At Biotium, our specialty is creating fluorescent dyes that simplify and improve your scientific experiments. For Microbiology, we offer a wide range of fluorescent dyes and assays kits to stain bacteria, yeast and fungi, including dyes to assess cell viability and bacterial gram stain type. We have also developed a complete toolkit of reagents for viability PCR, a revolutionary method for determining microbial viability using qPCR.
Also visit our Cellular Stains Table for a comprehensive list of cellular stains with their ability to stain various cell types.
BACTERIAL STAINS
For bacteria, we offer fluorescent dyes to stain live cells, dead cells, and gram+ cells. Combining these dyes in multi-color microscopy or flow cytometry experiments allows several parameters to be assessed at one time.
Bacterial Live Cell Stains
Often it can be useful to visualize or detect all bacteria present in a sample, regardless of species or metabolic state. For this purpose, we offer a selection of dyes that generally stain all bacteria, both gram-positive and gram-negative. The dyes are available in various colors and localizations:
- BactoView™ Live, RedDot™1, DMAO, Thiazole Orange, and Hoechst are cell membrane permeant nucleic acid binding dyes.
- SynaptoGreen™, SynaptoRed™, and CellBrite™ Fix are all cell membrane/cell periphery stains. CellBrite™ Fix dyes are a set of fixable membrane dyes available in multiple colors.
Live Cell Bacterial Stains |
Features |
|---|---|
| BactoView™ Live Fluorescent Bacterial Stains | • Nucleic acid binding dyes • Green and red options • Useful for fluorescence microscopy or flow cytometry |
| RedDot™1 Far-Red DNA Dye | • Nucleic acid binding dye • Far-red fluorescence • Useful for fluorescence microscopy |
| DMAO, 2 mM in DMSO | • Green nucleic acid binding dye • Useful for fluorescence microscopy or flow cytometry |
| Hoechst 33342, 10 mg/mL in H2O | • Blue nucleic acid binding dye • Useful for fluorescence microscopy or flow cytometry |
| Thiazole Orange | • Nucleic acid binding dye • Green fluorescence • Useful for fluorescence microscopy or flow cytometry |
| CellBrite™ Fix Membrane Stains | • Fixable membrane dyes • Green, red and far-red options • Useful for fluorescence microscopy |
| SynaptoGreen™ C4 | • Green fluorescent membrane dye • Useful for fluorescence microscopy |
| SynaptoRed™ C2 | • Red fluorescent membrane dye • Useful for fluorescence microscopy |
Fluorescent Gram Stains
A traditional colorimetric gram staining protocol is laborious, requiring up to 5 different solutions to stain cells, including toxic alcohol and acetone to decolorize the sample, and precise timing. In contrast, Wheat Germ Agglutinin (WGA) has been shown to bind specifically to N-acetylglucosamine in the peptidoglycan layer of the cell wall of gram-positive bacteria, and can be labeled with a number of different fluorescent dyes for one-step fluorescent cell labeling. We offer fluorescent WGA conjugates in 13 color options, as well as combination gram stain/viability kits and DNA dyes.
| Product Name | Features |
|---|---|
| Wheat Germ Agglutinin (WGA) CF® Dye conjugates | • Fast and sensitive gram stains • Available in 13 colors |
| Live Bacterial Gram Stain Kit | • CF®594 WGA stains gram-positive cells red • DAPI stains all cells blue |
| Bacterial Viability and Gram Stain Kit | • CF®488A WGA stains gram-positive cells green • EthD-III stains dead cells red • DAPI stains all cells blue |
Bacterial Viability Stains
Biotium offers a selection of different fluorescent viability dyes and kits, to allow for the differentiation of live and dead cells by microscopy or flow cytometry (see the Viability PCR section below for detection of viable bacteria by qPCR).
| Product Name | Features |
|---|---|
| Live-or-Dye™ Fixable Viability Staining Kits | • Fixable dead cell stains • Available in 8 fluorescent colors • Useful for flow cytometry or microscopy |
| Live-or-Dye NucFix™ Red Staining Kit | • Fixable, DNA-binding dead cell stain • Works in gram-negative bacteria only • Stains dead cells red |
| RedDot™2 Far-Red DNA Dye | • Nuclear-specific dead cell stain • Stains dead cells with far-red fluorescence |
| Ethidium Homodimer III (EthD-III) | • Nuclear-specific dead cell stain • Stains dead cells red |
| Viability/Cytotoxicity Assay Kit | • Green fluorescent DMAO stains DNA in all bacteria • Ethidium Homodimer III (EthD-III) stains dead cells red |
| Bacterial Viability and Gram Stain Kit | • CF®488A WGA stains gram-positive cells green • EthDIII stains dead cells red • DAPI stains alll cells blue |
| 5-Cyano-2,3-ditolyl tetrazolium chloride (CTC) | • Substrate for measuring bacterial respiratory activity • Healthy cells reduce CTC into an insoluble red fluorescent formazan product |
YEAST STAINS AND KITS
Fluorescent dyes and kits to stain yeast cells, including viability dyes, combination staining kits, and organelle stains. Combining these dyes in multi-color microscopy or flow cytometry experiments allows maximum experimental versatility.
Yeast Viability Stains
Biotium offers a selection of different fluorescent viability dyes and kits, to allow for the differentiation of live and dead yeast cells by microscopy or flow cytometry (see the Viability PCR section below for detection of viable yeast by qPCR).
| Product Name | Features |
|---|---|
| Live-or-Dye™ Fixable Viability Staining Kits | • Fixable dead cell stains • Choice of 8 fluorescent colors |
| Propidium Iodide | • Red dead cell stain • Not fixable |
| Ethidium Homodimer III (EthD-III) | • Far-red dead cell stain • Not fixable |
| RedDot™2 Far-Red Nuclear Stain | • Far-red, nuclear dead cell stain • Not fixable |
| NucSpot® 470 | • Green, nuclear dead cell stain • Not fixable |
| ViaVac™ Red/Green | • Yeast-specific vitality dye • stains the vacuole red in metabolically active cells |
| Yeast Live-or-Dye™ Fixable Live/Dead Staining Kit | • Thiazole Orange stains all cells green • Live-or-Dye™ 568/583 stains dead cells red • Fixable staining |
| Yeast Viability Staining Kit | • CF® Dye-labeled Concanavalin A (ConA) to label the cell walls of all cells • Live-or-Dye™ viability dye to label dead cells • Choose blue/green, green/red, or red/far-red color combinations |
| Yeast Vitality Staining Kit | • Calcofluor White labels all cell walls blue • ViaVac™ Red/Green stains the vacuole red in metabolically active cells |
Organelle Stains for Yeast
A number of our organelle and cellular stains can be used to stain yeast cells. We also offer stains for the fungal cell wall and bud scars of budding yeast.
| Product Name | Features |
|---|---|
| MitoView™ Dyes | • Mitochondrial dyes in five colors: • MitoView™ 633 is mitochondrial membrane potential-dependent |
| LysoView™ 540 & 633 | • Label vacuoles in live yeast cells • 2 LysoView dyes stain the yeast vacuole LysoView™ 540 & LysoView™ 633 |
| LipidSpot™ 488 | • Label vacuoles in live yeast cells • Stains intracellular membrane structures |
| Calcofluor White | • Blue fluorescent chitin stain stains cell walls • Strongly stains bud scars |
| CellBrite™ Fix | • Stains the cell membrane • Available in 3 dye colors • Staining is fixable |
| MemBrite™ Fix | • Stains the cell periphery • Available in 8 dye colors • Staining is fixable |
| CF® Dye Concanavalin A (Con A) Conjugates | • Con A lectin binds to a-mannopyranosyl and a-glucopyranosy in the cell wall of yeast and fungi • Available in 10 colors |
| CF® Dye Wheat Germ Agglutinin (WGA) Conjugates | • WGA lectin binds sialic acid and N-acetylglucosamine • Strongly labels bud scars • Available in 13 colors |
| Thiazole Orange | • Green nucleic acid binding dye • Can be used as an all-cell yeast stain • Staining in yeast is both nuclear and cytoplasmic in unfixed cells and cytoplasmic after fixation |
| NucSpot® 470 Nuclear Stain | • Green nucleic acid binding dye • Stains the nucleus of dead or fixed and permeabilized yeast |
| ViaFluor® CFSE | • Can be used as an all-cell cytoplasmic stain in yeast |
| Phalloidin conjugates | • Phalloidin stains F-actin cables and patches in fixed and permeabilized yeast • Available in 20 colors and biotin |
VIABILITY PCR WITH PMA & PMAXX™
Biotium is the inventor of the original viability PCR dye, PMA, and the new and improved viability PCR dye PMAxx™. We have also developed a large range of products and kits for viability PCR. To learn more about this technology and all of the associated products, please visit the Viability PCR Technology Page.
Introduction to viability PCR (v-PCR)
Viability PCR is a powerful technology for the sensitive and rapid detection of viable microorganisms. Unlike time-consuming culturing methods, qPCR is a fast and sensitive method of detection. However, normal qPCR does not distinguish between live and dead cells. With v-PCR using PMAxx™ or PMA, you get the speed, sensitivity and specificity of PCR, plus quantifiable viability. And because no culturing is required, you can even detect viable but not culturable (VBNC) bacteria.The v-PCR technology can be applied not only to bacteria but to other organisms like yeast, viruses, eukaryotes, and archaea.
How does v-PCR work?
The infographic below shows the basic mechanism of v-PCR. PMAxx™ and PMA are photoreactive dyes with high affinity for DNA. The dyes intercalate into dsDNA and form a covalent linkage upon exposure to intense visible light. The reaction inhibits PCR amplification of modified DNA templates by a combination of removal of modified DNA during purification and inhibition of template amplification by DNA polymerases. Because the dyes are cell membrane-impermeable, when a sample containing both live and dead bacteria is treated with dye, only dead bacteria with compromised cell membranes are susceptible to DNA modification. In a qPCR reaction, dead cell DNA will show delayed amplification and higher Ct than live cells.
PMA & PMAxx™ Dyes for Viability PCR
PMA is the original dye developed at Biotium for v-PCR. It has been validated in a wide variety of bacterial strains, as well as yeast and viruses (see PMA References). However, while PMA is generally effective at differentiating between live and dead bacteria by qPCR, it does not completely eliminate PCR products from dead cell DNA. This could potentially give false positive results.
PMAxx™ was designed by Biotium scientists to be a superior alternative to PMA. PMAxx™ is much more effective at eliminating PCR amplification of dead cell DNA, and therefore provides the best discrimination between live and dead bacteria.
Download the PMA™ and PMAxx™ flyer to learn more.
| Product Name | Catalog No. | Features |
|---|---|---|
| PMAxx™, 20 mM in H2O | 40069 | • Next-generation v-PCR dye • Gives the best live/dead discrimination |
| PMA Dye | 40013 | • Original v-PCR dye developed at Biotium • Validated in hundreds of publications and a wide variety of organisms |
| PMA Dye, 20 mM in H2O | 40019 |
Other Viability PCR Reagents
Viability PCR Starter Kits
The customizable Viability PCR Starter Kits contain the materials that you need for selective detection of viable cells using either PMA or PMAxx™ viability dye and qPCR. You also have the choice of selecting a kit with or without the Enhancer for Gram Negative Bacteria (not to be used with other cell types). The user will need to supply their own primers to amplify their species of interest .
| Product Name | Catalog No. | Viability Dye | Target Cell Type |
|---|---|---|---|
| Viability PCR Starter Kit with PMA | 31075 | PMA | Any cells |
| Viability PCR Starter Kit with PMAxx™ | 31075-X | PMAxx™ | Any cells |
| Viability PCR Starter Kit with PMA and Enhancer | 31076 | PMA | Gram-negative bacteria |
| Viability PCR Starter Kit with PMAxx™ and Enhancer | 31076-X | PMAxx™ | Gram-negative bacteria |
Strain-Specific Viability PCR Kits
Strain-specific v-PCR kits are designed for selective detection of viable bacteria from a specific strain using PMAxx or PMA dye and real-time PCR. The kits contain PMA dye OR PMAxx™ dye, Forget-Me-Not™ EvaGreen® qPCR Master Mix, and validated PCR primers for detection of selected strains of bacteria.
Strain-Specific Bacterial Viability PCR Kits
| Bacteria Strain | Gene name | Kit with PMA (catalog #) | Kit with PMAxx™ (catalog #) |
|---|---|---|---|
| Salmonella enterica | invA | 31033 | 31033-X |
| Mycobacterium tuberculosis | groEL2 | 31034 | N/A |
| Staphylococcus aureus | nuc | 31035 | N/A |
| MRSA | mecA | 31036 | N/A |
| E. coli O157:H7 | Z3276 | 31037 | 31037-X |
| E. coli | uidA | 31050 | 31050-X |
| Listeria monocytogenes | hly | 31051 | 31051-X |
| Legionella pneumophila | mip | 31053 | N/A |
PMA Enhancer for Gram-Negative Bacteria
PMA Enhancer for Gram Negative Bacteria was designed to improve discrimination between live and dead gram-negative bacteria during viability PCR. PMA Enhancer is provided as a 5X solution, and is added to a sample before the addition of viability dye.
| Product Name | Catalog No. | Features |
|---|---|---|
| PMA Enhancer for Gram Negative Bacteria, 5X Solution | 31038 | • Improves live/dead discrimination in gram-negative strains |
Photoactivation Device
The PMA-Lite™ 2.0 LED Photolysis Device allows for time- and temperature-controlled light treatment of PMAxx- or PMA-treated samples in microcentrifuge tubes.
| Product Name | Catalog No. | Features |
|---|---|---|
| PMA-Lite™ 2.0 LED Photolysis Device | E90006 | • Photoactivation device, holds 18 microcentrifuge tubes |
Associated products
Bacterial Viability and Gram Stain Kit
Concanavalin A (Con A) CF® Dye Conjugates
29015, 29016, 29017, 29018, 29019, 29020, 29058, 29074, 29075, - 29080View allHide
PMAxx™ Dye, 20 mM in H2O
Viability/Cytotoxicity Assay Kit for Bacteria Live & Dead Cells
Yeast Live-or-Dye™ Fixable Live/Dead Staining Kit
Yeast Vitality Staining Kit
Wheat Germ Agglutinin (WGA) Conjugates
29021, 29022, 29023, 29024, 29025, 29026, 29027, 29028, 29029, 29059, 29064, 29073, 29021-1, 29022-1, 29023-1, 29024-1, 29025-1, 29026-1, 29027-1, 29028-1, 29029-1, 29059-1, 29064-1, 29077-1, 29077, 29076-1, - 29076View allHide
Live Bacterial Gram Stain Kit
32000, - 32000-1View allHide