ORCID Profile
0000-0001-8966-9680
Current Organisation
Emory University
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Bacteriology | Microbiology | Biotechnology Not Elsewhere Classified
Publisher: Proceedings of the National Academy of Sciences
Date: 28-08-2002
Abstract: The 2,160,267 bp genome sequence of Streptococcus agalactiae , the leading cause of bacterial sepsis, pneumonia, and meningitis in neonates in the U.S. and Europe, is predicted to encode 2,175 genes. Genome comparisons among S. agalactiae , Streptococcus pneumoniae , Streptococcus pyogenes , and the other completely sequenced genomes identified genes specific to the streptococci and to S. agalactiae . These in silico analyses, combined with comparative genome hybridization experiments between the sequenced serotype V strain 2603 V/R and 19 S. agalactiae strains from several serotypes using whole-genome microarrays, revealed the genetic heterogeneity among S. agalactiae strains, even of the same serotype, and provided insights into the evolution of virulence mechanisms.
Publisher: Wiley
Date: 08-2011
Publisher: Centers for Disease Control and Prevention (CDC)
Date: 09-2009
Publisher: Wiley
Date: 07-09-2018
DOI: 10.1111/MEC.14840
Abstract: Pollen DNA metabarcoding-marker-based genetic identification of potentially mixed-species pollen s les-has applications across a variety of fields. While basic species-level pollen identification using standard DNA barcode markers is established, the extent to which metabarcoding (a) correctly assigns species identities to mixes (qualitative matching) and (b) generates sequence reads proportionally to their relative abundance in a s le (quantitative matching) is unclear, as these have not been assessed relative to known standards. We tested the quantitative and qualitative robustness of metabarcoding in constructed pollen mixtures varying in species richness (1-9 species), taxonomic relatedness (within genera to across class) and rarity (5%-100% of grains), using Illumina MiSeq with the markers rbcL and ITS2. Qualitatively, species composition determinations were largely correct, but false positives and negatives occurred. False negatives were typically driven by lack of a barcode gap or rarity in a s le. Species richness and taxonomic relatedness, however, did not strongly impact correct determinations. False positives were likely driven by contamination, chimeric sequences and/or misidentification by the bioinformatics pipeline. Quantitatively, the proportion of reads for each species was only weakly correlated with its relative abundance, in contrast to suggestions from some other studies. Quantitative mismatches are not correctable by consistent scaling factors, but instead are context-dependent on the other species present in a s le. Together, our results show that metabarcoding is largely robust for determining pollen presence/absence but that sequence reads should not be used to infer relative abundance of pollen grains.
Publisher: Oxford University Press (OUP)
Date: 15-04-2003
DOI: 10.1093/NAR/GKG321
Abstract: The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt with a plasmid of 7966 nt) was determined, representing the fourth species with a complete genome sequence from the Chlamydiaceae family of obligate intracellular bacterial pathogens. Of 1009 annotated genes, 798 were conserved in all three other completed Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack orthologs in any other completed chlamydial genomes, including tryptophan and thiamine biosynthesis determinants and a ribose-phosphate pyrophosphokinase, the product of the prsA gene. Notable amongst these was a novel member of the virulence-associated invasin/intimin family (IIF) of Gram-negative bacteria. Intriguingly, two authentic frameshift mutations in the ORF indicate that this gene is not functional. Many of the unique genes are found in the replication termination region (RTR or plasticity zone), an area of frequent symmetrical inversion events around the replication terminus shown to be a hotspot for genome variation in previous genome sequencing studies. In C.caviae, the RTR includes several loci of particular interest including a large toxin gene and evidence of ancestral insertion(s) of a bacteriophage. This toxin gene, not present in Chlamydia pneumoniae, is a member of the YopT effector family of type III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR is much more similar to orthologs in Chlamydia muridarum than those in the phylogenetically closest species C.pneumoniae, suggesting the possibility of horizontal transfer of genes between the rodent-associated Chlamydiae. With most genes observed in the other chlamydial genomes represented, C.caviae provides a good model for the Chlamydiaceae and a point of comparison against the human atherosclerosis-associated C.pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific genes in these important bacterial pathogens.
Publisher: Wiley
Date: 11-2021
DOI: 10.1002/ECE3.8281
Abstract: Molecular identification of mixed‐species pollen s les has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via licon sequencing, but whole‐genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per s le and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each s le using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k ‐mer identification method with reference libraries constructed from full‐genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 licon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but erged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS‐based pollen identification is the lack of representation of plant ersity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed‐species pollen s les.
Publisher: PeerJ
Date: 14-02-2015
DOI: 10.7287/PEERJ.PREPRINTS.837V1
Abstract: The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species and is therefore also the largest extant species of the paraphyletic assemblage commonly referred to as “fishes”. As both a phenotypic extreme and a member of the group basal to the remaining gnathostomes, which includes all tetrapods and therefore also humans, its genome is of substantial comparative interest. Whale sharks are also listed as a “vulnerable” species on the International Union for Conservation of Nature (IUCN)'s Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which assembled into 11,347,816 contigs and 3,606,038 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the Holocephali Elephant shark. The whale shark contained a novel Toll-like-receptor protein with sequence conservation to both the TLR4 and TLR13 proteins of mammals. The data are publicly available on a Galaxy bioinformatic server (whaleshark.georgiaaquarium.org). This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.
Publisher: Oxford University Press (OUP)
Date: 20-06-2011
Publisher: American Association for the Advancement of Science (AAAS)
Date: 09-10-2009
Abstract: More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data.
Publisher: Cold Spring Harbor Laboratory
Date: 28-06-2019
DOI: 10.1101/685743
Abstract: Chondrichthyes (cartilaginous fishes) are fundamental for understanding vertebrate evolution, yet their genomes are understudied. We report long-read sequencing of the whale shark genome to generate the best gapless chondrichthyan genome assembly yet with higher contig contiguity than all other cartilaginous fish genomes, and studied vertebrate genomic evolution of ancestral gene families, immunity, and gigantism. We found a major increase in gene families at the origin of gnathostomes (jawed vertebrates) independent of their genome duplication. We studied vertebrate pathogen recognition receptors (PRRs), which are key in initiating innate immune defense, and found erse patterns of gene family evolution, demonstrating that adaptive immunity in gnathostomes did not fully displace germline-encoded PRR innovation. We also discovered a new Toll-like receptor (TLR29) and three NOD1 copies in the whale shark. We found chondrichthyan and giant vertebrate genomes had decreased substitution rates compared to other vertebrates, but gene family expansion rates varied among vertebrate giants, suggesting substitution and expansion rates of gene families are decoupled in vertebrate genomes. Finally, we found gene families that shifted in expansion rate in vertebrate giants were enriched for human cancer-related genes, consistent with gigantism requiring adaptations to suppress cancer.
Publisher: American Society for Microbiology
Date: 13-05-2011
DOI: 10.1128/JB.00454-11
Publisher: American Society for Microbiology
Date: 12-2010
DOI: 10.1128/JB.00991-10
Abstract: The Gram-negative Burkholderia genus includes several species of intracellular bacterial pathogens that pose substantial risk to humans. In this study, we have generated draft genome sequences of 15 strains of B. oklahomensis , B. pseudomallei , B. thailandensis , and B. ubonensis to an average sequence read coverage of 25- to 40-fold.
Publisher: American Society for Microbiology
Date: 08-2011
DOI: 10.1128/JB.05277-11
Abstract: Chlamydia psittaci is a highly prevalent avian pathogen and the cause of a potentially lethal zoonosis, causing life-threatening pneumonia in humans. We report the genome sequences of C. psittaci 6BC, the prototype strain of the species, and C. psittaci Cal10, a widely used laboratory strain.
Publisher: American Society for Microbiology
Date: 06-2009
DOI: 10.1128/JB.00746-09
Abstract: Zoonotic infections are a growing threat to global health. Chlamydia pneumoniae is a major human pathogen that is widespread in human populations, causing acute respiratory disease, and has been associated with chronic disease. C. pneumoniae was first identified solely in human populations however, its host range now includes other mammals, marsupials, hibians, and reptiles. Australian koalas ( Phascolarctos cinereus ) are widely infected with two species of Chlamydia , C. pecorum and C. pneumoniae . Transmission of C. pneumoniae between animals and humans has not been reported however, two other chlamydial species, C. psittaci and C. abortus , are known zoonotic pathogens. We have sequenced the 1,241,024-bp chromosome and a 7.5-kb cryptic chlamydial plasmid of the koala strain of C. pneumoniae (LPCoLN) using the whole-genome shotgun method. Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) distribution, and phylogenetic analysis of conserved genes and SNPs against the human isolates of C. pneumoniae show that the LPCoLN isolate is basal to human isolates. Thus, we propose based on compelling genomic and phylogenetic evidence that humans were originally infected zoonotically by an animal isolate(s) of C. pneumoniae which adapted to humans primarily through the processes of gene decay and plasmid loss, to the point where the animal reservoir is no longer required for transmission.
Publisher: Elsevier BV
Date: 04-2014
DOI: 10.1016/J.GENE.2014.01.064
Abstract: The whale shark (Rhincodon typus) is the largest extant species of fish, belonging to the order Orectolobiformes. It is listed as a "vulnerable" species on the International Union for Conservation of Nature (IUCN)'s Red List of Threatened Species, which makes it an important species for conservation efforts. We report here the first complete sequence of the mitochondrial genome (mitogenome) of the whale shark obtained by next-generation sequencing methods. The assembled mitogenome is a 16,875 bp circle, comprising of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. We also performed comparative analysis of the whale shark mitogenome to the available mitogenome sequences of 17 other shark species, four from the order Orectolobiformes, five from Lamniformes and eight from Carcharhiniformes. The nucleotide composition, number and arrangement of the genes in whale shark mitogenome are the same as found in the mitogenomes of the other members of the order Orectolobiformes and its closest orders Lamniformes and Carcharhiniformes, although the whale shark mitogenome had a slightly longer control region. The availability of mitogenome sequence of whale shark will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this species.
Publisher: American Society for Microbiology
Date: 03-2007
DOI: 10.1128/JB.00378-06
Abstract: In Chlamydiaceae , the nucleotide sequence between the 5S rRNA gene and the gene for subunit F of the Na + -translocating NADH-quinone reductase ( nqrF or dmpP ) has varied lengths and gene contents. We analyzed this site in 45 Chlamydiaceae strains having erse geographical and pathological origins and including members of all nine species.
Publisher: Proceedings of the National Academy of Sciences
Date: 23-09-2002
Abstract: The 3.31-Mb genome sequence of the intracellular pathogen and potential bioterrorism agent, Brucella suis , was determined. Comparison of B. suis with Brucella melitensis has defined a finite set of differences that could be responsible for the differences in virulence and host preference between these organisms, and indicates that phage have played a significant role in their ergence. Analysis of the B. suis genome reveals transport and metabolic capabilities akin to soil lant-associated bacteria. Extensive gene synteny between B. suis chromosome 1 and the genome of the plant symbiont Mesorhizobium loti emphasizes the similarity between this animal pathogen and plant pathogens and symbionts. A limited repertoire of genes homologous to known bacterial virulence factors were identified.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 28-03-2003
Abstract: The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.
Publisher: Proceedings of the National Academy of Sciences
Date: 18-04-2003
Abstract: The 1,995,275-bp genome of Coxiella burnetii , Nine Mile phase I RSA493, a highly virulent zoonotic pathogen and category B bioterrorism agent, was sequenced by the random shotgun method. This bacterium is an obligate intracellular acidophile that is highly adapted for life within the eukaryotic phagolysosome. Genome analysis revealed many genes with potential roles in adhesion, invasion, intracellular trafficking, host-cell modulation, and detoxification. A previously uncharacterized 13-member family of ankyrin repeat-containing proteins is implicated in the pathogenesis of this organism. Although the lifestyle and parasitic strategies of C. burnetii resemble that of Rickettsiae and Chlamydiae , their genome architectures differ considerably in terms of presence of mobile elements, extent of genome reduction, metabolic capabilities, and transporter profiles. The presence of 83 pseudogenes displays an ongoing process of gene degradation. Unlike other obligate intracellular bacteria, 32 insertion sequences are found dispersed in the chromosome, indicating some plasticity in the C. burnetii genome. These analyses suggest that the obligate intracellular lifestyle of C. burnetii may be a relatively recent innovation.
Publisher: Springer Science and Business Media LLC
Date: 07-10-2002
DOI: 10.1038/NBT749
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 03-2005
End Date: 12-2008
Amount: $233,000.00
Summary: Kernel methods for the analysis of whole bacterial genomes. This project addresses the fundamental scientific problem of the identification of regulatory regions and specific promoters within bacterial genomes, with a focus upon two organisms of great social, economic and bioterrism significance. From the machine learning perspective, the project will be the first to produce a kernel-based approach directly tailored to the problem of the detection of regulatory regions. The methods developed wil .... Kernel methods for the analysis of whole bacterial genomes. This project addresses the fundamental scientific problem of the identification of regulatory regions and specific promoters within bacterial genomes, with a focus upon two organisms of great social, economic and bioterrism significance. From the machine learning perspective, the project will be the first to produce a kernel-based approach directly tailored to the problem of the detection of regulatory regions. The methods developed will be made available through a straightforward web-based interface, allowing biologists throughout the world to utilize the approach as a tool to be applied to a progressively widening class of bacterial genomes, and even to eukaryotes. Read more Read less
Funder: Australian Research Council
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