic methods, because they exchange genes regularly, no single gene is conserved across all phages. Here, we demonstrate how gene-level networks can provide high-resolution view of genetic diversity offer novel perspective...
Metagenomics has enabled sequencing of viral communities from a myriad different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete genomes have been constructed directly complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine identify raw reads representative mixed (viral and bacterial) communities. automates sequence...
Modern sequencing technologies have provided insight into the genetic diversity of numerous species, including human pathogen Pseudomonas aeruginosa. Bacterial genomes often harbor bacteriophage (prophages), which can account for upwards 20% genome. Prior studies found P. aeruginosa prophages that contribute to their host's pathogenicity and fitness. These advantages come in many different forms, production toxins, promotion biofilm formation, displacement other strains. While several genera...
The advent of sensitive enhanced culture (metaculturomic) and culture-independent DNA-based (metagenomic) methods has revealed a rich collection microbial species that inhabit the human urinary tract. Known as microbiome, this community microbes consists hundreds distinct range across entire phylogenetic spectrum. This new knowledge clashes with standard clinical microbiology laboratory methods, established more than 60 years ago, focus attention on relatively small subset universally...
We used a whole-genome scanning technique to identify the NADH dehydrogenase gamma subunit (nuoG) primer set that is sensitive and specific enough detect diverse number of Bartonella species in wide range environmental samples yet maintains minimal cross-reactivity mammalian host arthropod vector organisms.
Viruses are the most abundant component of human microbiota. Recent evidence has uncovered a rich diversity viruses within female bladder, including both bacteriophages and eukaryotic viruses. We conducted whole-genome sequencing bladder microbiome 30 women: 10 asymptomatic 'healthy' women 20 with an overactive bladder. These metagenomes include sequences representative human, bacterial viral DNA. This analysis, however, focused specifically on sequences. Using bioinformatic tool virMine, we...
Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance many similar bacterial taxa. As was once thought to be sterile, complex interactions between microbes within yet characterized. To initiate this process, we begun sequencing isolates, including clinically relevant genus Gardnerella. Herein, present genomic sequences four Gardnerella strains isolated from bladders women with symptoms urgency urinary incontinence; these are first genomes produced niche....
Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have less studied freshwaters, despite representing potentially more diverse environment. Lake Michigan is one of the largest bodies freshwater planet, yet to date diversity its phages be examined. Here, we present composite survey viral...
Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present first high-throughput molecular survey of Lake Michigan. Every two weeks from May 13 to August 5, 2014, collected surface water samples nearshore waters four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Calumet Beach. Four biological replicates were for each sampling date location, resulting 112 samples. Eighty-nine...
Infections caused by antibiotic-resistant
Average nucleotide identity analysis, based on whole genome sequences of 115 strains previously identified as Aerococcus urinae, an emerging uropathogen, discriminates at least six unique genomic taxa. The analysis affords clearer species boundaries over 16S rRNA gene sequencing and traditional phenotypic approaches for the identification phylogenetic organization species. newly described can be differentiated by matrix-assisted laser desorption ionization time-of-flight protein signatures....
Abstract Background In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed to translational selection, mutational bias and drift. Furthermore, correlations between within host genomes their viral pathogens been observed for myriad host-virus systems. As such, numerous investigated effort better understand how species evolve. Numerous metrics developed identify usage. addition, few...
ABSTRACT Recent research has debunked the myth that urine is sterile, having uncovered bacteria within bladders of healthy individuals. However, identity, diversity, and putative roles bacteriophages in bladder are unknown. We report draft genome sequences seven isolated from microbial communities adult female bladders.