Chapter 1: Odor and the Science of Olfaction
Chapter 2: Exploration of the Sources of Odor
Chapter 3: The Interrelationship Between Microorganisms and Odor
Chapter 4: Effective Odor Detection Techniques
Chapter 5: Process of Deodorization
Chapter 6: Process of Oxidation
Chapter 7: Process of Enzymatic Action
Chapter 8: Process of Chemical Deodorization
Chapter 9: Process of Sealing
Chapter 10: Deodorization Equipment and Supplies
Chapter 11: Remediating Protein and Chemical Odors
Chapter 12: Death Scene Restoration

In this chapter, we explore in depth the sources of the most stubborn, pervasive, and repugnant odors. At the heart of the discussion of sources of odors is a focused examination of why these odors occur in the first instance. At the foundation of the source of a malodorous smell are two elements:

  • Molecular structure of the item generating or emitting an odor
  • A specific catalyst that releases an odor

In investigating and researching specific odor issues that homeowners’ face, certain structure, and catalysts appear with regularity. These structures and catalysts as sources of odors represent the chief focus of this chapter.

Nitrogen and Sources of Odors

Nitrogen represents the most common element involved in the molecular structure of item (or source) generating an odor. In many ways, the presence of nitrogen as an element in an odorous source is not surprising. Nitrogen is fundamental to life on Earth. Nitrogen is a component of all living systems on the planets, including all plants, animals, and microorganisms.

We are in contact with nitrogen in its gaseous state. Nitrogen boils at -320 degrees Fahrenheit. Thus, in any natural setting on the planet, nitrogen is encountered as a gas. The fact that it is gaseous renders it an ideal conduit for odorous vapors.

Nitrogen itself has no odor. Nitrogen has the capacity to take on additional atoms, in a multitude of combinations, that can result in the formation of a myriad of different types of malodorous compounds. These are compounds that contain molecules capable of becoming airborne and impacting the human olfactory system.

An example of a nitrogen-based compound is ammonia. Ammonia consists of one atom of nitrogen and three atoms of hydrogen. This is an inorganic compound.

As noted previously, nitrogen is a major element in organic compounds. One of these organic compounds is called methylamine. Scientifically speaking, methylamine consists of a methyl group, which is carbon and three hydrogen atoms, linked with an amine group, which is nitrogen and two hydrogen atoms. The carbon added to the chemical formulation is what makes the compound organic.

Amine groups added to chemical formulations is what makes the resulting compounds foul smelling. The amine group illustrated a moment ago is the simplest of them all. Research reveals that the more complex an amine group (meaning the more amine atoms in the group) the more severe the generated foul odor.

Examples of complex amine groups that result in the more significant of foul odors include:

  • Tri Methyl Amine – related to spoiled or decayed fish
  • Putrescine – related to cadavers
  • Cadaverine – related to cadavers

As previously discussed, nitrogen is an underlying element in a myriad of unpleasant odors. Malodorous smells associated with nitrogen needing to be addressed in a household setting typically are associated with what is known as nitrogenous waste, which is primarily pet urine. In addition, nitrogen-associated odors are also associated with a living organism that has died and is undergoing decomposition. In most situations in a residential setting, this is something along the lines of a mouse that has somehow died somewhere in a house. It can also be associated with a human death scene under certain circumstances discussed later in this chapter as well.

The odors associated with urine contamination continue to prove particularly problematic for remediation specialists. More often than not, the situation involves a cat or dog urine. Strategies for remediation or eliminating pet urine odor are discussed later in this book.

Urine is a mammal’s primary means of eliminating nitrogenous waste from the body. This is waste containing nitrogen.

Some basic points about urine need to be noted. Normal or “healthy” urine is a sterile, clear fluid with a bit of a yellowish tinge to it. The pH of urine depends upon both the species of the animal as well as its overall health condition. Carnivores including cats and dogs, have acidic urine. Herbivores have alkaline urine.

Urine is far more complex than most people realize. Urine contains:

  • Water
  • Urea
  • Uric acid
  • Creatinine
  • Sodium
  • Potassium
  • Calcium
  • Magnesium
  • Chloride
  • Phosphate
  • Sulfate
  • Ammonia


After water, which makes up 90 percent of urine, urea is the largest component. Urine is made up of about 2 percent urea.

Urea is a tacky, sticky substance. Urea contains about 80 percent of the nitrogen excreted from a body, including that of a cat or dog. The more protein an animal consumes, the more urea that will be found in urine.

In theory, cats should eat primarily protein. They are carnivores that should consume things like fish, chicken, and meats. They tend to eat more protein than do dogs. Some researchers contend this is a reason why cat urine is more malodorous and more difficult to remediate than is the case with that discharged from a dog.

Uric Acid

Uric acid is the third most significant compound contained in human urine. With that said, uric acid is almost nonexistent in cat and dog urine. This is important to understand because many retail cat and dog urine cleanup products sold today purport that they eliminate the smell or uric acid. In the end, that simply is not a smell that needs to be remediated when it comes to cat and dog urine.


One of the reasons cats and dogs lack uric acid is because much of it is converted into allantoin in an animal’s body. This is part of a process that aids in removing toxic compounds from a cat or dog’s body.

Amino Acids

Researchers believe that between 10 to 15 amino acids are present in a dog’s urine. The level of amino acids in cat urine is not yet clear. Amino acids tend to increase the intensity of odor in a urine contaminated area.


Ammonia is a major contributing factor when it comes to pet urine odor. Ammonia contains nitrogen although it initially is excreted in the form of salts that include chloride and sulfates. The salts break down following urination, which results in increased odor associated with urine.

Death Scene and Nitrogen

Up to 400 different types of gases can be released as a result of the human decomposition process. This includes gases that include the element of nitrogen. (As an aside, there are odors that are emitted associated with sulfur, which is discussed later in this chapter.)

The most common odor associated with a death scene and human (and other animals) decomposition are:

  • Cadaverine and putrescine (rotting fish odor)
  • Skatole (feces odor)
  • Indole (mothball-like odor)
  • Hydrogen sulfide (rotten egg odor)
  • Methanethiol (rotting cabbage odor)
  • Dimethyl disulfide and trisulfide (foul garlic odor)

Sulfur and Sources of Odors

Although nitrogen is at the foundation of a majority of foul odors, not all of them can be explained by this element. Rather, sulfur is the culprit as the element underlying some types of foul odors. Sulfur becomes malodorous when it is acted upon by a catalyst. In addition, it creates a stench when bonded with other atoms.

The examination of sulfur as a source of odors necessitates the categorization of sulfur-associated compounds into a number of different groups.


Mercaptans are also known as thiol groups or sulphydryl groups. The sulfur-associated compounds in these groups generate what are described as both repulsive and pervasive odors. Indeed, these odors are so intense that they can be detected down to a quantity of only seven million-millionth parts of an ounce. Despite being repulsive and furiously avoided, mercaptans have limited practical use. For example, very small levels of mercaptans are added to otherwise odorless natural gas to render its dangerous presence readily detectable.

Hydrogen Sulfide

Hydrogen sulfide is another of the sulfur groups. This compound produces the well-recognizable stench of rotten eggs. Hydrogen sulfide is also detectable at many fire scenes. It is perceptible even if only less than a one-millionth part per ounce.

Allyl Groups

Allyl groups are also sulfur-based. These groups do give off pungent odors, although they are not always considered repugnant. For example, the allyl groups give the following edibles their distinctive odors:

  • Onion
  • Garlic
  • Broccoli (cooked)
  • Cauliflower (cooked)


90 percent of sulfur found in urine is inorganic sulfate. Bacteria contained in urine reduces the sulfate to hydrogen sulfate. The remaining 10 percent of sulfur contained in urine is in the form of:

  • Cresol
  • Indole
  • Skatole

The different manifestations of sulfur in urine is a contributing factor to the pervasiveness and intensity of pet urine. The fact that sulfate is acted upon by a catalyst, coupled with the variants of organic sulfur-based compounds, results in urine having the potential to have varying degrees of a foul and even challenging to remediate odors.

Pet Fur

Pet fur has a notable high sulfur content. When it is shed, pet fur begins to be reduced by microorganisms. That biological process creates an unpleasant odor, sometimes referred to as “doggy smell” or “doggy odor.”

Pet fur odor is challenging to eliminate or remediate. In point of fact, it can permeate pervasively throughout a home, infesting porous material of all types, including furnishings. In fact, pet fur odor can prove to be as challenging to eliminate or neutralize as is pet urine.

Incomplete Combustion (Burnt Food)

When it comes to a homeowner, incomplete combustion is most often associated with cooking, baking, and burnt food. Proteins contained in items being cooked and ending up burnt contain nitrogen as well as sulfur-associated compounds. When it comes to foul odors stemming from incomplete combustion or burnt food, the element of sulfur is what is primarily responsible. The net effect of burnt food can be intense unpleasant odors.

When it comes to odors generated via incomplete combustion, the molecules not only disperse as vapor. They can also be absorbed into porous materials, which makes the remediation of these odors especially challenging.

These absorbed residues oftentimes are colorless, rendering visual detection highly difficult. In other words, a room might have a malingering foul smell, but the precise location of it can be challenging for a homeowner to identify.

As noted, and fortunately, a homeowner typically only encounters incomplete combustion when something goes awry when preparing a meal. The most extreme form of foul odors associated with incomplete combustion stems from a residential fire. One of the most challenging parts of the cleanup and restoration process is removing the “smoke odor” from all manner of porous materials at a fire-damaged residence.

Death Scene and Sulfur

In addition to death scene odors associated with nitrogen and organic compounds, sulfur also contributes to the powerfully repugnant associated with death, decay, and putrefaction. Indeed, discovering the remains of a person who dies an unattended death can prove to be one of the most devastating, traumatic experiences in a person’s lifetime. An unattended death is one in which a person not only dies alone but his or her remains are not promptly discovered. The horrific stench ultimately associated with the human decomposition process renders a death scene virtually incomprehensible.

In the immediate aftermath of a death, bacteria and other microbes begin to breakdown the organic material comprising the human body. This results in the release of an array of different types of gases as well as fluids, come which contain sulfur.

Armed with this primer on sources of odor, in the next chapter we explore the machinations of microorganisms in the creation and enhancement of odors. Specifically, a discussion is provided about how bacteria play a role in the creation and enhancement of odors. 


Emily Kil

Co-Owner of Eco Bear Biohazard Cleaning Company

Together with her husband, Emily Kil is co-owner of Eco Bear, a leading biohazard remediation company in Southern California. An experienced entrepreneur, Emily assisted in founding Eco Bear as a means of combining her business experience with her desire to provide assistance to people facing challenging circumstances. Emily regularly writes about her first-hand experiences providing services like biohazard cleanup, suicide cleanup, crime scene cleanup, unattended death cleanup, and other types of difficult remediations in homes and businesses.