Profile
Vincent Richards
Biological Sciences
Associate Professor
Jordan Hall 111A [Lab]
Jordan Hall 111C [Office]
Jordan Hall 111D [Research Laboratory Service]
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
Profile/About Me
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.
Courses Taught
Introduction to Applied Genomics - BIOL4030/6030
Micro Core II - MICR8040
Selected Publications
Since 2015
Hassler HB, Probert B, Moore C, Lawson E, Jackson RW, Russell BT, Richards VP (2022) Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. Microbiome, 10, 104. https://doi.org/10.1186/s40168-022-01295-y
O’Connell LM, Blouin T, Soule A, Burne RA, Nascimento MM, Richards VP (2022) Optimization and evaluation of the 30S-S11 rDNA gene for taxonomic profiling of oral streptococci. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.00453-22
Rathbone T, Ates I, Fernando L, Addlestone E, Lee CM, Richards VP, Cottle RN (2022) Electroporation-mediated delivery of cas9 ribonucleoproteins results in high levels of gene editing in primary hepatocytes. The CRISPR Journal, https://doi.org/10.1089/crispr.2021.0134
Ma X, Agudelo P, Richards VP, Baeza JA (2022) Genome survey sequencing of the phyto-parasitic nematode Hoplolaimus galeatus. PeeJ 10:e12749, https://doi.org/10.7717/peerj.12749
Coker MO, Akhigbe P, Osagie E, Idemudia NL, Igedegbe O, Chukwumah N, Adebiyi R, Mann AE, O’Connell LM, Obuekwe O, Omoigberale A, Charurat M, Richards VP (2021) Dental caries and its association with the oral microbiomes and HIV in young children – Nigeria (DOMHaIN): a cohort study. BMC Oral Health 21, 620 https://doi.org/10.1186/s12903-021-01944-y
Richards VP, Nigsch A, Pavinski Bitar P, Sun Q, Stuber T, Ceres K, Robbe Austerman S, Schukken Y, Grohn YT, and Stanhope MJ (2021) Evolutionary genomic and bacteria GWAS analysis of Mycobacterium avium subsp. paratuberculosis and dairy cattle Johne’s disease phenotypes. Applied and Environmental Microbiology, https://doi.org/10.1128/AEM.02570-20
O'Connell LM, Santos R, Springer G, Burne RA, Nascimento MM, and Richards VP (2020) Site-specific profiling of the dental mycobiome reveals strong taxonomic shifts during progression of early childhood caries. Applied and Environmental Microbioogy, 18;86(7), https://doi.org/10.1128/AEM.02825-19
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, https://doi.org/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, https://doi.org/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, https://doi.org/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, https://doi.org/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, https://doi.org/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; https://doi.org/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; https://doi.org/10.1128/mSystems.00158-18.
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). https://doi.org/10.1128/microbiolspec.GPP3-0042-2018
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, https://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, https://doi.org/10.1093/jhered/esy045
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, https://doi.org/10.1016/j.ympev.2018.03.034
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, https://doi.org/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, https://doi.org/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, https://doi.org/10.1186/s12864-016-3411-x
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, https://doi.org/10.1093/gbe/evw255
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, https://doi.org/10.1111/1348-0421.12439
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. https://doi.org/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, https://doi.org/10.1007/s00338-016-1435-y
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, https://doi.org/10.1128/AEM.03887-15
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, https://doi.org/10.1371/journal.pone.0119799
Honors and Awards
2020: Junior Researcher of the Year - Clemson University
2017: Nova Southeastern University - Distinguished Alumni Achievement Award
