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.

20 thoughts on “Chasing Coliform Counts

  1. Your approach to dealing with the E-coli count reminded me of the calm, professional and caring approach of an emergency room physician. The upshot shows that simple, step-by-step measures taken with a cool head can be amazingly successful. Bravissima!

  2. My father-in-law is a microbiologist. His lab tests bacteria in milk. They are going to teach my husband and I how to do it. The lab isn’t State certified. I thought they were, but they know how. He is also going to teach me how to fecal tests, as apparently we can do that ourselves.


  3. GREAT article. We produce raw milk right across the border from you in Northern CA, and just began using the 3M films to regularly measure coliform and APC in our milk. We also use a certified lab that is not local, so the on-farm testing is a great compliment and allows us to monitor batches much more frequently. It is a great tool! Our cfu’s tend to stay very low, but we find that when we do have an issues, the culprit is usually our milking equipment. Our strategy is to do that “hyper-cleaning” of our milker that you mention at the first sign of rising counts, and that usually drops us back down to <5 or non-detect.

    We've also learned that some types of mastitis are caused by gram-negative bacterias. If no other root cause can be found, it can be helpful to test each cow or goat directly from the teat to see if they are shedding coliform straight from the udder. 🙂

  4. intresting article, I have a question. Currently we are making artisan cheese (double camembert / brie) from pasteurized milk and some of our batches get high total coliforms >1000cfu/g (no e.coli). What could be the cause ? We ensure pH are achieved at all times.

  5. Hello Gianaclis Caldwell! I am a cheese producer in Turkey and i’ve been reading your books for several years to support my cheese making. First of all thank you for those great helpers 🙂
    I produce both fresh, aged and blue cheeses. In my blue cheese as well as fresh cheeses there is a slight bitterness that can be tasted at the back of the mouth/tongue. Can this bitterness come from coliform bacteria? Thanks. Buket

  6. Hi Buket! Thank you for your kind words, it’s always nice to picture my books with cheesemakers all over the world. 🙂
    No, probably not, unless you are also getting coliform gas production in those cheeses? Does the milk you are using have any off or metallic taste? What type of rennet are you using and are you able to do precise measurements?
    Bitterness typically comes from too rapid protein breakdown which could happen from rennet or from enzymes in the milk or bacteria in the milk. With blue cheese, aging at a cooler temperature can help too.
    Good luck!

    • Hello Gianaclis, thank you for your quick reply! This is the specifications of the rennit i am using Strength 1/10 000
      500 mg of active chymosine
      IMCU ≥ 140

      I am today sending a cheese sample to the lab for E.Coli count.
      Most probably as you said we will find out it is not due to E.Coli but from rapid breakdown of the proteins by enzymes. I am using %70 percent of rennet for soft cheeses (60mins coagulation time at 32 degrees) and %50 for hard cheeses (60mins 34 degrees).

      Thanks alot for your comments! and looking forward to visiting your farm some day 🙂

      Best wishes,

    • Test results are negative; no coliform in the cheese 🙂 500mg of active chymosin in 1000mg of bottle. (%2) No i don’t have that book, will try to get it! By the way we are waiting for the results of the referandum here in Turkey right noıw! If the result is “yes” i will move to state, can i come and work with you :))

      Sevgilerimle, Buket Ulukut

      On Sun, Apr 16, 2017 at 4:41 PM, Gianaclis Caldwell wrote:

      > Gianaclis Caldwell commented: “Let me know what the tests are. Do you have > my Small-Scale Dairy book? It has a lacto-fermentation test you can do > yourself to check for coliforms. Can you tell what the percentage of > chymosin is?” >

  7. Well, I hope the referendum results are favorable, then! Great on the coliforms. It sounds as if the chymosin amount might be a bit low (the other portion being pepsin, which is known to more readily cause bitterness). If you can ever find 80% Chymosin that would be better, but I imagine your choices are limited.

    • Well i am bringing the enzyme as well cultures from France. The amount of chymosin and pepsin should have been a well balanced portion as this product is already sold in the catalouge of company coquard!? I should better check with them. I know wrong proportions of pepsin can cause bitterness but i didnt think this could be the case from a product bought from a dairy supplier. Anyway i will check with the technical department of coquard.

      Thanks alot 🙂

      Best wishes, Buket

      Sevgilerimle, Buket Ulukut

      On Tue, Apr 18, 2017 at 4:32 PM, Gianaclis Caldwell wrote:

      > Gianaclis Caldwell commented: “Well, I hope the referendum results are > favorable, then! Great on the coliforms. It sounds as if the chymosin > amount might be a bit low (the other portion being pepsin, which is known > to more readily cause bitterness). If you can ever find 80% Chymosin th” >

    • Dear Mrs Gianaclis,

      How are you? I hope you are having a good winter.

      I would like to hear your thoughts about aging blue cheese. Do you suggest wrapping the pinned cheeses in aluminium foil during aging? We pin our blue cheeses when we first see the blue dots; in about 10 days after making.

      Today i checked the blue cheeses in the cellar and there were almost no blue veins. I sed to wrap them in aluminium foil couple of years ago. But i am not doing it now. Can this be a reason?

      I use a liquid p.roqueforti mold. I was using 20 drops for 100 liter, this season i increased it to 30 drops for 100 litres to have more blue in side, but there was almost no blue veins. So even though we increased the amount of the mould, the result was less blue compared to last season.

      The brevibacterium population on our blue cheeses are more compared to last season as well. What can be the reason?

      After we pin the cheeses, normally the lines that the needle passes through should be blue, but this time there are orange/brown lines in the cheese instead of blue.

      Sorry if i am bothering too much with my questions.

      Hope to hear from you,

      Best wishes Buket

      Sevgilerimle, Buket Ulukut

  8. Hello, sorry you are having trouble with your blue! I’m not a blue expert, but it does sound as if the red surface flora (usually yeasts with the brevabacterium) are growing instead of the blue. Increasing the blue mould dose won’t help. Wrapping might help, and is often done to keep the humidity up and surface contamination down, but this might also be a seasonal development. Do you remember if you had a lot of B. linens type growth this time of year in the past? It is almost impossible to avoid once there. Let me know and I’ll see if I can think of any other options for you!

  9. Dear Mrs Caldwell,

    I hope you and your family are healthy.
    I have a question which you may have experience with;

    My camembert type soft cheeses have started melting right after salting. I didnt change anything in the receipe, neighter the salt brand/type nor the cultures i am using. This has happened 2-3 times over the last 3 years and lastly happened this week. I searched for articles and couldnt find a relevant answer.
    The melting is strange. After I take the cheeses out from the molds, they start becoming liquidish and start dripping. What can cause such a problem, do you have any experience? Can antibiotics n milk cause this? I am buying the milk from another company in the village.

    Thank you for your time and considertion,

    Best wishes,

    Buket Ulukut

    • Sorry to take so long! Do you monitor pH? That would be the key to determining proper acidification and ruling out antibiotic issues. I’d love to see a picture of this melting. You can email me (link from website)

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