Microbiomes of pathogenic Vibrio species reveal environmental and planktonic associations

2019 ◽  
Author(s):  
Rachel E. Diner ◽  
Ariel J. Rabines ◽  
Hong Zheng ◽  
Joshua A. Steele ◽  
John F. Griffith ◽  
...  
Keyword(s):  
Distinct Species ◽  
Human Infection ◽  
Model Systems ◽  
Taxonomic Resolution ◽  
Environmental Preferences ◽  
Pathogenic Vibrio ◽  
Photosynthetic Organism ◽  
One Year ◽  
Species Specific ◽  
Planktonic Community

Abstract Background Many species of coastal Vibrio spp. bacteria can infect humans, representing an emerging health threat linked to increasing seawater temperatures. Vibrio interactions with the planktonic community impact coastal ecology and human infection potential. In particular, interactions with eukaryotic and photosynthetic organism may provide attachment substrate and critical nutrients (e.g. chitin, phytoplankton exudates) that facilitate the persistence, diversification, and spread of pathogenic Vibrio spp. Vibrio interactions with these organisms in an environmental context are, however, poorly understood.Results We quantified pathogenic Vibrio species, including V. cholerae, V. parahaemolyticus, and V. vulnificus, and two virulence-associated genes for one year at five coastal sites in Southern California and used metabarcoding to profile associated prokaryotic and eukaryotic communities, including vibrio-specific communities. These Vibrio spp. reached high abundances, particularly during Summer months, and inhabited distinct species-specific environmental niches driven by temperature and salinity. Associated bacterial and eukaryotic taxa identified at fine-scale taxonomic resolution revealed genus and species-level relationships. For example, common Thalassiosira genera diatoms capable of exuding chitin were positively associated with V. cholerae and V. vulnificus in a species-specific manner, while the most abundant eukaryotic genus, the diatom Chaetoceros, was positively associated with V. parahaemolyticus. Associations were often linked to shared environmental preferences, and several copepod genera were linked to low-salinity environmental conditions and abundant V. cholerae and V. vulnificus.Conclusions This study clarifies ecological relationships between pathogenic Vibrio spp. and the planktonic community, elucidating new functionally relevant associations, establishing a workflow for examining environmental pathogen microbiomes, and highlighting prospective model systems for future mechanistic studies.

Coastal Microbiomes Reveal Associations between Pathogenic Vibrio Species, Environmental Factors, and Planktonic Communities

2020 ◽  
Author(s):  
Rachel E. Diner ◽  
Drishti Kaul ◽  
Ariel Rabines ◽  
Hong Zheng ◽  
Joshua A Steele ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Communities ◽  
Antibiotic Resistance Genes ◽  
Human Infection ◽  
Vibrio Species ◽  
Model Systems ◽  
Laboratory Model ◽  
Environmental Preferences ◽  
Pathogenic Vibrio ◽  
Vibrio Spp

Abstract Background Many species of coastal Vibrio spp. bacteria can infect humans, representing an emerging health threat linked to increasing seawater temperatures. Vibrio interactions with the planktonic community impact coastal ecology and human infection potential. In particular, interactions with eukaryotic and photosynthetic organism may provide attachment substrate and critical nutrients (e.g. chitin, phytoplankton exudates) that facilitate the persistence, diversification, and spread of pathogenic Vibrio spp.. Vibrio interactions with these organisms in an environmental context are, however, poorly understood. Results After quantifying pathogenic Vibrio species, including V. cholerae , V. parahaemolyticus , and V. vulnificus, over one year at 5 sites, we found that all three species reached high abundances, particularly during Summer months, and exhibited species-specific temperature and salinity distributions. Using metabarcoding we established a detailed profile of the both prokaryotic and eukaryotic coastal microbial communities, finding that pathogenic species were frequently associated with specific ASVs of chitin-producing eukaryotes such as diatoms and copepods. Furthermore, environmental variables had a significant effect not only on pathogenic Vibrio species but entire microbial communities, suggesting in some cases shared environmental preferences. Several significant ASV-level associations were revealed, indicating that commonly used broad taxonomic classifications (e.g. based on microbial class or Vibrio as a genus) likely mask ecologically important interactions. Shotgun metagenomic analyses revealed diverse vibrio communities that harbored additional potential vibrio pathogens, antibiotic resistance genes, and genes associated with virulence. Conclusions Taken together, this data shows that abundant pathogenic Vibrio species likely containing both antibiotic resistance and virulence-associated genes are associated with chitin producing organisms which could act as an attachment substrate, facilitating environmental persistence and horizontal gene transfer. Shared environmental conditions such as high temperatures were associated with both high levels of pathogenic vibrios and potential environmental reservoirs, which should be taken into consideration when modelling vibrio infection risk in the face of climate change and identifying biomarkers of pathogen species. Furthermore, ASV-level associations may be critical to understanding vibrio microbial ecology and should be taken into consideration while developing environmentally relevant laboratory model systems.

Pathogenesis of Gram-Negative Bacteremia

2021 ◽  
Vol 34 (2) ◽  
Author(s):  
Caitlyn L. Holmes ◽  
Mark T. Anderson ◽  
Harry L. T. Mobley ◽  
Michael A. Bachman
Keyword(s):  
Immune Responses ◽  
Global Economy ◽  
Human Infection ◽  
Model Systems ◽  
Small Subset ◽  
Gram Negative ◽  
Content Type ◽  
Capsule Production ◽  
Gram Negative Bacteremia ◽  
Species Specific

SUMMARY Gram-negative bacteremia is a devastating public health threat, with high mortality in vulnerable populations and significant costs to the global economy. Concerningly, rates of both Gram-negative bacteremia and antimicrobial resistance in the causative species are increasing. Gram-negative bacteremia develops in three phases. First, bacteria invade or colonize initial sites of infection. Second, bacteria overcome host barriers, such as immune responses, and disseminate from initial body sites to the bloodstream. Third, bacteria adapt to survive in the blood and blood-filtering organs. To develop new therapies, it is critical to define species-specific and multispecies fitness factors required for bacteremia in model systems that are relevant to human infection. A small subset of species is responsible for the majority of Gram-negative bacteremia cases, including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. The few bacteremia fitness factors identified in these prominent Gram-negative species demonstrate shared and unique pathogenic mechanisms at each phase of bacteremia progression. Capsule production, adhesins, and metabolic flexibility are common mediators, whereas only some species utilize toxins. This review provides an overview of Gram-negative bacteremia, compares animal models for bacteremia, and discusses prevalent Gram-negative bacteremia species.

scholarly journals Sequence Comparison of Vaginolysin from Different Gardnerella Species

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 86
Author(s):  
Erin M. Garcia ◽  
Myrna G. Serrano ◽  
Laahirie Edupuganti ◽  
David J. Edwards ◽  
Gregory A. Buck ◽  
...  
Keyword(s):  
Amino Acid ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Distinct Species ◽  
Vaginal Swab ◽  
Metagenomic Data ◽  
Gardnerella Vaginalis ◽  
Vaginal Epithelial Cells ◽  
Species Specific

Gardnerella vaginalis has recently been split into 13 distinct species. In this study, we tested the hypotheses that species-specific variations in the vaginolysin (VLY) amino acid sequence could influence the interaction between the toxin and vaginal epithelial cells and that VLY variation may be one factor that distinguishes less virulent or commensal strains from more virulent strains. This was assessed by bioinformatic analyses of publicly available Gardnerella spp. sequences and quantification of cytotoxicity and cytokine production from purified, recombinantly produced versions of VLY. After identifying conserved differences that could distinguish distinct VLY types, we analyzed metagenomic data from a cohort of female subjects from the Vaginal Human Microbiome Project to investigate whether these different VLY types exhibited any significant associations with symptoms or Gardnerella spp.-relative abundance in vaginal swab samples. While Type 1 VLY was most prevalent among the subjects and may be associated with increased reports of symptoms, subjects with Type 2 VLY dominant profiles exhibited increased relative Gardnerella spp. abundance. Our findings suggest that amino acid differences alter the interaction of VLY with vaginal keratinocytes, which may potentiate differences in bacterial vaginosis (BV) immunopathology in vivo.

scholarly journals Performance of Five Commercial Identification Platforms for Identification of Staphylococcus delphini

2019 ◽  
Vol 57 (11) ◽  
Author(s):  
Matthew C. Canver ◽  
Tsigereda Tekle ◽  
Samantha T. Compton ◽  
Katrina Callan ◽  
Eileen M. Burd ◽  
...  
Keyword(s):  
Distinct Species ◽  
Human Infection ◽  
Species Level ◽  
Accurate Identification ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Staphylococcus Intermedius ◽  
Animal Pathogens ◽  
Tof Ms

ABSTRACT The Staphylococcus intermedius group (SIG) is a collection of coagulase-positive staphylococci consisting of four distinct species, namely, Staphylococcus cornubiensis, Staphylococcus delphini, Staphylococcus intermedius, and Staphylococcus pseudintermedius. SIG members are animal pathogens and rare causes of human infection. Accurate identification of S. pseudintermedius has important implications for interpretation of antimicrobial susceptibility testing data and may be important for other members of the group. Therefore, we sought to evaluate the performance of five commercially available identification platforms with 21 S. delphini isolates obtained from a variety of animal and geographic sources. Here, we show that automated biochemical platforms were unable to identify S. delphini to the species level, a function of its omission from their databases, but could identify isolates to the SIG level with various degrees of success. However, all automated systems misidentified at least one isolate as Staphylococcus aureus. One matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system was able to identify S. delphini to the species level, suggesting that MALDI-TOF MS is the best option for distinguishing members of the SIG. With the exception of S. pseudintermedius, it is unclear if other SIG members should be routinely identified to the species level; however, as our understanding of their role in animal and human diseases increases, it may be necessary and important to do so.

scholarly journals Depression in Men and Women One Year Following Traumatic Brain Injury (TBI): A TBI Model Systems Study

2017 ◽  
Vol 8 ◽  
Author(s):  
Sarah Lavoie ◽  
Samantha Sechrist ◽  
Nhung Quach ◽  
Reza Ehsanian ◽  
Thao Duong ◽  
...  
Keyword(s):  
Traumatic Brain Injury ◽  
Brain Injury ◽  
Model Systems ◽  
Men And Women ◽  
One Year

Genetic diversity of three Aegla species (Decapoda, Anomura) revealed by AFLP and mtDNA markers

Crustaceana ◽  
2019 ◽  
Vol 92 (4) ◽  
pp. 445-462
Author(s):  
Bianca L. Zimmermann ◽  
Jober V. De Vargas Machado ◽  
Sandro Santos ◽  
Marlise L. Bartholomei-Santos
Keyword(s):  
Genetic Diversity ◽  
Distinct Species ◽  
Genetic Distances ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Similar Species ◽  
Southern Brazil ◽  
Low Levels ◽  
Management And Conservation ◽  
Mtdna Markers

Abstract Representatives of the genus Aegla present a conserved morphology; thus, the increased use of molecular markers has raised many taxonomic issues. We used AFLP and mtDNA to investigate the genetic differentiation and phylogenetic relationships of morphologically similar species with overlapping distribution areas in southern Brazil: A. georginae, A. ludwigi, and A. platensis. While A. platensis is widely distributed, the critically endangered A. georginae and A. ludwigi have limited distributions. Although both markers showed populations with low levels of genetic variability, they differed markedly in revealing relationships between populations; according to AFLP, the genetic distances between A. platensis populations were as high as those between distinct species, a result not observed when considering mtDNA data. We emphasize that the use of multiple lines of evidence is necessary for defining correct levels of genetic diversity and a good species-level taxonomic resolution. Such features are essential for the management and conservation of Aegla species.

Genetic, morphometric, and molecular analyses of interspecies differences in head shape and hybrid developmental defects in the wasp genus Nasonia

2019 ◽  
Author(s):  
Lorna B Cohen ◽  
Rachel Edwards ◽  
Dyese Moody ◽  
Deanna Arsala ◽  
Jack H Werren ◽  
...  
Keyword(s):  
Parasitoid Wasp ◽  
Gene Interaction ◽  
Distinct Species ◽  
Diploid Male ◽  
Gene Interactions ◽  
Morphological Development ◽  
Head Shape ◽  
Developmental Defects ◽  
Primary Driver ◽  
Species Specific

AbstractMales in the parasitoid wasp genus Nasonia (N. vitripennis, N. giraulti, N. longicornis) have distinct, species specific, head shapes. Fertile hybrids among the species are readily produced in the lab allowing genetic analysis of the evolved differences. In addition, the obligate haploidy of males makes these wasps a uniquely powerful model for analyzing the role of complex gene interactions in development and evolution. Previous analyses have shown that complex gene interactions underpin different aspects of the shape differences, and developmental incompatibilities that are specific to the head in F2 haploid hybrid males are also governed by networks of gene interaction. Here we use the genetic tools available in Nasonia to extend our understanding of the gene interactions that affect development and morphogenesis in male heads. Using artificial diploid male hybrids, we show that alleles affecting head shape are codominant, leading to uniform, averaged hybrid F1 diploid male heads, while the alleles mediating developmental defects are recessive, and are not visible in the diploid hybrids. We also determine that divergence in time, rather than in morphological disparity is the primary driver of hybrid developmental defects. In addition, we show that doublesex is necessary for the male head shape differences, but is not the only important factor. Finally we demonstrate that we can dissect complex interspecies gene interaction networks using introgression in this system. These advances represent significant progress in the complex web of gene interactions that govern morphological development, and chart the connections between genomic and phenotypic variation.

scholarly journals 31P-NMR Metabolomics Revealed Species-Specific Use of Phosphorous in Trees of a French Guiana Rainforest

Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 3960
Author(s):  
Albert Gargallo-Garriga ◽  
Jordi Sardans ◽  
Joan Llusià ◽  
Guille Peguero ◽  
Dolores Asensio ◽  
...  
Keyword(s):  
Tree Species ◽  
French Guiana ◽  
31P Nmr ◽  
Principal Component ◽  
Distinct Species ◽  
Community Diversity ◽  
N:P Ratios ◽  
High Concentrations ◽  
Species Specific ◽  
Total P

Productivity of tropical lowland moist forests is often limited by availability and functional allocation of phosphorus (P) that drives competition among tree species and becomes a key factor in determining forestall community diversity. We used non-target 31P-NMR metabolic profiling to study the foliar P-metabolism of trees of a French Guiana rainforest. The objective was to test the hypotheses that P-use is species-specific, and that species diversity relates to species P-use and concentrations of P-containing compounds, including inorganic phosphates, orthophosphate monoesters and diesters, phosphonates and organic polyphosphates. We found that tree species explained the 59% of variance in 31P-NMR metabolite profiling of leaves. A principal component analysis showed that tree species were separated along PC 1 and PC 2 of detected P-containing compounds, which represented a continuum going from high concentrations of metabolites related to non-active P and P-storage, low total P concentrations and high N:P ratios, to high concentrations of P-containing metabolites related to energy and anabolic metabolism, high total P concentrations and low N:P ratios. These results highlight the species-specific use of P and the existence of species-specific P-use niches that are driven by the distinct species-specific position in a continuum in the P-allocation from P-storage compounds to P-containing molecules related to energy and anabolic metabolism.

The Anopheles maculipennis complex (Diptera: Culicidae) in Iran: molecular characterization and recognition of a new species

2003 ◽  
Vol 93 (6) ◽  
pp. 527-535 ◽  
Author(s):  
M.M. Sedaghat ◽  
Y.-M. Linton ◽  
M.A. Oshaghi ◽  
H. Vatandoost ◽  
R.E. Harbach
Keyword(s):  
New Species ◽  
Distinct Species ◽  
Nuclear Rdna ◽  
Pcr Assay ◽  
Dna Evidence ◽  
Anopheles Maculipennis Complex ◽  
Anopheles Maculipennis ◽  
Species Specific ◽  
A New Species ◽  
Maculipennis Complex

AbstractMosquitoes of the Anopheles maculipennis complex were collected in nine provinces of Iran (Esfahan, Fars, Gilan, Golestan, Kohkiluyeh va Boyerahmad, Mazandaran, Tehran, Azarbaijan-e Gharbi and Zanjan) between June 1983 and September 2002. The nuclear rDNA ITS2 sequences of 86 specimens were compared with those of seven species of the complex available in GenBank. Three genetically distinct species of the complex were distinguished: A. maculipennis Meigen, A. sacharovi Favre and a previously unrecognized species. The last species is most similar to, but clearly distinct from, A. martinius Shingarev and A. sacharovi. The taxonomy of A. martinius and A. sacharovi is critically reviewed, and justification is provided for formally recognizing the third species as Anopheles persiensissp.n. The new species is the first culicid to be characterized and named principally on the basis of DNA evidence. Anopheles persiensis was collected only in the northern Caspian Sea littoral provinces of Gilan and Mazandaran, and it seems likely that this species could be responsible for malaria transmission in this region that was previously attributed to A. maculipennis. A species-specific RFLP–PCR assay based on ITS2 sequences was developed to facilitate further studies of the three species in Iran.

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