Chasing Coliform Counts

I was recently visiting England to attend “The Science of Artisan Cheesemaking” conference and had the great additional luck to visit an amazing farmstead creamery- Hill Dairy in Somerset. Not only was the facility quite possibly one of the most well thought out and constructed small creameries that I have ever visited, but owners Will and Caroline Atkinson, were as charming and lovely as their picturesque English farm. Since I got back to the US, we have been corresponding about a problem that Hill Dairy was experiencing both during my visit and on and off for a good part of this fall. A problem, unfortunately, that caused the loss of many batches of cheese milk and is a problem that plagues many farmstead cheesemakers (sometimes even without their knowing). High coliform counts.

3M coliform petri film with count at about 400cfu/ml (black dots from Sharpie marker on a few) look for a red dot surrounded by or up against an tiny air bubble. each dot with air bubble is one cfu.

First a bit about the large bacterial family called coliforms. These microbes live in the environment of the farm, especially bedding, feed, and soil. But some of them also live in the lower intestine (not only of cows and goats, but of people too) the most well-known being Escherichia coli, better known by its abbreviated name “E. coli”. The presence of E. coli in milk or cheese can be translated as the presence of feces, that’s right, poo. While E. coli and poo in milk are not desirable in any circles, it doesn’t necessarily mean that the milk is unsafe. It is the ne’re-do-well coliform cousin E. coli 0157:H7 that can wreak horrible damage when ingested. (There is another variant that surfaced recently in Germany that is just as nasty and there will no doubt be more variations in the future that will cause horrific food borne illnesses, sickness, and death). So while coliforms do not necessarily mean the presence of pathogens (illness causing microbes) their numbers are a good gauge of milk cleanliness. The higher the general coliform count, the higher your odds that some might be bad.

Currently most data say that high quality raw milk should have fewer than 10 cfu’s (that’s colony forming units) per milliliter of milk.  Some states allow for higher counts and the “fewer than 10”number is somewhat arbitrary, but let’s pretend for now that it’s a great standard. Here at our farm our petri-film plate counts (done on every cheese batch – see my previous posts if you want to know how to do these) show our total coliforms at usually 3-5 cfu’s per ml. Awesome, right? Well, when I got back from England our counts shot up to over 400cfu/ml.  Fortunately for both us and Hill Dairy, tests showed that none of the coliforms were from fecal sources, no E. coliforms. (You can buy petri film plates that will grow E. coli’s in a different color than regular coliforms). Interestingly, but not surprisingly, our APC (which counts total bacteria numbers) didn’t look that bad – until you looked closely and could see that there were tiny air bubbles all over the plate (from the gas produced by the coliforms) and these bubbles had lifted the film from the plate – making it look as though there were not that many colonies growing.

Aerobic plate count showing red dots of bacteria colonies (cfu’s) and lots and lots of tiny air bubbles from coliforms making the plate “uncountable”.

So what do high numbers of “harmless” coliforms do to milk and cheese? Well, these guys eat lactose – that’s milk sugar, (as do starter cultures) and produce both lactic acid and carbon dioxide – that’s gas. The problem with them is that they grow very fast and can often out-compete the added starter culture during a slow fermentation, just like what is done to make most fresh cheeses and lactic set bloomy rinds (like the Atkinson’s were making – and yes it is legal to make them with raw milk in the UK). At Pholia Farm, we make long-aged, low moisture cheese that use a faster acid development and rennet, so we would not have known about our high coliform counts if we were not doing routine lab tests on every batch. While these coliform types are unlikely to make our cheese unsafe, it tells us that something is far from ideal with our process – something that could lead to unsafe food. We don’t only make cheese, we drink our raw milk – we care that it is of the best quality possible for many reasons.

Okay, so both our farm and Hill Dairy had much higher than normal counts, what did it mean and what did we do about it to resolve the problem? The most common causes of high coliforms are dirty teats, poor milking technique, and dirty equipment. While this may seem like an easy fix, when your counts suddenly go from great to horrendous, it can be very confusing.  So let’s go over a step by step procedure for trouble shooting coliform counts – with as little financial investment as possible!

  1. Observe that animals are coming into the parlor relatively free of manure and debris – dairy clipping udders can help.
  2. Verify that established teat and udder cleaning methods are being performed properly and that udder cleaning solutions and sanitizers are effective.
  3. Verify that milking equipment with parts that need replacing, especially rubber parts, are up to date for recommended replacement times.
  4. Verify that cleaning steps for equipment are effective – this includes chemical strength and effectiveness for your water type, temperatures, time, air slug velocity, etc. Swabs can be taken at various points in system and cultured for total bacteria counts to verify effectiveness.
  5. Perform “hyper-cleaning” following guidelines from chemical manufacturer or other dairy representative. This often includes a double strength, double time cleaning and manual cleaning to verify the removal of bio-films and residue that might have occurred from less than ideal parlor practices.
  6. Verify milk chilling process, if used (even with proper chilling, high enough coliform counts will be a problem in lactic technology cheeses)

Don’t be surprised if trouble shooting takes place over many days before you completely conquer the problem. All it takes is one step to be missed, and the problem reasserts itself. For example, our problem seems to have come from our neglect (later in the season) of dairy clipping our ladies udders, combined with wet weather, combined with me forgetting to replace a couple of rubber parts inside of the milking claws , combined with a bit too casual milking and udder cleaning techniques. I would fix one problem, but not all problems at one time. Everything needed to be zeroed out, you might say, before our counts went completely back to our normal low.  It took several weeks of implementing new techniques and replacing parts and hyper-cleaning to shape things back up. During that time the count dropped from the 400, to 100 plus, then to the high 30’s, and finally to under 10.

Coliform petri film showing 3 cfu’s (circled with black ink). This is great!

If you experience a similar extended issue, here are some things you can do so that you don’t lose product, and future income, while you whip things back into shape:

  1. Pasteurize the milk.
  2. Thermize, aka heat shock, the milk (lower temperature than pasteurization, not recognized in the US, so cheeses made from thermized milk are not considered pasteurized)
  3. Switch from lactic cheeses (such as surface ripened and fresh soft) to an aged, quickly cultured and rennet style cheese. (Verify that no E. coli is present)
  4. Switch from freeze-dried direct set culture to bulk starter or mother culture that will provide a faster growing starter bacteria population. (if coliform counts are too high, though, this may not be enough)

Remember that if you are not testing each batch of cheese milk and are making a rennet coagulated, quickly acidified cheese, you may never know that your milk is less clean than it could be! If you do experience a problem, don’t feel alone and remember that keeping sanitation standards high on the small farm, or any farm for that matter, is an ongoing, major challenge. It is a great reminder of how quickly things can change – for the worst.

Keeping your Home Milk Supply Clean

Here is another article I wrote about a year ago.  I did a little study using several local volunteer farms who promised to not change anything about their milking techniques and allowed me to take samples of their milk, which I then sent to a certified laboratory for testing.

How Clean is Your Home Milk Supply-Really?

By Gianaclis Caldwell

First Printed in United Caprine News, September 2010

Like most people who have a few dairy goats you probably believe the milk you drink and feed to your family (and maybe even sell) is clean and safe.  But you might want to think again.

We run a small, licensed cheese dairy inOregon.  We too thought our Grade A milk produced in our inspected, licensed facility was as pure as it could be.  After all, the state conducts routine tests on our milk to verify its safety, but when we first got started I didn’t know how to correctly read the results from these tests. I assumed that if the numbers were less than stellar, that someone would tell me, but in reality, only when the bacteria counts reach the official violation level is the dairy owner usually informed.

Without our noticing, the bacteria counts began a slow and steady climb that suddenly shot sky high.  While the milk was still technically safe to use for cheese, it was far below the standards that are ideal.  This was a pivotal moment for us.  It did three things: It caused me to study and learn how to read and interpret milk lab tests, inspired me to pay close attention to the lab results when they arrived, and completely changed our approach to sanitation in our milk processing areas.

After experiencing this from the standpoint of a licensed producer that believes in the right to drink raw milk, I started thinking about the home producer and their milk quality.  If a licensed dairy performing rigorous cleaning rituals could find their milk not clean, what about the home producer?  Here inOregon, raw milk can be sold legally direct from the farm, as long as only a specific herd size is not exceeded and other criteria are met.  So not only could the home producer be serving tainted milk to their families, but they could be selling it to any number of people for whom bacterial contamination might cause health concerns.  Even beyond the health issues, there is the flavor concern.  A common cause of poor flavor in milk (especially goat milk) is the breakdown of fats by bacterial enzymes. So, for quality milk from all standpoints, cleanliness is paramount.


The Study


I decided to recruit some volunteer farms that would allow me to collect samples of their milk to send to a lab for testing, as well as fill out a questionnaire about their milk sanitation practices. Each producer promised to keep their cleaning and collecting routine the same.  The results of the lab tests were amazing; from milk that was extremely clean, to one that was over the usual violation level. The good news was that even the “dirtiest milk” did not have high levels of the most common pathogenic (illness causing) bacteria e.coli. (The samples were not tested for another bad bug, listeria)

I collected two milk samples from five farms.  One sample was fresh, one just a few days old. Two of the farms hand milked and three used milking machines.  The samples were packed on ice and overnight shipped to Agrimark Central Laboratory inMassachusetts. (I chose Agrimark for their easy to read and order “raw milk profile”)  Before we go into the results, lets go over a little background on just what kind of tests can be done on milk and what these tests can tell you.


Milk Quality Tests


Everyone who milks their goats, cows, or sheep should know a little bit about milk quality tests.  The first thing you should know is that anyone can have their milk tested.  It is not expensive (the tests run in this study cost about 20.00 for each sample) and can be very helpful in you quest for producing good, safe food for your family and neighbors.

The first, and most common, test done on milk is the raw standard plate count (SPC) (some times called simply “raw count”). The SPC counts the TOTAL amount (measured in colony forming units) of bacteria in the milk.  Both good and bad.  It is a starting point for looking at the milk quality.  For example, if the SPC is extremely low, you can bet that the bad bacteria count is also low.  But if the SPC is high, it doesn’t necessarily mean that the milk is “bad”.  If you are a cheesemaker, then you know that by adding culture, you are adding bacteria to your milk.  Sometimes the home milk supply is “pre-cultured” with some pretty good bacteria from your animals.

The next test is the pasteurized count.  For this test, the milk is pasteurized and then the bacteria units are counted.  Remember, normally pasteurized milk (in other words NOT ultra-pasteurized) is not sterile, a certain number of bacteria do survive.  These are the heat loving bacteria (thermophiles).  For most of us who are drinking and using our milk raw, the pasteurized count is of little significance.

The test that I find most interesting is the preliminary incubation count (PI or PIC).  For the PI, milk is held at 50 degrees F for a period of time and then the bacteria colonies are counted.  Bacteria that like the cold (psychrohiles) will grow well under these conditions.  They are of great importance for issues regarding milk flavor when the milk is stored for periods of time.  Once the milk is chilled, the cold loving bacteria will continue to grow (very slowly if the milk is about 38 degrees F).  Some bad bacteria are psychrophiles too, such as listeria (a potentially deadly pathogen).  So knowing what your milk’s PI is after it has been stored for a while, can be very useful information.

Then there are specific tests for certain bad bacteria such as e. coli, staph aureus, and listeria.  First a count is done for the total number of coliforms (of which e. coli is the worst).  If that number is low, then the e.coli number will be of little value, but if it is high, then it is important to know just how much of those coliform colonies are e. coli.

Staph. aureus is a very common cause of clinical and subclinical mastitits in lactation animals.  It is also of increasing concern for human health.


The Study Results

First lets take a look at the lab results as a chart as well as the acceptable ranges, then I’ll break it down to analyze each farm and their procedures, test results, and some possible remedies where needed. Remember, I took a sample of milk that was 5 days old when tested (numbered “1”) and a sample that was 2 days old when tested (numbered “2”).  Then I will go over the suggested cleaning regimen for milking equipment.  But, as you will see from the volunteer farms, many of them perform cleaning procedures that vary greatly from those suggested and are evidently working quite well! ( If you are unsure of how to determine measurements of products and proper use, contact the supplier, they should be able to help you.)


Bacterial Testing Results


Farm Sample


Past. Count


Total Coli

E. coli


































































Milk Test Result Ranges (From Dairy Practices Council)





Common Industry*

Regulatory Limit

Raw Count





300,000/commingled tanker




20,000/ml (pasteurized milk)

PIC (should be <3-4x SPC)



No legal limit




<10/ml (pasteurized milk)


*Related to premium payments within industry

 Farm A

This farm’s milk was pretty clean. They hand milk into a hooded pail in a fairly typical setting- milk stand is in the barn with the animals. Teats are not dipped after milking (note, the farm with the cleanest milk in the study did not post dip either). The milk is chilled by placing in a refrigerator next to the vent from the freezer compartment.  They were unsure of how long it took for the milk to cool completely.

If you will notice, their raw counts are not too bad, but the PI is quite high on the older milk sample.  This indicates that there has been a significant growth of cold loving bacteria while the milk was stored, usually indicating that the milk did not reach ideal storage temperatures rapidly enough, or that it warmed up a bit during storage.  Interestingly, the fresher sample had a higher bacteria count and the staph count was elevated, but the PI was low.  The fresh sample was warm when I collected it from the farm.  I cooled it rapidly in my collection ice, this probably led to the much reduced PI count.

Suggestions: Cool the milk more rapidly and check the milking does for subclinical mastitis with an on-farm somatic cell (SCC) test such as the California Mastitis Test (CMT).


Farm B

This farm’s milking procedure, according to their questionnaire, sounds pretty thorough- so it was initially baffling to see the very high bacteria counts.  Farm B uses a milking machine, washes the udders with hot water and a wash cloth, pre-strips, post dips, cools the milk in a refrigerator, and cleans the milking equipment with chemicals and cleaners designed for the job.

The older milk sample has a raw count far beyond the violation level and an extremely high PI. The fresher sample has a much lower raw count, but still has an out of proportionally high PI.  It also has a coliform count 10 times the ideal.  So what could the problem be?

Suggestions: The first place troubleshooting should be checking the milking equipment for cleanliness. Using a magnifying glass and strong flashlight, each component should be disassembled and inspected. A common area for buildup is in the typical goat claw used on many milking machines. In addition rubber gaskets and hoses might need replacing.  Remember, microscopic nicks and grooves can easily harbor colonies of bacteria that your fresh milk will wash over during each milking- providing food for these colonies and contamination for your milk. After addressing these issues, a ramped up cleaning should be preformed using double the amount of detergent, utilizing 140 degree water (140 degrees at the start of cleaning will ensure it is still hot enough at the end of the cycle), and performed for 10-15 minutes (or until the water drops below 120 degrees).  This should be followed with a 5 minute acid wash. After this “super cleaning”, they will want to ensure that their water is the right temperature (usually 120-140 degrees) during daily cleaning.  When wash water drops below the ideal, it re-deposits proteins and fats on the equipment. The other factor that can limit the effectiveness of cleaning is the pH and hardness of the water source.  Farm B also does not pre-sanitize their milking hoses, this step should be considered as well.  The last thing that Farm B should do is chill the milk more rapidly, this will help prevent that elevated PI.


Farm C

This farm hand milks into open pails, does not post dip teats, cleans the milking equipment in an automatic dishwasher and routinely uses an acid wash.  They milk two goats and then filter that milk and begin its cooling before proceeding with the next goats, this is probably contributing to their lower PI counts.

The older sample has a remarkable low raw count and an acceptable PI, the newer sample has a bit higher raw count and an elevated staph count (probably leading to the higher raw count).

About the only suggestion I have for this farm is routinely checking does with a somatic cell detecting test such as the California Mastitis Test (CMT), as staph is often present in mastitic milk, even in subclinical cases (where no clumping, stringing, or udder heat is present).  Good job!


Farm D

This farm uses a milking machine, uses single use wash clothes for cleaning udders, and does not post dip teats.  The milk is chilled within 10 minutes of milking by filtering into a container which is then set into an ice water filled pail. They use antibacterial dish soap to manually clean their milking hoses and equipment.

While I spilled the fresher of the two milk samples when preparing them for shipping, Farm D’s older milk sample is amazingly clean.  This farm claimed that their milk would maintain its flavor for up to two weeks, and I believe it!

Suggestions: Keep doing what you are doing!  Bravo!


Farm E

This farm uses a milking machine, cleans udders with a quaternary udder wash, and post dips teats. The milk is filtered into a clean container within 30 minutes of beginning to milk and placed in a refrigerator. The milking equipment is cleaned by pumping rinse, wash, and acid rinse solutions through the hoses.  155-180 degree water (although water temperature does not need to be higher than 140, especially when low temp detergent is used) is used with lo-temp automatic dishwashing detergent with chlorine added.

Both samples have raw counts above the acceptable level and PI counts out of proportion to the raw count (remember, the PI is typically 3-4x as high as the raw count). Total coliforms on the older sample are quite high as well.

Suggestions: The cleaning procedure sounds good on first examination, but obviously something is missing. One thing to remember is that each cleaning step has an ideal amount of chemical, temperature of water, and length of time. Any gap in these steps can lead to problems. It is possible that the length of cleaning time is inadequate, the amount of detergent is not sufficient, or even the water type is negatively effecting the performance of the chemicals.  As with Farm B, the equipment should be disassembled and thoroughly inspected and a super cleaning should be performed.  The milk chilling time and temperature goals should also be improved, rarely is chilling by setting the container in a refrigerator sufficient.


Proper Daily Cleaning of Milking Equipment




Common Errors


Rinse all equipment with 100-110 degree water. Too hot of water causing proteins to bind to surfaces or too cold causing fats to form a greasy film.


Use a chlorinated alkaline detergent mixed in the right amount for your water type (hard or soft and pH) in water that is 120-140 degrees F.

For hand washing, soak all parts in this solution for five minutes and then clean with brushes.

If pumping through the lines, clean for 5-10 minutes, making sure water does not cool below 120 degrees.

Drain wash water.

Water too cold or cooled to below 120 by end of cleaning, causing the re-depositing of fats and proteins.

Not cleaning for long enough.

Not disassembling and manually cleaning parts not cleaned well by pumping or brushes.

Acid Rinse

Mix acid rinse in lukewarm or cool water in amount directed. Soak or circulate solution for 2-3 minutes.

Drain and hang equipment to air dry.

Not using an acid rinse at the proper pH can leave a residue of the alkaline detergent, allow buildup of minerals, and leave the equipment more vulnerable to bacterial contamination between uses.


Just before use, sanitize all equipment with a chlorine or other type sanitizer mixed as directed in cool water for 30 sec min.

Drain well.

Too strong of a solution will pit and erode stainless steel and leave a residue on hoses. Too weak will be ineffective.

Putting it all Together

As they say, milk was never meant to see the light of day- it was meant to go directly from the mother into the mouth of her offspring.  Once we interrupt that cycle and attempt to collect and keep a product that was never intended to be handled in that fashion, we increase the odds of reducing its quality and safety.

While using a milking machine is often thought of as the cleanest method available for collecting milk, this only holds true when a very strict regimen of cleaning is adhered to.  Milking hoses and paraphernalia have many nooks and crannies which make thorough cleaning a challenge. Other than cleaning of equipment, proper chilling of the milk seems to be the most common area that needs improving.  I think once the milk is in our refrigerators, we kind of let our guards down, it seems safe in there! But if you try to picture the milk as a growth medium, for not only your family, but for the hoards of bacteria, both good and bad, that are on the animals, in the air, and possibly on our equipment, then you more likely establish procedures for ensuring the safest and tastiest home milk supply possible.

GC’s Ten Tips for Collecting Clean Milk and Keeping it Clean

  1. Give your doe a dairy clip- clip hair from udder, belly, legs and around her tail for the latest in trendy, dairy fashion!
  2. Milk with dry, clean hands- never wet!- or even better, use a pair of disposable gloves while milking. They say that dirty gloves are probably cleaner than clean hands!
  3. Milk in to a hooded pail or place your stainless strainer (with a fresh, clean, single use filter in it) on top of the pail during milking!
  4. Make sure your milk jars are clean and sanitized before adding warm milk. Remember, any bacterial residue in the container will love the warm milk!
  5. Keep it on ice- right after milking, set the filtered milk into a pail of ice water and stir.  If you can get the temperature to 40 degrees within 2 hours of milking, you are chilling perfectly.
  6. Clean up immediately! Never put off cleaning your milking equipment.
  7. Use cleaning detergents and sanitizing chemical in exacting amounts and with the right temperature water.
  8. Let equipment dry between use- bacteria need moisture to surviv- a wet surface is likely a contaminated surface!
  9. Don’t forget to replace any rubber, plastic, or silicone parts of your set-up as recommended!
  10. And last, use your milk within a week, it might still taste good, but any cold loving bacteria will be developing a population by then.