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Biological Sciences Profiles


Vincent Richards

Assistant Professor
Biological Sciences Department

Office: 111C Jordan Hall
Phone: 864-656-2207
Email: vpricha@clemson.edu
Personal Website: http://www.vprichards-lab.com/

 

 Educational Background

Ph.D. Population Genetics
Nova Southeastern University 2010

M.Sc. Population Genetics
Nova Southeastern University 2006

B.Sc. Marine Biology
Nova Southeastern University 2001

 Courses Taught

Introduction to Applied Genomics BIOL4030/6030
Biology in the News BIOL2000

 Profile

Professional Experience
2013 - 2014 Research Associate, Cornell University
2010 - 2013 Postdoctoral Associate, Cornell University
2009 - 2009 Adjunct Professor of Biology, Nova Southeastern University
2000 - 2010 Research Assistant, National Coral Reef Institute and Guy Harvey Research Institute

 Research Interests

My lab's primary research objective is to better understand how pathogenic bacteria evolve and adapt to their environment. Specific topics include understanding how these bacteria (i) invade, colonize, and respond to different environments and hosts, (ii) evade host defenses, (iii) acquire virulence factors, and (iv) interact at the community level.

Central to this endeavor is the study of genetic variation and differential gene expression. With the advent of next generation sequencing technology, these processes can now be examined at the genomic level, and we utilize this technology to examine genomic variation in nucleotide sequence, gene content, and gene expression. Through a combination of these approaches, genes associated with particular disease states and tropisms can be identified, population genetic structure can be precisely delineated, information regarding demographic history and transmission dynamics can be obtained, and bacteria communities can be profiled.

The human microbiome is an exciting new field of genomic study and the profiling of communities from the perspective of species, genes, and gene expression has the potential to aid in the development of novel disease therapeutic and prevention strategies. We have a strong interest in the oral microbiome, with a particular emphasis on the impact of HIV infection in children and the interplay between adaptive immunity and the development of oral disease.

Lastly, information obtained from population studies can help control the spread of disease, elucidate outbreak causal factors, aid post infection source tracking, and assist in the management of livestock. Parallel to this specific interest in bacterial pathogens, we maintain a wide interest in evolutionary biology and population genetics.

 Publications

Richards VP, Velsko IM, Alam TM, Zadoks RN, Manning SD, Pavinski Bitar PD, Hasler HB, Crestani C, Springer G, Probert B, Town CD, Stanhope MJ (2019) Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae. Molecular Biology and Evolution, doi: 10.1093/molbev/msz169

Nascimento MM, Alvarez AJ, Huang X, Browngardt C, Jenkins R, Sinhoreti MC, Ribeiro APD, Dilbone DA, Richards VP, Garrett TJ, Burne RA (2019) Metabolic profile of supragingival plaque exposed to arginine and fluoride. Journal of Dental Research, doi: 10.1177/0022034519869906

Kaspar J, Godwin M, Velsko IM, Richards VP, Burne RA (2019) Spontaneously arising Streptococcus mutans variants with reduced susceptibility to chlorhexidine display genetic defects and diminished fitness. Antimicrobial Agents and Chemotherapy, doi: 10.1128/AAC.00161-19

Velsko IM, Perez MS, Richards VP (2019) Resolving phylogenetic relationships for Streptococcus mitis and Streptococcus oralis through core and pan genome analyses. Genome Biology and Evolution, pii: evz049. doi: 10.1093/gbe/evz049

Nascimento MM, Alvarez AJ, Huang X, Hanway S, Perry S, Luce A, Richards VP, Burne RA (2019). Arginine metabolism in supragingival oral biofilms as a predictor of caries risk. JDR Clinical & Translational Research. doi: 10.1177/2380084419834234

Marra NJ, Stanhope MJ, Jue N, Wang M, Sun Q, Pavinski Bitar P, Richards VP, Komissarov A, Rayko M, Kliver S, Stanhope BJ, Winkler C, O'Brien SJ, Antunes A, Jorgensen S, Shivji MS (2019) White shark genome: ancient elasmobranch adaptations addressing genome stability. PNAS 201819778; DOI: 10.1073/pnas.1819778116

Velsko IM, Chakraborty B, Nascimento M, Burne RA, Richards VP (2018) Species designations belie phenotypic and genotypic heterogeneity in oral Streptococci. mSystems, 3 (6) e00158-18; doi: 10.1128/mSystems.00158-18.

Richards VP, DeBiasse M, Shivji MS (2018) Deep mitochondrial lineage divergence among populations of the southern stingray (Hypanus americana) throughout the Southeastern United States and Caribbean. Marine Biodiversity, doi.org/10.1007/s12526-018-0930-5

Bernard AM, Richards VP, Stanhope MJ, Shivji MS (2018) Transcriptome derived simple sequence repeats confirm the genetic isolation of Northeast Pacific white sharks. Journal of Heredity, 109, 771 - 779.

Chen Y, Hammer EE, Richards VP. (2018) Phylogenetic signature of lateral exchange of genes for antibiotic production and resistance among bacteria highlights a pattern of global transmission of pathogens between humans and livestock. Molecular Phylogenetics and Evolution, 125, 255 - 264.

He J, Kim D, Zhou X, Ahn S, Burne R, Richards VP, Koo H. (2017). RNA-seq reveals transcriptomic changes of Streptococcus mutans co-culturing with Candida albicans within mixed-species biofilms. Frontiers in Microbiology, doi: 10.3389/fmicb.2017.01036

Richards VP, Alvarez AJ, Luce A, Perry S, Bedenbaugh M, Mitchell M, Hong H, Shaddox LM, Burne RA, Nascimento MM. (2017). Microbiomes of site-specific dental plaque of children with different caries status. Infection and Immunity, doi: e00106-17

Marra NJ, Richards VP, Early A, Bogdanowicz SM, Pavinski Bitar P, Stanhope MJ, Shivji MS. (2017) Comparative transcriptomics of elasmobranchs and teleosts highlight important processes in adaptive immunity and regional endothermy. BMC Genomics, 18:87.

Jacob A, O'Brien Andersen L, Pavinski Bitar P, Richards VP, Shah S, Stanhope MJ, Stensvold R, Clark G (2016). Blastocystis mitochondrial genomes appear to show multiple independent gains and losses of start and stop codons. Genome Biology and Evolution, 8, 3340 - 3350.

Palmer A, Painter J, Hassler H, Richards VP, Bruce T, Morrison S, Brown E, Kozak NA, Lucas C, McNealy TL (2016) Legionella clemsonensis sp. nov., a green fluorescing Legionella strain from a patient with pneumonia. Microbiology and Immunology, 60, 694 - 701.

DeBiasse MB, Richards VP, Shivji MS, Hellberg ME (2016) Shared phylogeographic breaks in a Caribbean coral reef sponge and its invertebrate commensals. Journal of Biogeography. doi:10.1111/jbi.12785

Richards VP, Bernard AM, Feldheim KA, Shivji MS (2016) Patterns of population structure and dispersal in the long-lived "redwood" of the coral reef, the giant barrel sponge (Xestospongia muta). Coral Reefs, 1 - 11.

Huang X, Palmer SR, Ahn SJ, Richards VP, Williams ML, Nascimento MM, Burne R (2016) A Highly Arginolytic Streptococcus Species That Potently Antagonizes Streptococcus mutans. Applied and environmental microbiology. 82, 2187 - 2201.

Richards VP, Lefabure T, Pavinski Bitar PD, Simpson KW, Schukken YH, Stanhope MJ. (2015) Genome based phylogeny and comparative genomic analysis of intra-mammary pathogenic Escherichia coli. PLOS One, 10(3):e0119799.

Richards VP, DeBiasse MB, Shivji MS. (2014) Genetic evidence supports larval retention in the Western Caribbean for an invertebrate with high dispersal capability (Ophiothrix suensonii: Echinodermata, Ophiuroidea). Coral Reefs, 34, 313 - 325.

Choi SC, Parker J, Richards VP, Ross K, Jilly B, Chen J. (2014) Draft genome sequence of an atypical strain of Streptococcus pneumoniae isolated from a respiratory infection. Genome announcements, 2, 4.

Richards VP, Palmer SR, Highlander S, Pavinski Bitar PD, Qin X, Weinstock GM, Highlander SK, Town CD, Burne RA, Stanhope MJ (2014) Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biology and Evolution, 6, 741 - 753.

Richards VP, Choi SC, Pavinski Bitar PD, Gurjar AA, Stanhope MJ (2013) Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment. BMC Genomics, 14, 920.

Richards VP, Suzuki H, Stanhope MJ, Shivji MS (2013) Characterization of the heart transcriptome of the white shark (Carcharodon carcharias). BMC Genomics, 14, 697.

Richards VP, Greig TW, Fair PA, McCulloch SD, Politz C, Natoli A, Driscoll CA, Hoelzel RA, David V, Bossart GD, Lopez JV (2013) Patterns of population structure for inshore bottlenose dolphins along the eastern United States. Journal of Heredity, 104, 765 - 778.

Palmer SR, Miller JH, Abranches J, Zeng L, Lefabure T, Richards VP, Lemos JA, Stanhope MJ, Burne RA (2013) Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans. PLOS One, 10(1371): e0061358.

Richards VP, Lefabure T, Pavinski Bitar PD, Stanhope MJ (2012) Comparative characterization of the virulence gene clusters (lipooligosaccharide [LOS] and capsular polysaccharide [CPS]) for Campylobacter coli, Campylobacter jejuni subsp. jejuni and related Campylobacter species. Infection Genetics and Evolution, 14, 200 - 213.

Richards VP, Zadoks RN, Pavinski Bitar PD, Lefabure T, Lang P, Werner B, Tikofsky L, Moroni P, Stanhope MJ (2012) Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis. BMC Microbiology, 12, 293.

Cornejo OE, Lefabure T, Pavinski Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Carlos D. Bustamante CD, Stanhope MJ (2012) Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Molecular Biology and Evolution, 30, 881 - 893.

Bernard AM, Feldheim KA, Richards VP, Nemeth RS, Shivji MS (2012) Development and characterization of fifteen novel microsatellite loci for the Nassau grouper (Epinephelus striatus) and their utility for cross-amplification on a suite of closely related species. Conservation Genetic Resources, 4, 983 - 986.

Lefabure T, Richards VP, Lang P, Pavinski-Bitar P, Stanhope MJ (2012) Gene repertoire evolution of Streptococcus pyogenes inferred from phylogenomic analysis with Streptococcus canis and Streptococcus dysgalactiae. PLOS One, 7(5): e37607.

Richards VP, Stanhope MJ, Shivji MS (2012) Island endemism, morphological stasis, and possible cryptic speciation in two coral reef, commensal Leucothoid amphipod species throughout Florida and the Caribbean. Biodiversity and Conservation, 21, 343 - 361.

Richards VP, Lang P, Bitar PD, Lefabure T, Schukken YH, Zadoks RN, Stanhope MJ (2011) Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae. Infection Genetics and Evolution, 11, 1263 - 1275.

Feldheim KA, Chapman DD, Simpfendorfer CA, Richards VP, Shivji MS, Wiley TR, Poulakis GR, Carlson JK, Eng R, Sargarese S (2009) Genetic markers to support conservation of the endangered smalltooth sawfish, Pristis pectinata: rapid forensic identification, sawfish DNA-barcodes and polymorphic microsatellites. Conservation Genetics Resources, 2, 105 - 113.

DeBiasse MB, Richards VP, Shivji MS (2009) Genetic assessment of connectivity in the common reef sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) reveals high population structure along the Florida reef tract. Coral Reefs, 29, 47 - 55.

Smith WD, Bizzarro JJ, Richards VP, Nielsen J, Marquez-Fara­as F, Shivji MS (2009) Morphometric convergence and molecular divergence: the taxonomic status and evolutionary history of Gymnura crebripunctata and Gymnura marmorata in the eastern Pacific Ocean. Journal of Fish Biology, 75, 761 - 783.

Richards VP, Henning M, Witzell W, Shivji MS (2009) Species delineation and evolutionary history of the globally distributed spotted eagle ray (Aetobatus narinari). Journal of Heredity, 100, 273 - 283.


CHAPTERS AND BOOKS
Abranches J, Zeng L, Kajfasz JK, Palmer SR, Chakraborty B, Wen ZT, Richards VP, Burne, RA, Brady LJ, Lemos JA. Biology of oral Streptococci (2018). Microbiol Spectrum 6(5): doi:10.1128/microbiolspec.GPP3-0042-2018

Banks KW, Riegl BM, Richards VP, Walker BK, Helmle KP, Jordan LKB, Phipps J, Shivji MS, Spieler RE, Dodge RE (2008) The reef tract of continental Southeast Florida (Miami-Dade, Broward and Palm Beach Counties, USA). In: Coral reefs of the USA (eds. Riegl BM, Dodge RE), pp 175 220. Springer.com.

 Links

Postdoc and PhD student openings
HIV and oral disease
Pathogen transmission
Oral probiotic
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