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1. Euprymna berryi as a comparative model host for Vibrio fischeri light organ symbiosis

   https://doi.org/10.1128/aem.00001-25  

   Imes, Avery M; Pavelsky, Morgan N; Badal, Klodia; Kamp, Derrick L; Briseño, John L; Sakmar, Taylor; Vogt, Miranda A; Nyholm, Spencer V; Heath-Heckman, Elizabeth_A C; Grasse, Bret; et al (July 2025, Applied and Environmental Microbiology)

   Rudi, Knut (Ed.)

   ABSTRACT Functional studies of host-microbe interactions benefit from natural model systems that enable the exploration of molecular mechanisms at the host-microbe interface. BioluminescentVibrio fischericolonize the light organ of the Hawaiian bobtail squid,Euprymna scolopes, and this binary model has enabled advances in understanding host-microbe communication, colonization specificity,in vivobiofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid,Euprymna berryi,can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which theE. berryilight organ symbiosis parallels known processes inE. scolopes. However, the nature of theE. berryilight organ, including its microbial constituency and specificity for microbial partners, has not been examined. In this report, we isolated bacteria fromE. berryianimals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes inE. berryiandE. scolopeshatchlings. This study revealsE. berryito be a valuable comparative model to complement studies inE. scolopes.IMPORTANCEMicrobiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. TheEuprymna scolopes-Vibrio fischerisystem has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and forin vivobiofilm formation in development and specificity of an animal’s microbiome.Euprymna berryiis a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifiesE. berryias a strong symbiosis model host due to features that are conserved with those ofE. scolopes, which will enable the extension of functional studies in bobtail squid symbioses. 

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2. Nascent flagellar basal bodies are immobilized by rod assembly in Bacillus subtilis

   https://doi.org/10.1128/mbio.00530-25  

   Dunn, Caroline M; Foust, Daniel J; Gao, Yongqiang; Biteen, Julie S; Shaw, Sidney L; Kearns, Daniel B (June 2025, mBio)

   Salama, Nina R (Ed.)

   ABSTRACT Flagella are complex, trans-envelope nanomachines that localize in species-specific patterns on the cell surface. Here, we study the localization dynamics of the earliest stage of basal body formation inBacillus subtilisusing a fluorescent fusion to the C-ring protein FliM. We find thatB. subtilisbasal bodies do not exhibit dynamic subunit exchange and are largely stationary at steady state, consistent with flagellar assembly through the peptidoglycan (PG). However, rare mobile basal bodies were observed, and the prevalence of mobile basal bodies is elevated both early in basal body assembly and when the rod is mutated. Thus, basal body mobility is a precursor to patterning, and we propose that rod polymerization probes the PG superstructure for pores of sufficient diameter to permit rod transit. Furthermore, mutation of the rod disrupts basal body patterning in a way that phenocopies mutation of the cytoplasmic flagellar patterning protein FlhF. We infer that rod synthesis and the cytoplasmic regulators coordinate flagellar assembly by interpreting a grid-like pattern of pores, pre-existent in the PG. IMPORTANCEBacteria insert flagella in a species-specific pattern on the cell body, but how patterns are achieved is poorly understood. In bacteria with a single polar flagellum, a marker protein localizes to the cell pole and nucleates the assembly of the flagellum at that site.Bacillus subtilisassembles ~25 basal bodies over the length of the cell in a grid-like pattern and lacks proteins required for their polar targeting. Here, we show thatB. subtilisbasal bodies are mobile soon after assembly and become immobilized when the flagellar rod transits the peptidoglycan (PG) wall. Moreover, defects in the flagellar rod lead to a more-random distribution of flagella and an increase in polar basal bodies. We conclude that the peritrichous patterning of flagella ofB. subtilisis different from the polar patterning of other bacteria, and we infer that theB. subtilisrod probes the PG for holes that can accommodate the machine. 

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3. Maintaining microbiota across diverse symbiotic organs in Euprymna scolopes : Insights into shared immune responses

   https://doi.org/10.1073/pnas.2512903122  

   Vijayan, Nidhi; Briseño, John; Simakov, Oleg; Nyholm, Spencer V (January 2026, Proceedings of the National Academy of Sciences)

   Many animals have multiple organs or tissues that are colonized by diverse microbiota. The female Hawaiian bobtail squid,Euprymna scolopes, has two organs with distinct symbiotic communities: the accessory nidamental gland (ANG) and the light organ (LO). The ANG hosts a bacterial consortium, whereas the LO has a binary relationship withVibriofischeri, housed in extracellular crypt spaces as part of the central core (CC). To understand how the host maintains distinct symbiotic communities, we used transcriptomics to identify immune-related genes that are uniquely and similarly expressed in the ANG and LO-CC compared to organs without a known microbiota. Genes such as peptidoglycan recognition proteins EsPGRP2 and EsPGRP3, cathepsin-Z, alkaline phosphatase, and acidic phospholipase exhibited significant upregulation in the symbiotic organs compared to other tissues like gills, skin, mantle, optic lobe, ovaries, and brain. Moreover, EsPGRP2 displayed distinct localization patterns within the ANG, inversely correlating with bacterial presence, whereas the protein was colocalized withV. fischeriin the LO-CC. Notably, 10 different galaxins (EsGal) were uniquely highly expressed in both the ANG and LO-CC, with EsGal1 messenger RNA predominantly localized to the LO-CC epithelium, while EsGal2 and EsGal3 were primarily found in the epithelia of ANG tubules. Furthermore, antimicrobial assays using partial peptides derived from EsGal1 and EsGal2 showed varying and distinct patterns of inhibitory activity for these peptides. In summary, our findings identify similar immune gene families expressed across functionally distinct symbiotic organs inE. scolopes, suggesting that common immunomodulatory factors may maintain distinct symbiotic niches in the host. 

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4. 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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5. 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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