About

Thomas M. Stephens is a Professor of Spanish in the Department of Spanish and Portuguese at Rutgers, The State University of New Jersey, a position he has held since 1981. He also serves as the Assistant Graduate Director and Faculty Director of The Language Center. His educational background includes a B.A. in Spanish Education and an M.A. in Spanish Language and Literature from the University of South Carolina, as well as a Ph.D. in Romance Linguistics from the University of Michigan. His research and teaching focus on race and ethnicity in Latin America and questions of language in social contexts. He is the author of the 'Dictionary of Latin American Racial and Ethnic Terminology' and 'A Game of Mirrors: The Changing Face of Ethno-racial Constructs and Language in the Americas,' along with numerous journal articles. Currently, he is working on the third edition of his dictionary, which includes revisions and extensions to the lexical items related to ethnicity and race, and a manuscript tentatively titled 'Convenient Untruths: Language, Race, Ethnicity, and Racism in a Non-Post-Racial Latin America.' Stephens has served on various departmental, college, university, and national committees, including roles in the American Association of Teachers of Spanish and Portuguese, the American Portuguese Studies Association, the Brazilian Studies Association, and Rutgers' Faculty Athletics Representative to the NCAA.

Research topics

• Biology
• Evolutionary biology
• Genetics
• Ecology

Selected publications

• In <i>Staphylococcus aureus</i> , MbcS is a refunctionalized acyl-CoA synthetase that confers a fitness advantage during intra-species competition

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-29

  articleOpen access

  Abstract Staphylococcus aureus is one of the most frequently co-isolated pathogens in polymicrobial infections, where interspecies interactions contribute to enhanced virulence, persistence, and antimicrobial tolerance. Nutrient availability plays a central role in these interactions as microorganisms compete for resources required to sustain essential cellular processes. For instance, branched-chain amino acids (BCAAs) are critical for protein synthesis, and valine synthesis pathway precursors are essential for energy production. In S. aureus , BCAAs are also the precursors for branched-chain fatty acids (BCFAs), the dominant fatty acids in the S. aureus membrane. We previously identified a second pathway that uses branched-chain carboxylic acids (BCCAs) and the high-affinity acyl-CoA synthetase MbcS to catalyze the synthesis of BCFA precursors. However, the physiological role of this pathway and the conditions triggering its activation remain unclear. Here, we show that mbcS is restricted to S. aureus and closely related human-associated staphylococci. Phylogenetic analyses suggest that MbcS arose from a refunctionalization event and represents a non-orthologous replacement for the phosphotransbutyrylase (Ptb) and butyrate kinase (Buk) enzymes. Consistent with this model, Ptb and Buk from Staphylococcus pseudintermedius catalyze the formation of branched-chain acyl-CoAs from BCCAs, but only at high substrate concentrations. We further show that mbcS expression is upregulated in a codY mutant, implicating this pathway in BCAA-limited conditions. In support, we show that mbcS is required for optimal fitness during intra-species competition. Together, our findings support a model in which the MbcS-dependent pathway enables S. aureus to scavenge BCFA precursors under nutrient-limited conditions, providing a competitive advantage in polymicrobial environments. Importance Staphylococcus aureus is a major contributor to polymicrobial infections, where competition for nutrients can influence bacterial physiology and survival. A deeper understanding of how S. aureus adapts to nutrient limitation is therefore essential to explain its success as a human pathogen. In S. aureus , the acyl-CoA synthetase MbcS supports BCFA synthesis from BCAA-derived carboxylic acids and aldehydes, which are released into the environment as by-products of bacterial metabolism. Herein, we provide evidence that S. aureus acquired the acyl-CoA synthetase MbcS as an adaptive trait. This metabolic innovation allows this bacterium to maintain membrane homeostasis under nutrient limitation and compete against neighboring bacteria. Our findings highlight an adaptive strategy that may contribute to the persistence of S. aureus in polymicrobial infections.

  PublisherOA PDFDOI

• A portable, low-cost, point-of-care DNA amplification kit with impedance-based detection for decentralized antimicrobial resistance diagnostics

  Lab on a Chip · 2026-01-01 · 1 citations

  articleOpen access

  copies per μl) in a complex background DNA mixture demonstrated detection results that strongly correlated with quantitative PCR (qPCR). These findings demonstrate that the amplification kit achieves performance parity with gold-standard nucleic acid detection methods while offering portability, affordability, and ease of use. By enabling accurate, rapid, and decentralized diagnostics without reliance on laboratory infrastructure, this combined workflow holds promise for advancing infectious disease monitoring and antimicrobial resistance surveillance, among other applications, at the point of care.

  PublisherOA PDFDOI

• Metaproteome Analysis of Short‐Term Thermal Stress in Three Sympatric Coral Species Reveals Divergent Host Responses

  Ecology and Evolution · 2026-03-01

  articleOpen access

  ABSTRACT Anthropogenic climate change has contributed to the accelerating loss of coral reefs worldwide. This crisis has led to a myriad of studies aimed at understanding the basis of coral resilience to support reef conservation. Here, we compare physiological, proteomic, and metabolomic responses to acute thermal stress to identify both diverged and conserved stress response strategies and molecular markers of bleaching susceptibility in three different coral species. We find species‐specific responses with the thermally sensitive Acropora hyacinthus exhibiting a rapid decline in endosymbiont physiology (~19% decline in photosynthetic efficiency and a −1.88 fold change in abundance), coupled with one‐third of proteins showing a reduction in abundance. In contrast, Porites lobata displayed a delayed physiological and proteomic (~5% initial; ~14% prolonged) response to stress, suggesting greater resilience. Stylophora pistillata initially showed shifts in the proteome (~11%) followed by colony “bail‐out”, that is, rapid tissue loss. Overall, we observed markedly different responses in most biochemical pathways in the three coral species. Nonetheless, some known biomarkers of stress, including heat‐shock proteins, showed conserved, cross‐species responses to thermal stress with differences in temporal abundance reflecting bleaching resistance. Metabolomic profiling revealed an increase in stress‐associated dipeptides and free amino acids in all three species, although species‐specific and temporally variable responses occurred. Our results underscore the species‐specific nature of coral responses to thermal stress and highlight proteomic signatures associated with symbiosis breakdown, offering mechanistic insights into coral bleaching susceptibility and resilience. Overall, these findings enhance our ability to identify early‐warning indicators of bleaching and underscore the challenges associated with the development of universal coral stress biomarkers.

  PublisherDOI

• The Host Coral Bleaching Response Viewed Through the Lens of Multi‐Omics

  BioEssays · 2026-01-01

  articleOpen accessSenior author

  We review recent multi-omics analyses of the coral heat stress response to explore the generality of the Oxidative Theory of Coral Bleaching (OTCB), which posits that algal symbiont release is the final act of defense by the coral host to survive alga-derived oxidative stress. The OTCB is particularly relevant given that ocean warming, which is accelerating under climate change, has proven devastating for corals, leading to the bleaching phenotype and widespread reef loss. Multi-omics results, in combination with other data, such as genome-wide association studies, support the idea that coral bleaching is a multifactorial response that reflects a wide array of causes and effects and is population-specific under most conditions, with coral ploidy and genotype being critical to bleaching sensitivity. This perspective leverages the location, algal and prokaryotic microbiome, and host genotype-specific aspects of coral resilience to promote a new "personal genomics" approach to coral conservation, analogous to that used in human health.

  PublisherOA PDFDOI

• Rafts of change: microbial and functional dynamics in simulated <i>Sargassum</i> strandings

  Applied and Environmental Microbiology · 2026-03-31

  articleOpen access

  ABSTRACT Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum -derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future. IMPORTANCE This work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum , which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.

  PublisherDOI

• Genetic Transfer in Action: Uncovering <scp>DNA</scp> Flow in an Extremophilic Microbial Community

  Environmental Microbiology · 2025-02-01 · 3 citations

  articleOpen access

  Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.

  PublisherOA PDFDOI

• Gene transfer drives community cooperation in geothermal habitats

  Trends in Microbiology · 2025-06-20 · 2 citations

  reviewOpen accessSenior author

  Cyanidiophyceae red algae dominate many geothermal habitats and provide important tools for investigating the evolution of extremophilic eukaryotes and associated microbial communities. We propose that resource sharing drove genome reduction in Cyanidiophyceae and enabled the neofunctionalization of genes in multi-enzyme pathways. Utilizing arsenic detoxification as a model, we discuss how the sharing of gene functions by other members of the microbial assemblage weakened selection on homologs in the Cyanidiophyceae, allowing long-term gene persistence via the putative gain of novel functions. This hypothesis, referred to as the Integrated Horizontal Gene Transfer (HGT) Model (IHM), attempts more generally to explain how extremophilic eukaryotes may have transitioned from 'hot start' milieus by functional innovations driven by the duplication and divergence of HGT-derived genes.

  PublisherDOI

• Green fluorescent proteins show divergent patterns among species and strains of Porites from the Great Barrier Reef

  Coral Reefs · 2025-11-09

  articleOpen access

  Abstract GFP-like and RFP-like proteins serve diverse functional roles in corals, including photoprotection, prey capture, and algal symbiont attraction. This study investigated the diversity of biofluorescence patterns in 27 coral colonies of Porites cf. lutea and Porites cf. lobata from the Great Barrier Reef, Australia. We used comparative methods to characterize the extant fluorescence patterns under blue and green light for excitation, their relationship to the Porites phylogeny built using host animal 18S-28S rDNA sequence data. We also studied the impact of thermal stress on green and red fluorescence in a single coral genotype to assess stability of the observed signal. Overall, we identified six broad fluorescence patterns: star, uniform, absent, tentacles, oral region, and tentacle tips. Population analyses demonstrate that a single lineage of Porites may express divergent and distinct GFP-like patterns that are shared by all polyps in a colony. This suggests that biofluorescent proteins may confer an array of adaptive functions that allow Porites species to thrive in different ecosystems under different stressors. The reorganization of both green and red fluorescence distributions to uniform patterning under thermal stress suggests these proteins may provide a biomarker of thermal stress. Thus, the potential for GFP/green fluorescence and RFP/red fluorescence screening as a non-invasive tool to assess reef health and adaptive responses warrants further investigation, particularly in the context of climate change-driven stress events.

  PublisherOA PDFDOI

• Green fluorescent proteins show divergent patterns among species and strains of Porites from the Great Barrier Reef

  Research Square · 2025-07-17

  preprintOpen access
  PublisherDOI

• Metaproteome analysis of short-term thermal stress in three sympatric coral species reveals divergent host responses

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-26 · 2 citations

  preprintOpen access

  Abstract The accelerating loss of coral reefs worldwide due to anthropogenic climate change has led to a myriad of studies aimed at understanding the basis of coral resilience to support reef conservation. Here, we integrate physiological measurements with proteomic and metabolomic profiles to examine species-specific responses to increased temperature in three sympatric reef-building corals from the Great Barrier Reef: Acropora hyacinthus , Porites lobata , and Stylophora pistillata . We find species-specific stress response strategies with A. hyacinthus , a thermally sensitive species, exhibiting rapid decline in endosymbiont physiology, coupled with a one-third reduction in protein abundance. In contrast, P. lobata displayed a delayed physiological response to stress and a muted proteome response, suggesting greater resilience. S. pistillata initially showed minor shifts in the proteome followed by colony “bail-out”. Overall, we observed markedly different responses in most biochemical pathways in the three coral species. Nonetheless, some known biomarkers of stress, including heat-shock proteins, showed conserved responses to thermal stress with differences in temporal abundance reflecting bleaching resistance. Our results underscore the species-specific nature of coral responses to thermal stress and highlight proteomic signatures associated with symbiosis breakdown, offering mechanistic insights into coral bleaching susceptibility and resilience.

  PublisherOA PDFDOI

Frequent coauthors

• Debashish Bhattacharya

  Rutgers, The State University of New Jersey

  54 shared

• Cheong Xin Chan

  Monash University

  32 shared

• Mark A. Ragan

  21 shared

• Raúl A. González‐Pech

  Shepherd University

  20 shared

• Amin R. Mohamed

  New York University

  15 shared

• Hollie M. Putnam

  University of Rhode Island

  13 shared

• Igor V. Grigoriev

  Lawrence Berkeley National Laboratory

  12 shared

• Lauren E. Fuess

  Texas State University

  11 shared

Education

• Ph.D.

  University of Michigan