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1. Pathogenic Vibrio Species Are Associated with Distinct Environmental Niches and Planktonic Taxa in Southern California (USA) Aquatic Microbiomes

   https://doi.org/10.1128/mSystems.00571-21  

   Diner, Rachel E.; Kaul, Drishti; Rabines, Ariel; Zheng, Hong; Steele, Joshua A.; Griffith, John F.; Allen, Andrew E.; Seyler, Lauren Marie (August 2021, mSystems)

   Bernstein, Hans C. (Ed.)

   ABSTRACT Interactions between vibrio bacteria and the planktonic community impact marine ecology and human health. Many coastal Vibrio spp. can infect humans, representing a growing threat linked to increasing seawater temperatures. Interactions with eukaryotic organisms may provide attachment substrate and critical nutrients that facilitate the persistence, diversification, and spread of pathogenic Vibrio spp. However, vibrio interactions with planktonic organisms in an environmental context are poorly understood. We quantified the pathogenic Vibrio species V. cholerae , V. parahaemolyticus , and V. vulnificus monthly for 1 year at five sites and observed high abundances, particularly during summer months, with species-specific temperature and salinity distributions. Using metabarcoding, we established a detailed profile of both prokaryotic and eukaryotic coastal microbial communities. We found that pathogenic Vibrio species were frequently associated with distinct eukaryotic amplicon sequence variants (ASVs), including diatoms and copepods. Shared environmental conditions, such as high temperatures and low salinities, were associated with both high concentrations of pathogenic vibrios and potential environmental reservoirs, which may influence vibrio infection risks linked to climate change and should be incorporated into predictive ecological models and experimental laboratory systems. IMPORTANCE Many species of coastal vibrio bacteria can infect humans, representing a growing health threat linked to increasing seawater temperatures. However, their interactions with surrounding microbes in the environment, especially eukaryotic organisms that may provide nutrients and attachment substrate, are poorly understood. We quantified three pathogenic Vibrio species monthly for a duration of 1 year, finding that all three species were abundant and exhibited species-specific temperature and salinity distributions. Using metabarcoding, we investigated associations between these pathogenic species and prokaryotic and eukaryotic microbes, revealing genus and amplicon sequence variant (ASV)-specific relationships with potential functional implications. For example, pathogenic species were frequently associated with chitin-producing eukaryotes, such as diatoms in the genus Thalassiosira and copepods. These associations between high concentrations of pathogenic vibrios and potential environmental reservoirs should be considered when predicting infection risk and developing ecologically relevant model systems. 

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2. Isolation and characterization of four novel Vibrio parahaemolyticus bacteriophages from oysters

   https://doi.org/10.1371/journal.pone.0339894  

   Aldaroub, Joud; Walsky, Chrissy M; Ewell, Rylee E; Aylward, Frank O; Stevens, Ann M; Burke, Alison Kernell (December 2025, PLOS One)

   Fernández_Robledo, José A (Ed.)

   Vibrio parahaemolyticus(VP) is a bacterial pathogen found in brackish and marine water that infects many marine organisms, such as oysters and shrimp. Consumption of raw or undercooked seafood contaminated withV. parahaemolyticusis a primary cause of seafood-borne gastroenteritis in humans. Due to increasing ocean temperatures,V. parahaemolyticuscontamination of oyster beds in the United States has spread up the east and west coasts to the northern-most states. Promising new research is exploring the isolation of bacteriophages againstV. parahaemolyticuswith a long-term goal to possibly decontaminate oyster beds, thereby expanding the harvest season and allowing for safer consumption of seafood. In this study, store-bought oysters harvested from the Chesapeake Bay in Virginia were used to isolate four bacteriophages with activity against a specificV. parahaemolyticusstrain. A standard double agar overlay plaque assay was used to identify phage activity. After phage isolation, the genomes were sequenced, and transmission electron microscopy (TEM) was performed to visualize the virions. The genomes and TEM images revealed four distinct phages. Three of the phages are distinct isolates that exhibit podovirus-like morphology with short tails and genome sizes of approximately 43 kbp. One phage has siphovirus-like morphology and is a mid-sized tailed phage with a genome size of 80 kbp. Although spot tests performed with the oyster homogenates on up to 10 differentV. parahaemolyticusstrains recovered activity across a wide range of hosts, plaque assays with the isolated phages showed limited host range. Future work will be necessary to determine the viability of using the bacteriophages for elimination ofV. parahaemolyticusin harvested oysters, treatment of aquaculture seed and spat, and/or the environment. 

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3. Hybridization capture sequencing for Vibrio spp. and associated virulence factors

   https://doi.org/10.1128/mbio.00516-25  

   Brumfield, Kyle D; Enke, Sana; Swan, Brandon K; Carrasquilla, Lakeshia; Lee, Michael D; Stern, David B; Gieser, Linn; Hasan, Nur A; Usmani, Moiz; Jutla, Antarpreet S; et al (August 2025, mBio)

   Hinton, Deborah (Ed.)

   ABSTRACT Proliferation ofVibriospp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundanceVibriospp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69Vibriospp. and 162Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition,Vibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenicVibriospp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specificVibriospp., yielded significantly greater metagenomic insight, notably a variety of otherVibriospp., including detection ofVibrio cholerae,Vibrio fluvialis, andVibrio aestuarianus, in addition toVibrio parahaemolyticusandVibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios.IMPORTANCEThe increasing prevalence of pathogenicVibriospp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenicVibriospp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundanceVibriospp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing ofVibrio parahaemolyticusandVibrio vulnificusstrains isolated from the samples. Results suggest pathogenicVibriospp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance. 

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4. Machine learning in understanding environmental variability of vibriosis in coastal waters

   https://doi.org/10.1128/aem.00716-25  

   Magers, Bailey M; Brumfield, Kyle D; Kumar, Sunil; Colwell, Rita R; Jutla, Antarpreet S (September 2025, Applied and Environmental Microbiology)

   van_Kessel, Julia C (Ed.)

   ABSTRACT Vibrio spp.comprise ecologically significant bacteria that thrive in warm, moderately saline water, and their incidence and proliferation are strongly influenced by environmental factors. In recent years,Vibrio spp. infections have been reported more frequently and over a greater geographical area along the US eastern seaboard. This study provides an analysis ofVibrio spp. infections, notably caused byVibrio alginolyticus,Vibrio choleraenon-O1/non-O139,Vibrio fluvialis,Vibrio mimicus,V. parahaemolyticus, andV. vulnificus, extracted from the Centers for Disease Control and Prevention’s Cholera and OtherVibrioIllness Surveillance system, located within 200 km of the eastern US coast, to analyze latitudinal distribution trends between 1990 and 2019. For eachVibrio spp., case incidence (presence/absence) was modeled, including environmental data and employing extreme gradient boosting machine learning algorithms (XGBoost). Environmental parameters associated with the incidence of vibriosis were clustered using k-means clustering. The northern limit of total cases of vibriosis was found to have increasedca. 40 km/year, withV. alginolyticus(ca. 70 km/year),V. fluvialis(ca. 60 km/year), andVibrio parahaemolyticus(ca. 60 km/year) showing the greatest latitudinal shifts. These changes were found to be linked to environmental parameters that enhance the proliferation ofVibrio spp. The average accuracy of the XGBoost models was 60.9%–71.0%, with temperature and salinity being the most significant predictors. Relationships among other environmental parameters were complex and nonlinear, but phytoplankton and precipitation served to differentiate the models. Clustering using k-means yielded results that supported temperature, salinity, and phytoplankton as important environmental parameters. Research in progress will aid in developing global predictive risk models forVibrio spp. infections.IMPORTANCEVibrio spp. are ecologically significant bacteria, and their incidence and proliferation are strongly influenced by environmental factors. In recent years,Vibrio spp. infections have been reported more frequently and over a greater geographical area along the US eastern seaboard. This study provides an analysis of latitudinal distribution trends ofVibrio spp. infections, notably caused byVibrio alginolyticus,Vibrio choleraenon-O1/non-O139,Vibrio fluvialis,Vibrio mimicus,Vibrio parahaemolyticus, andV. vulnificus, within 200 km of the eastern US coast. The northern limit of total cases of vibriosis was found to have increasedca. 40 km/year. These changes were found to be linked to environmental parameters that enhance the proliferation ofVibrio spp. Temperature and salinity were the most significant predictors of vibriosis case presence and absence. Phytoplankton and precipitation changes served to differentiateVibrio sp. presence. Research in progress will aid in developing global predictive risk models forVibrio spp. infections. 

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5. Microbial ecology of coral-dominated reefs in the Federated States of Micronesia

   https://doi.org/10.3354/ame01961  

   Apprill, A; Holm, H; Santoro, AE; Becker, C; Neave, M; Hughen, K; Richards Donà, A; Aeby, G; Work, T; Weber, L; et al (April 2021, Aquatic Microbial Ecology)

   Microorganisms are central to the functioning of coral reef ecosystems, but their dynamics are unstudied on most reefs. We examined the microbial ecology of shallow reefs within the Federated States of Micronesia. We surveyed 20 reefs surrounding 7 islands and atolls (Yap, Woleai, Olimarao, Kosrae, Kapingamarangi, Nukuoro, and Pohnpei), spanning 875053 km 2 . On the reefs, we found consistently higher coral coverage (mean ± SD = 36.9 ± 22.2%; max 77%) compared to macroalgae coverage (15.2 ± 15.5%; max 58%), and low abundances of fish. Reef waters had low inorganic nutrient concentrations and were dominated by Synechococcus, Prochlorococcus, and SAR11 bacteria. The richness of bacterial and archaeal communities was significantly related to interactions between island/atoll and depth. High coral coverage on reefs was linked to higher relative abundances of Flavobacteriaceae, Leisingera, Owenweeksia, Vibrio, and the OM27 clade, as well as other heterotrophic bacterial groups, consistent with communities residing in waters near corals and within coral mucus. Microbial community structure at reef depth was significantly correlated with geographic distance, suggesting that island biogeography influences reef microbial communities. Reefs at Kosrae Island, which hosted the highest coral abundance and diversity, were unique compared to other locations; seawater from Kosrae reefs had the lowest organic carbon (59.8-67.9 µM), highest organic nitrogen (4.5-5.3 µM), and harbored consistent microbial communities (>85% similar), which were dominated by heterotrophic cells. This study suggests that the reef-water microbial ecology on Micronesian reefs is influenced by the density and diversity of corals as well as other biogeographical features. 

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