A5076522093- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Insect symbiosis and bacterial influences
- Escherichia coli research studies
- Probiotics and Fermented Foods
- Salmonella and Campylobacter epidemiology
- Vibrio bacteria research studies
- Plant Virus Research Studies
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- Diet and metabolism studies
- Clostridium difficile and Clostridium perfringens research
- Mollusks and Parasites Studies
- Legume Nitrogen Fixing Symbiosis
- Aquatic Invertebrate Ecology and Behavior
- Antibiotic Resistance in Bacteria
- Primate Behavior and Ecology
- Protist diversity and phylogeny
- Plant Pathogenic Bacteria Studies
- Entomopathogenic Microorganisms in Pest Control
The University of Texas at Austin
2016-2025
Integra (United States)
2020
Yale University
2011-2015
University of Arizona
2002-2014
University of Connecticut
2013
University of New Haven
2013
University of Houston
2010-2011
University of California, Irvine
2010-2011
University of Chicago
2010-2011
Georgia Institute of Technology
2011
Pathogenic Escherichia coli cause over 160 million cases of dysentery and one deaths per year, whereas non-pathogenic E. constitute part the normal intestinal flora healthy mammals birds. The evolutionary pathways underlying this dichotomy in bacterial lifestyle were investigated by multilocus sequence typing a global collection isolates. Specific pathogen types [enterohaemorrhagic coli, enteropathogenic enteroinvasive K1 Shigella] have arisen independently repeatedly several lineages, other...
Abstract A method is presented for the rapid in vitro amplification of DNA sequences that flank a region known sequence. The uses polymerase chain reaction (PCR), but it has primers oriented reverse direction usual orientation. template restriction fragment been ligated upon itself to form circle. This procedure inverse PCR (IPCR) many applications molecular genetics, example, and identification flanking transposable elements. In this paper we show feasibility IPCR by amplifying an IS1...
Massively parallel pyrosequencing of the small subunit (16S) ribosomal RNA gene has revealed that extent rare microbial populations in several environments, 'rare biosphere', is orders magnitude higher than previously thought. One important caveat with this method sequencing error could artificially inflate diversity estimates. Although per-base 16S rDNA amplicon been shown to be as good or lower Sanger sequencing, no direct assessments errors on estimates have reported. Using only...
The availability of the complete sequence Escherichia coli strain MG1655 provides first opportunity to assess overall impact horizontal genetic transfer on evolution bacterial genomes. We found that 755 4,288 ORFs (547.8 kb) have been introduced into E. genome in at least 234 lateral events since this species diverged from Salmonella lineage 100 million years (Myr) ago. average age genes was 14.4 Myr, yielding a rate 16 kb/Myr/lineage divergence. Although most acquired subsequently were...
A set of 72 reference strains Escherichia coli isolated from a variety hosts and geographical locations has been established for use in studies variation genetic structure natural populations. The strains, which have characterized by multilocus enzyme electrophoresis, are representative the range genotypic species as whole.
The evolutionary origins of the bacterial lineages that populate human gut are unknown. Here we show multiple predominant taxa in arose via cospeciation with humans, chimpanzees, bonobos, and gorillas over past 15 million years. Analyses strain-level diversity within hominid microbiomes revealed clades Bacteroidaceae Bifidobacteriaceae have been maintained exclusively host across hundreds thousands generations. Divergence times these cospeciating bacteria congruent those hominids, indicating...
Multiple factors over the lifetime of an individual, including diet, geography, and physiologic state, will influence microbial communities within primate gut. To determine source variation in composition microbiota among species, we investigated distal gut harbored by great apes, as present fecal samples recovered their native ranges. We found that branching order host-species phylogenies based on these is completely congruent with known relationships hosts. Although initially continuously...
Attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar those higher eukaryotes, or few taxa for which ancestors can be reliably dated from ecological geological evidence. Despite similarities substitution estimated some lineages, comparisons relative at different classes nucleotide sites indicate no basis their universal application all bacteria. However, there is evidence a constant genome-wide mutation...
Journal Article Production of single-stranded DNA templates by exonuclease digestion following the polymerase chain reaction Get access Russell G. Higuchi, Higuchi Search for other works this author on: Oxford Academic PubMed Google Scholar Howard Ochman 1Department Human Genetics, Washington University School MedicineSt Louis, MO 63110, USA Nucleic Acids Research, Volume 17, Issue 14, 25 July 1989, Page 5865, https://doi.org/10.1093/nar/17.14.5865 Published: 1989
Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this is believed to result mainly from duplication and loss, but prokaryotes, lateral transfer (LGT) can also contribute substantially genome contents. To determine histories inventories, we conducted an exhaustive analysis phylogenies for all families widely sampled group, γ-Proteobacteria. We show that, although these bacterial genomes display striking differences...
Significance Human lifestyles profoundly influence the communities of microorganisms that inhabit body, is, microbiome; however, how microbiomes humans have diverged from those found within wild-living hominids is not clear. To establish gut microbiome has changed since diversification human and ape species, we characterized microbial assemblages residing hundreds wild chimpanzees, bonobos, gorillas. Changes in composition accrued steadily as African apes diversified, but at an accelerated...
Genetic drift, which is particularly effective within small populations, can shape the size and complexity of genomes by affecting fixation deleterious mutations. In Bacteria, assessing contribution genetic drift to genome evolution problematic because usual methods, based on intraspecific polymorphisms, be thwarted difficulties in delineating species' boundaries. The increased availability sequenced bacterial allows application an alternative estimator genome-wide ratio replacement silent...
Chimpanzee social activity is associated with diversity in the gut microbiome.
Animals are distinguished by having guts—organs that must extract nutrients from food yet also bar invasion pathogens. Most guts colonized nonpathogenic microorganisms, but the functions of these microbes, or even reasons why they occur in gut, vary widely among animals. Sometimes microorganisms have codiversified with hosts; sometimes live mostly elsewhere environment. Either way, gut often benefit hosts. Benefits may reflect evolutionary addiction, whereby hosts incorporate into normal...
The variation and taxonomic diversity among mammalian gut microbiomes raises several questions about the factors that contribute to rates patterns of change in these microbial communities. By comparing microbiome compositions 112 species representing 14 orders, we assessed how host ecological diversification. Except rare cases, same bacterial phyla predominate microbiomes, there has been some convergence according dietary category across all mammalians lineages except Chiropterans (bats),...