Using animal manure in the home or school garden while minimizing the risk of E. coli

With the recent Escherichia coli outbreak at Chipotle still occasionally in the news, a colleague suggested that it might be time for a post on how integrated pest management ties in to pathogen transmission like E. coli in a small garden.

Typically when many of us think of integrated pest management, we think about something coming into a planting area and affecting the physical qualities of a crop or plant, changing its appearance or taste. We don’t usually link IPM with a food-borne illness unless it’s caused by a household pest like mice or rats, or by pesticide exposure.

The truth is that the risk of contamination by pathogens like E. coli can be reduced by using some IPM tactics and timing planting appropriately.

Pathogens like E. coli can be absorbed through the roots of home-grown vegetables and herbs if you’re not careful, whether or not you fence your garden. An unfenced garden is subject to visits by deer, small wild animals like rabbits and squirrels, or loose neighborhood dogs looking for a good place to relieve themselves.

I want to emphasize that the comments and recommendations in this post are for people with smaller growing areas, such as home or school gardens. Farms have their own set of best management practices for avoiding E. coli contamination.


Deer often come to farms and gardens looking for food and relief.

While some people tend to think of animal dung as “good fertilizer,” unseasoned droppings can transmit pathogens to growing plants. In 2011, for instance, deer droppings in an Oregon strawberry farm caused one death and 12 E. coli-borne illnesses. News stories about the outbreak stated that officials tracked the contamination to the strawberry farm, where they found deer tracks and droppings.

Although accidental contamination like this always can happen, gardeners may not realize that some of their deliberate fertilization practices raise their risk of contamination. For instance, a fertilizer that is gaining in popularity in home and school gardens is rabbit pellets and rabbit manure tea. Using rabbit manure on its own is not dangerous; the danger is in the timing between applying the manure and planting the seeds or plants.

For families or teachers who raise rabbits, using the manure in the garden is an economical and sustainable way to fertilize plants organically. Hobby Farms, one of the websites that promotes rabbit manure as fertilizer, recommends composting the pellets first; you can also till them into the ground fresh and wait at least 60 days before planting. If you use rabbit manure tea, you must use the same guidelines to wait before planting.

“There have been experiments that show E. coli can be taken up by roots in a process called ‘internalization’ and it is the subject of much study,” says Nancy Kurul, Extension Master Gardener volunteer in Pender County, NC.

According to an article in Applied and Environmental Microbiology, experiments demonstrate that E. coli O157:H7 can enter the lettuce plant through the root system and migrate throughout the edible portion of the plant.

The National Organic Program recommends waiting 90 to 120 days after applying fresh manure to harvest crops. Those recommendations, however, do not consider the waiting period between manure application and planting. If you waited 60 days before planting, you would wait 30 to 60 days before harvesting.

A study done in 2010 revealed that waiting at least 60 days between laying manure and seeding or planting significantly reduced the transmission of bacteria to the mature plant. The study, conducted by scientists at the University of Georgia, sought to determine how pathogens like E. coli were absorbed into a plant and to test whether a waiting period would reduce the risk of infection.

wild rabbit

Wild rabbit

They infected the soil in several containers containing radish and lettuce seeds with E. coli bacteria and discovered that the plant collects E. coli through the roots. However, they found that numbers of bacteria in the phyllosphere (the part of the plant that grows above ground) were low at harvest of older plants even when the soil had high numbers of bacteria. Because younger plants are often harvested with mature plants, the researchers cautioned that bacterial transmission from the younger plant to the older plants may be possible. The 60-day waiting period reduced the possibility of transmission even from young plants.

For those gardeners who can’t wait 60 days before planting, place the rabbit manure in an area that will not touch any edible plants. The manure must compost for 60 days before adding it to a garden, so those who need to fertilize should use another type of organic fertilizer that IS composted when they plant. Note that composting is different from aging the manure. See the publication on guidelines for using animal manures included below.

Farmers who use IPM for their crops sometimes have to time their planting at certain dates to avoid a certain stage of a pest. Delaying planting after fertilizing the soil with either fresh mammal manure or manure tea isn’t very different.

To reduce the chance of visits by uninvited mammal guests, be sure to use some kind of physical deterrent like a fence and keep an eye on unfenced gardens to make sure that you don’t have any unplanned applications of “nature’s fertilizer.”

Article reference: Habteselassie, M.Y., Bischoff, M., Applegate, B., Reuhs, B. and Turco, R.F. (2010). Understanding the role of agricultural practices in the potential colonization and contamination by Escherichia coli in the rhizospheres of fresh produce. Journal of Food Protection. 73 (11): 2001-2009.

For more information:

Guidelines for Using Animal Manures and Manure-Based Composts in the Garden. University of New Hampshire Extension publication.

Using Manure in the Home Garden. Colorado State University Extension publication.


One Response

  1. Hello i came across your article i am interested in aquaponics but its the use of worms in aquaponics that concern me could they pass on ecoli ?I see alot of youtube of people just putting them straight into there aquaponic grow beds where did they get there worms how do they know what soil microbes they are carrying . Thank you

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