Compost Magazine

Composting tips, advice and science.

Cartoon image of microorganisms killing pathogens.

The Pathogen-Destroying Power of Composting

Composting is a magical process that has been used for thousands of years to improve the soil.

Still, there was a time when people worried about what was in compost – in fact, at one point gardeners often sterilised compost before using it. 

However, in recent years, composting has also been recognized for its ability to kill and suppress various pathogens – especially if you have a well constructed compost heap. As we’ll see, even finished compost may help suppress pathogens too.

In this guide, you’ll find out about the pathogen-killing power of compost and how it works. You’ll also find how to maximise the disease suppressing power of your own compost heap. 

Let’s get started…


What are pathogens?

3d render illustration of a pathogen.
Above: 3d render of a viral pathogen.

Pathogens are organisms which can cause a wide range of illnesses in both you and your plants. They can include bacteria, viruses, fungi, and parasites. 

People can get anything from the common cold to influenza, while plants can get a host of different diseases varying from downy mildew to black rot. 

Where do pathogens in compost come from?

Unfortunately, the germs in your compost can come from a wide variety of sources. Some of these are under your control, and others are not! 

One review attempted to classify common sources of contamination – and while it focussed on soil in fields, the sources are likely to be the same for compost. They included:

  • Airborne sources
  • Contaminated soils
  • Use of raw manure 
  • Exposure to contaminated water or groundwater
  • Transfer by insects
  • Contamination from wild animals

What pathogens can you find in compost? 

You’ll probably recognise bacterial pathogens such as Salmonella, E. coli, and Staphylococcus – you might not be as familiar with fungi such as Aspergillus, Fusarium, and Penicillium. 

Viral pathogens such as Norovirus and Poliovirus can also be found in compost, as well as parasitic pathogens such as Cryptosporidium and Giardia.

Fortunately, the process of composting helps significantly reduce the amount of pathogens. Let’s take a look at this in more detail. 

How Composting Kills Pathogens

Infographic showing the different ways in which microorganisms in compost kill pathogens.


As we saw in the science of composting, if you have a large, well constructed compost heap, it will soon start to warm up. 

As the temperature increases, the metabolic rate of microorganisms increases and the activity of thermophilic bacteria rises. In addition to speeding up the breakdown of compost material, it also generates the heat that kills pathogens.

Just how hot – and how many pathogens are killed – is a matter of some debate. However, the US Department of Agriculture advises maintaining a minimum heat of 55 degrees for at least three days. 

Higher temperatures may speed up the process. A 2007 study by Ceustermans et al found that when compost reaches 60 degrees, and moisture levels are maintained, Salmonella pathogens were killed within 10 hours. However, this study only looked at one type of pathogen.

It’s also worth bearing in mind that you don’t want your compost to get too hot. Too much heat can destroy the diversity of beneficial bacteria, including bacteria that can combat pathogens. This lead one researcher to note that:

Research has indicated that temperature is not the only mechanism involved in pathogen suppression, and that the employment of higher than necessary temperatures may actually constitute a barrier to effective sanitization under certain circumstances.

(Shuval et al, quoted in the Humanure Handbook.)

When I discussed this with Sophie from the Charles Dowding team, she agreed, telling me:

Municipal waste is turned many times to speed up the process but it raises the temperature too high which in turn kills beneficial microbes. The compost becomes effectively inert with perhaps only one or two types of Bacteria remaining. It is best to keep the temperature below 66 to ensure a balanced compost.

Let’s take a look at some of the other ways pathogens are removed from compost. 

Competition for resources

Beneficial organisms compete with pathogens for resources – a battle which can take place over carbon, nutrients or space. 

Fortunately, the beneficial organisms are often better at this competition and the pathogens we want to get rid of.  For example, in more mature compost, thay have a better ability to digest the remains of rotting plants and wood (a characteristic known as saprophytic).

Microorganisms attack pathogens

Some studies have found that microorganisms that are found in compost attack and consume pathogens.

Yitzhak and Papadopoulou explain that some microorganisms can recognise a pathogen. They release enzymes that weaken the cell wall of the pathogen before penetrating and killing it. 

Antimicrobial and antibacterial properties

Compost also contains certain compounds that are known to have antimicrobial properties. For example, compost contains lignin, which has antifungal properties, as well as phenols, which has antibacterial properties. 

In addition, compost also contains humic and fulvic acids, which are known to have antiviral properties. These acids can bind to and inactivate viruses, preventing them from infecting cells and spreading disease. 

Soil scientist Professor Deborah Neher also told me:

Many bacteria and fungi in soil naturally produce anti-microbial compounds naturally. They represent a microbe’s natural defense against other species.

These include antibiotics which can attack pathogens. Indeed, as Neher pointed out, many of the antibiotics we use now, such as penicillin and ampicillin, were first discovered in soil. 

It’s likely that more compounds in compost may have applications for human medicine in the future. One 2022 study by Verillo et al concluded that humic substances from compost:

..may be indeed exploited as substrates to produce novel materials not only to improve plant productivity but also for medical applications.

Could worms help too?

Worms in maturing compost.
Worms help eliminate pathogens – and improve the quality of the compost too.

As compost cools down and enters the maturing compost stage, worms will find and enter the heap. A number of studies have suggested that these worms can reduce pathogens. Indeed, a 2011 research article described worms’ bodies as ‘biofilters’ which can purify, disinfect and detoxify solid waste. 

Another 2012 study by Hill and Baldwin looked at composting toilets. The study found that vermicomposting toilets (which use worms to compost human waste) outperformed compost toilets that didn’t use worms. 

Also see: Why you need worms in your compost 

Does composting kill all pathogens?

There’s still more research needed on just how effective compost is at killing pathogens. However, a 2004 review by Noble and Roberts found that composting at high temperature for a reasonable amount of time kills most of most types of pathogens. 

If you’re still worried about pathogens, it’s worth bearing in mind that they exist everywhere (including in your nose!) And even if you killed all the pathogens in a compost heap, more will transfer from wind, your hands, wildlife or other sources. 

I think it’s important not to worry too much about this. It’s a bit like washing your hands. You’re not going to kill every germ on your hands, but you do it because you kill most of them. If you are still worried, or are not in the best of health, it may be worth wearing gloves when you handle compost.

Finally, it’s worth remembering that compost doesn’t just contain pathogens – it also contains beneficial organisms which are good for both your garden and for you. 

Still, one pathogen you do need to be aware of is Aspergillus fumigatus. This is an airborne pathogen which thrives at high temperatures, although populations drop rapidly after that. 

This can cause respiratory problems. It tends to attack those with an illness such as asthma or a compromised immune system. If that applies to you, it’s worth taking extra care.

A second area of concern is rats and mice. Both can carry leptospirosis or Weil’s disease. Hot composting can kill this disease, but rats and mice may infect your compost bin after the compost has cooled down. 

(Here’s 11 ways to stop mice in compost bins!)

I always let my compost cool down before turning it, which should reduce the chances of Aspergillus fumigatus. If my compost is dry, I also give each layer a soak before turning. 

If you’re concerned or have poor health, do consider wearing a mask and gloves while turning your compost.

Can finished compost kill pathogens in soil? 

Finished compost held in hand.
The application of compost itself helps control many plant diseases.

So far we have focussed on the composting process. But what about compost itself?

Simply applying compost can suppress and kill some pathogens. For example, a 2003 study by Cheuk et al found that compost was effective at killing the pathogens that cause root rot in tomato and pepper plants.

However, it’s important to note that compost is not a magic cure-all. A 2006 study by A.J.Termorshuizen et al which attempted to quantify this found that compost only significantly suppressed disease in 54% of cases. 

Professor Neher, who I quoted earlier in the post, has found that the effectiveness of compost in preventing a particular disease varies can depend on the ingredients and process used.

For example, in one study she looked at the impact of applying compost to fields with brassicas. All the brassica fields with compost had reduced disease, but the compost containing hardwood carbon had the least disease. 

She pointed out that commercial pressures and government guidelines means many compost makers focus on the thermophilic stage of compost (i.e. the stage at which compost is hot.) By leaving compost to mature (which you should anyway), you may obtain a compost which is better able to suppress pathogens. 

When I asked Neher about this, she explained:

As a general rule of thumb (not universal however), mature compounds containing some wood in the recipe tend to be more suppressive than immature composts without wood as an ingredient…

Wood contains more of the cellulose and lignin which tips the balance in favor of biological control (beneficial) organisms. Soilborne plant pathogens tend to like high nutrient (easy to degrade) food supplies and are poorer competitors on substrates relatively high in cellulose and lignin.

(For those interested in learning more, Neher recommended chapter 17 of the Compost Handbook.)

How to ensure your compost heap kills pathogens 

HotBin Thermometer.
Heat helps – but you wouldn’t want it any hotter than this!

To maximise the potential of your compost to kill pathogens, it’s important to have a well constructed pile. That means considering factors such as: 

  • Size a larger pile enables the compost to get hotter. An alternative is to use an insulated hot composting bin.
  • Composition: A combination of high carbon (browns) and high nitrogen materials greens) also helps keep the compost hot for longer. Ideally, you don’t want the nitrogen too high, as research in 1997 by Hoitink et al. found that high nitrogen heaps can encourage certain pathogens.
  • Moisture levels: Dry compost heaps are the perfect environment for certain pathogens such as Pyhtium. Moisture is also needed to feed the beneficial microbes that populate the compost heap in the maturing phase and deter pathogens. Hoitink, Stone and Han suggest a minimum level of 40-50% moisture levels.
  • Oxygen levels: Oxygen levels are also essential for beneficial microbes. This can be achieved in a number of ways such as turning the compost or using bulking material in your compost heap. 

You can find advice on constructing a good compost pile in our guide to home composting and in our 16 tips for speeding compost up.

At the same time, it’s important not to let a desire for perfection stop you from composting! While a large, hot heap will kill more pathogens, researchers have emphasised that there is significant pathogen reduction even in cool heaps. 

Should you sterilise your compost?

As mentioned previously, it used to be common to sterilise compost – but that harks back to the time when gardeners thought soil health was all about nutrients, and had little awareness of soil biology. 

So in most cases it is not necessary to sterilise soil, as the process kills beneficial microorganisms and reduces the ability of compost to suppress disease. The exceptions, Sophie emphasised, come about when the compost is used for a specific purpose or contains specific materials:

For growing mushrooms it is important to sterilise before using to stop any competition from other fungal spores. For other uses normal green waste should not be sterilised. 

When using Home Acres Compost for mulching beds and growing plants we are looking for a balanced ratio of bacteria to fungi present that will inoculate the soil as well as providing organic matter to feed microbes already present in the soil.

Wrapping up

I’m always amazed by the magic of composting. It can turn waste into black gold, remove heavy metals from soil – and may even help with mental health. 

Removing pathogens and bringing us the potential to treat human diseases is just one more to add to the list!