Microbes with Good and Bad Smell

Last updated on June 21st, 2021


Microorganisms can produce different types of volatile compounds that may give characteristics smell, pleasant scent, or pungent odor. Production of these volatile chemicals depends on the metabolic characteristics of that particular organism. Sometimes scent or odor produced by bacteria can give important clues in the identification of microorganisms, but it is not a reliable rule.

You may have seen a microbiologist/technician trying to “smell the difference” between bacterial cultures. Though, some laboratory personnel regard sniffing as a useful tool others regard it as a biohazard (1).

I suggest you be cautious while sniffing culture plates. Sniffing culture plates is not a good idea and you may contract a disease (2).

Table: Characteristics odor of selected microbes 

Alkaligenes faecalis Freshly cut apples
Candida spp.Yeast
Citrobacter spp.Dirty sneakers
Clostridium difficile Putrid, fecal
Corynebacterium spp.Fruity
Eikenella corrodensBleach or cracker
Haemophilus spp.Wet fur
Nocardia spp.Musty basement
Pasteurella multocidaPungent (indole)
Peptostreptococcus anaerobiusFecal
Pigmented Bacterioides groupAcrid
Proteus spp.Burnt chocolate
Pseudomonas aeruginosaFruity, grape-like
Staphylococcus spp.Dirty sneakers
Certain viridans group Streptococcus spp.Butter/butterscotch
Streptomyces spp.Musty basement

Pungent/Unpleasant smell
Anaerobes are particularly pungent due to their reliance on sulfhydryl compounds to maintain redox balance. When an anaerobic infection is suspected, the specimen is often foul-smelling. Gram-negative anaerobes are often responsible for ‘morning breath’.

Bacterioides fragilis: Pus containing Bacteroides species has a very unpleasant smell.

Under anaerobic conditions, Clostridium perfringens multiplies and produces alpha-toxin and other toxins which result in the rapid destruction of tissue carbohydrate with the production of gas in decaying tissues, particularly muscle. The affected tissue is foul-smelling.

Yeast like smell: The colonies of Candida albicans have a distinctive yeast smell.

Smell like a soil
Certain cyanobacteria and actinomycetes synthesize geosmin, a volatile chemical that is reminiscent of potting soil.

Rotten cooked fishy odor: Proteus mirabilis produces a very distinct fishy odour. On Salmonella-Shigella (SS) agar, Proteus usually smells like “rotten cooked fish”.

Sweet grape-like scent
Pseudomonas aeruginosa produces a sweet grape-like scent, so wound dressings and agar plates are often sniffed for organism identification. Pseudomonas aeruginosa can famously generate a “grape juice” smell in infected burn patients (3). Cultures of Pseudomonas have a distinctive smell due to the production of 2-aminoacetophenone.

Ammoniacal smell

Woman infected with Gardnerella complaints of grey, offensive, fishy ammoniacal smell. Fishy ammoniacal smell becomes more intense after adding a few drops of 10% potassium hydroxide.

Burkholderia pseudomallei cultures give off an ammoniacal smell.

Bleach-like odor: Eikenella corrodens, a gram-negative rod, responsible for wound infections gives a bleach-like odor when grown in Blood Agar or Chocolate Agar.

Caramel odor: Streptococcus milleri produces diacetyl (caramel odor). The detection of diacetyl (caramel odor) can be used in presumptive identification of the “Streptococcus milleri” group (4).

Further Reading and references

  1. Sniffing Bacterial Cultures on Agar Plates: a Useful Tool or a Safety Hazard?
  2. Brucellosis from sniffing bacteriological cultures
  3. A Microbe By Any Other Name Would Smell As Sweet
  4. Detection of diacetyl (caramel odor) in presumptive identification of the “Streptococcus milleri” group

About Acharya Tankeshwar 476 Articles
Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. I am working as an Asst. Professor and Microbiologist at Department of Microbiology and Immunology, Patan Academy of Health Sciences, Nepal. If you want me to write about any posts that you found confusing/difficult, please mention in the comments below.


  1. You should add Clostridium difficile to your list. Most people working in hospitals and nursing homes are unfortunately familiar with this highly unpleasant odor emitted. To illustrate the potential of using smell as a diagnostic tool, a trained beagle detected C diff stool samples and patients themselves with surprising accuracy. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675697/

  2. Hello Dr Acharya,
    Do you know if bacteria on the surface of fish coats can also give out odor? I have caught a Mulloway fish species (Jewfish) with a very pleasant distinct smell. I believe this may be from the slime coat which can collect bacteria overtime before they shed? No other fish species smells this way. Any information would be most appreciated. Thank you so much for your time.

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