Microbes with Good and Bad Smell

Microorganisms can produce different types of volatile compounds that may give characteristics smell, pleasant scent, or pungent odor. The production of these volatile chemicals depends on that particular organism’s metabolic factors.

Characteristics smell of microorganisms

When anaerobic bacteria like Clostridium decompose organic matters (mainly proteins), various foul-smelling, incompletely oxidized odoriferous compounds like H2S, methyl mercaptan, cadaverine, putrescine, and ammonia. Cadaverine and putrescine smell like rotting flesh, whereas methyl mercaptan smells like rotten cabbage.

Sometimes odor produced by these microorganisms may give essential clues in the identification of microorganisms. For example, foul-smelling diarrhea and the absence of blood or mucus in the stool distinguish giardiasis from bacterial or viral diarrhea.

You may have seen a technician trying to “smell the difference” between bacterial cultures. Though some laboratory personnel regard sniffing as a helpful 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).

Characteristics odor produced by selected microbes 

Microorganisms do not have odor on their own, but they may produce various metabolites that have distinguished smells of their own. For example, spoiled seafood’s odor is primarily due to trimethylamine oxide (TMAO) produced by the action of bacteria. The earthy odor of soil is caused by the production of a series of complex metabolites called geosmin by Streptomycetes. Many cyanobacteria are also responsible for the production of earthy odors and flavors in some freshwater.

Some of the characteristics smell produced by microorganisms is tabulated here;

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 Bacteroides 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.’

Anaerobic bacteria produce fatty acids and other odoriferous compounds while decomposing organic matters (putrefaction).  Major such compounds are hydrogen sulfide (H2S), methyl mercaptan (from sulfur amino acids), cadaverine (from lysine), putrescine (from ornithine), and ammonia. H2s smell like rotten eggs at low concentration levels in the air. Cadaverine and putrescine smell like rotting flesh, methyl mercaptan smells like rotten cabbage, and ammonia has a strong odor that smells like urine or sweat.

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

Under anaerobic conditions, Clostridium perfringens multiplies and produces alpha-toxin and other toxins, resulting in the rapid destruction of tissue carbohydrates 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.

It smells like soil

Certain cyanobacteria and actinomycetes synthesize geosmin, a volatile chemical reminiscent of potting soil.

Rotten Fish like Smell

Proteus mirabilis produces a very distinct fishy odor. 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 a grey, offensive, fishy ammoniacal smell. The fishy ammoniacal smell becomes more intense after adding a few drops of 10% potassium hydroxide. Burkholderia pseudomallei cultures also give off an ammoniacal odor.

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 the presumptive identification of the “Streptococcus milleri” group (4).

Frequently Asked Questions

  1. What kind of bacteria is present in a pond with black water that smells like rotten eggs?

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

Acharya Tankeshwar

Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. As an asst. professor, I am teaching microbiology and immunology to medical and nursing students at PAHS, Nepal. I have been working as a microbiologist at Patan hospital for more than 10 years.

5 thoughts on “Microbes with Good and Bad Smell

  1. Dear Dr Tankeshwar,

    Can I contact you via your email about some interesting projects we can collaborate on? I am on gunturu.revathi@aku.edu. I am a microbiologist working in Kenya, East Africa.

  2. 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/

  3. 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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