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New name and URL

Animal Science Review is now Fur, Farm, & Fork! Because I graduated from OSU, I have had to move the hosting for this blog to a wordpress URL.

I will continue to generate new content, with a completely unpredictable schedule as usual, at the new location. So if you’re someone who actually likes to read my content, be sure to change your bookmarks and RSS over to furfarmandfork.wordpress.com, as I will no longer update at this address.






Shigella penetrating the intestinal wall. Source: cellimagelibrary.org

If the world was enriched and homogenized, we would actually have a very good idea of what the microbiological community within looks like. Fortunately, the world is much more complex than the miniature environments we culture in the lab, and high throughput sequencing (HTS) is allowing us to fully appreciate micro-biodiversity. As new information becomes available, many of our models for microbial communities continue to be challenged by the actual composition of species in natural environments.

In the world of food safety, we rely on these models to set policy on a regulatory level, and to set critical limits down at the production level. Which tests we run on what products depend directly on what organisms (that cause food borne illness or spoilage) are supposed to be found on that type of food. The authors of this study that came out in PLOS ONE this February examined the microbiome associated with poultry products from farm to fork (meaning from clucking chicken to packaged poultry product) using HTS rather than culture/enrichment methods. The results indicate that there is an unappreciated amount of diversity between different stages of the poultry production process, and that we may not acknowledge the presence of some organisms as much as we should.

In the study, samples were taken from multiple steps in the poultry production process: wet and dry litter, fecal samples, fluid from carcasses collected during the cooling process following slaughter, and fluid from raw retail poultry products (legs, wings, and breasts). Other than the retail portion, all of the samples collected were from the same batch of birds from start to finish. The available RNA from viable cells in each sample was amplified and identified as belonging to specific species using a combination of Illumina sequencing and database referencing (blastn and usearch).

From this pile of data, lists of organisms were compiled to compare the ecosystem profile for each point in production.

The numbers refer the the number of unique taxa found in each group

The authors were very surprised by the amount of diversity between the two litter samples (wet and dry) and the fecal sample. They expected to see very similar profiles, as all of the predicted microbes in those groups would be inoculated from contact with fecal material (young chicks have no inherited microflora, and are coprophagous); however, all of the groups’ microbial communities had very little in common. As shown above, of the hundreds of unique species identified, only 52 were actually found at every stage from farm to fork.

In evaluating food safety, several results are of concern. The first was that the authors found significant amounts of Shigella spp., which have traditionally not been associated with poultry products and may not be a part of many sanitation programs. The second is that in one of their dry litter samples, the authors found a large amount of C. jejuni. It’s presence was interesting as previous studies have found it difficult to cultivate C. jejuni onto dry litter, suggesting that it will not grow in that environment. This discovery further shows that our attempts to cultivate bacteria are not indicative of their behavior in “the wild”. There may be nutrient gradients or a symbiont in play that allows C. jejuni to grow; therefore the possible contamination of dry litter has to be acknowledged in that facility’s Campylobacter monitoring program.

The last point of interest I’ll discuss here is the large amount of unique species that were found in samples following slaughter. This suggests that these species did not come from the farm, but rather were introduced during slaughter and processing. Interestingly, among Campylobacter spp., there was little to no abundance of C. jejuni in the samples, but differing amounts of other Campylobacter spp. This is revealing, as we have been predisposed to expect C. jejuni to be present due to our use of selective media.

Let’s fully appreciate the amount of diversity found within the processing facility, the authors collected two post-processing samples labeled carcass rinse and carcass weep. The rinse was composed of fluid shaken off of the carcass following its removal from the chlorinated chill tanks, and the weep was the drippings from the same carcass 48 hours later. 2/3 of the unique species found the weep samples were not found in the rinse. The authors interpret this as being due to the fact that the sterilization of carcasses is not the goal of poultry processing, and provide the example that viable Salmonella can be recovered from carcasses even after they are sent through the standard antimicrobial processes. The goal is to reduce enumeration, not sterilization.

Finally, in examining the retail samples, we get what we expect. Similar organisms as the weep, with some new faces, presumably because they persisted through processing at undetectable levels, and slowly grew as the product was stored in refrigeration.

The authors conclude by examining some potential symbionts that would allow C. jejuni to persist, but ultimately say that due to the high number of environments C. jejuni can occupy, attempting to exclude it in a universal way will not be very effective.

So all in all, a thorough example of the misdirection we receive from culture bias, and a startling look at how, given enough incubation time, properly processed meat can still support a huge amount of microbial diversity, including many food borne pathogens.

Appreciate this diversity, and make sure you cook your chicken to temperature.



Oakley BB, Morales CA, Line J, Berrang ME, Meinersmann RJ, Tillman GE, Wise MG, Siragusa GR, Hiett KL, & Seal BS (2013). The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations. PloS one, 8 (2) PMID: 23468931

Circadian rhythms and jet lag.  There, cyclic crowing behavior explained.

Quite a lot of people are discussing this study from Japan examining the effect of light on the crowing behavior of roosters. The authors observed several birds in experimental conditions where light intensity and duration were controlled, taking observations with audio recorders and cameras. The scenarios presented were a daylight cycle of 12 hours of light and dim light respectively, and constant dim light. Observations were recorded for a period of 14 days, producing this graph.

So many reporters on the study have run with this, making declarations about what great timekeepers roosters are, and how cool it is that they don’t need the sun to know when dawn is.

Well, approximately when dawn is.

“Under dimLL conditions, a free-running rhythm of crowing was observed with a period of 23.7 ± 0.1 h (n = 4), but this free-running rhythmicity gradually damped out”

Interesting, so the sun is unnecessary until it’s been gone for a while, then we start to get some variation. This dampening effect is even more obvious when you place testosterone implants in the roosters.

Testosterone implant roosters calling out “Bro, do you even lift?”

Don’t get me wrong, the fact that Roosters have this accurate of a circadian clock is impressive! It’s very interesting biologically, but it’s not some infallible atomic clock. While many news sites are toting that Roosters are independent of the sun, the opposite is true. Circadian rhythms are directly calibrated primarily by light cycling, with temperature being another important environmental cue. To confirm the roosters knew what time it was, the authors examined the effect of light or recorded crowing sounds at different times of day. They found that there were fewer crowing behaviors at random dawn times than at the “correct time” of day.

This doesn’t mean the roosters know it’s 5pm, but their circadian rhythm is telling them that it isn’t dawn. However, the sun still “came up” so we witness some halfhearted crowing. Anyone who has ever traveled out of their timezone knows exactly how this feels: these roosters have jet lag. While the sun may be coming up, their circadian clocks are telling them that it feels like a different time of day, so they crow in response to the light, but with reluctance and confusion, much in the same way you sleepily get up on vacation when the Louvre opens, even though it feels like 5PM to you.

“But Austin,” you tell me, “aren’t you anthropomorphizing?” While I admit roosters may not empathize with trans-Atlantic vacations, we know that chickens are dependent on daylight to calibrate their biological rhythms because we do it all the time. We increase egg production by simulating summer lighting year round, and alter feed intake in broilers by changing their daylight cycle. We also use this trick to bring mares into heat.

The loss of rhythm observed in 24 hour dim light is likely to become more and more sporadic, and even more so if the roosters were housed singly (as there is some group consensus due to competitive crowing). I would propose that if you could keep the roosters on a light cycle that progressively moved forward an hour a day until dawn was at 2pm, the roosters would crow with the same strict rhythm independent of the actual sun. If the authors of the study choose to pursue this hypothesis, an easy test would be to simply progress their artificial sun’s rise and fall over time.

Alternatively, we could fly several roosters with us to Paris, and see if they wake us up before the Louvre opens.


Shimmura, T., & Yoshimura, T. (2013). Circadian clock determines the timing of rooster crowing Current Biology, 23 (6) DOI: 10.1016/j.cub.2013.02.015

It appears that the agencies that we rely on to track disease outbreaks need to start tracking disease, not just their own jurisdiction.

An article in Sociology of Health and Illness piqued my interest this last week that reveals the amount of segregation different government agencies have when dealing with zoonotic disease. The understanding of the goals and connections between livestock, wildlife, and human health among these agencies are often apathetic at best, and antagonistic at worst.

The author of the article took it upon himself to interview several government agencies with different species and regional jurisdictions, and was able to reveal what he calls “organizational silos” that develop when the values and cultures of these different agencies prevent them from working with outside groups. When attempting to monitor emerging infectious disease (EID), identification of cross-species movement is critical to predicting and preventing pandemics. Unfortunately, while they may be able to acknowledge the geographical movement of EID’s, many organizations are blinded by their specific oversight of humans or animals.

Copied from the article: Diagram showing the crossover between domestic animals, wildlife, and human EID. Important emergence factors for each circle are listed on the outside.

There are many telling comments contained in his interviews, and I encourage you to read the article to get the whole scope of the problem, but I’ve chosen to list a few of my favorites here:

From the Director of Animal Health Division at a state Department of Agriculture:

“‘We got a positive [flu result] on one of our routine surveillance tests’ of a poultry farm, Spencer complained, and ‘we were required to contact the USDA right away because of the pandemic Asian strain’. Spencer added, ‘It seems a little silly because there was no clinical illness on the property, and the strain came back something pretty common…’ In Spencer’s eyes, it was ‘hard to justify’ reporting the flu strain to the USDA… These days, Spencer said he passes on information about disease events to the state DOH and leaves it to them to tell local health boards. ‘If somebody screws up’, he shrugged, ‘at least we can blame the [Department of Health]’.”

Not an uncommon perspective for many organizations, or even coworkers! Let’s hear from another director at the USDA Animal and Plant Health Inspection Service (APHIS):

 ”Clinton argued that the ‘single biggest threat for disease’ comes from ‘wildlife intermingling with domestic livestock’. He told me, ‘You can’t control the birds’ and he rightly pointed out that ducks are flu incubators. If the bird flu – which Clinton called the top priority of his agency – becomes pandemic in humans, he told me, it will come from waterfowl.”

Interesting, I might argue that we have much more interaction with domestic fowl (can’t remember the last time I handled a wild duck), but let’s see what others had to say about this viewpoint.

“Nina Marano, a zoonotic disease expert at the CDC, told me that ‘most of the outbreaks have occurred through interaction with domestic poultry’. Another example: though poultry farmers singled out wild birds called cattle egrets as the source of a 2004 flu outbreak in California, the egrets tested negative – it turned out that contaminated egg containers circulating between farms were the culprit (McNeil 2004).”

Finally, one last example of how a zoonotic disease often isn’t treated as such by human health agencies. From a Director of the Infectious Disease Bureau of a city Public Health Commission:

“When I asked Sanders to describe a zoonose that she responded to, she mentioned a recent outbreak of salmonella…and she believed that the pathogen came from two live poultry markets in Chinatown. What I found telling was that, in Sanders’ lengthy discussion of this outbreak, she did not mention any communication with veterinary medicine agencies.While the Disease Bureau’s response to salmonella followed protocol, it did not turn to the Department of Agriculture, the USDA, or any other agencies involved in animal health for help or information. Nor did it share information with them.”

Clearly here the city health board considered this a food safety issue, but payed no attention to the implications of getting meat from an approved source (a domain which definitely belongs to the USDA), or the fact that other agriculture agencies may be interested in a salmonella outbreak. There are many other telling quotes within these interviews, and I again encourage you to check out the article.

The author of the study concludes that the only examples we get of harmonious collaboration are for those diseases which are in the public eye such as rabies and influenza (H5N1 and H1N1), though we still have lines drawn even when the public is asking for action (“‘we have enough H1N1 to worry about without worrying about turkeys’. He
concluded that turkey infection is ‘a Department of Agriculture issue’”). The most shining example of the failure to communicate by these institutions in the article is the discovery of Bird Flu in the US.

The first human cases of H5N1 in the US were wrongly diagnosed with St. Louis encephalitis, resulting in the deaths of 3 patients. A veterinary pathologist at the Bronx zoo observed neurological symptoms in some of the zoo’s birds and suspected a link, however encephalitis would not have killed her birds. Both the CDC and local DOH would not accept new information from her, instead keeping the encephalitis diagnosis. She then sent specimens to a friend at an Army Medical Research Institute of Infectious Diseases, who revealed the etiology of the disease and I’m sure had a hilarious conversation with the CDC and DOH (could you please explain to us why this veterinarian is doing your job casually on the side, and doing it better?). By the time the CDC received/accepted this information, H5N1 was endemic in the area.

Nothing against the CDC, it’s a fantastic organization, but this highlights the closed lines of communication that exist between human and animal agencies the author discusses. In order to prevent the next EID crisis, rigorous epidemiology is critical. Refusing to acknowledge the importance of cross-species movement to the virulence and emergence of a disease that falls under your agency does not only prevent you from identifying the next source of infection, but leaves you with nothing but reactive measures catered to a epidemic that you refuse to fully appreciate.


Jerolmack, C. (2012). Who’s worried about turkeys? How ‘organisational silos’ impede zoonotic disease surveillance Sociology of Health & Illness DOI: 10.1111/j.1467-9566.2012.01501.x

This is the first study I’ve found that was interested in cataloging bacterial diversity among subclinical (or asymptomatic) infections. While they may be less threatening to the animal’s overall health, these infections have great significance in the world of animal agriculture, where they restrict growth (or in this case, milk production), and encourage the use of medicated feeds which in turn motivate people to purchase organic products. Identifying the risk factors and causes of these infections could therefore impact both the management of food animals, and any legislation defining how and when medications can be used. With that in mind, let’s jump back into mastitis, and everyone’s favorite gram-positive, S. aureus.

It’s because of my plasmids, people can’t help but stare.
Image from http://cellimagelibrary.org/

S. aureus is one of many bacteria that cause mastitis, however it is of additional importance as it often causes chronic or recurring cases of mastitis that result in unusable milk and discomfort of the animal. In this study, the authors investigated 11 dairy farms where they expected to find S. aureus, based on previous culture findings at each farm. They defined cows that they took milk samples from as having new or chronic infections based on somatic cell counts (SCC) in the milk. If values were >200,000 cells/mL for the month of collection the infections were considered new, whereas if cell counts were  >200,000 cells/mL for more than 2 months, those infections were considered chronic. They took a single milk sample from each teat of the infected cows, for a total of 1,354 mammary glands from 350 cows.

Pulse field electrophoresis was used to identify the different subspecies/serotypes/pulsotypes (pick your word), and to identify the genes coding for enterotoxin production that had been amplified by PCR. An ELISA test was used last to detect the presence of several enterotoxins.

As the majority of exposure to enterotoxins produced my S. aureus is through milk and dairy products, subclinical infections of S. aureus are very important as a food safety control point. Unlike cows with clinical cases that are removed from production, cows with subclinical infections continue to contribute milk that makes it to the consumer, provided that the SSC is <750,000 cells/mL. The authors were unable to detect a large amount of enterotoxin in their samples, but many of the pulsotypes contained the genes coding for their production. Other studies cited by the author report the common presence of these genes in S. aureus  samples, but expression rates are inconclusive or unexplored. This means that theoretically, subclinical cows could be introducing these bacterial toxins into consumer milk in small amounts.

It’s difficult to tell how significant these amounts might be. Toxic doses of one of the enterotoxins, “Toxic Shock Syndrome Toxin 1″, has been found to be as low as 100 micrograms/Kg in miniature pigs. The concentrations that may be introduced through contaminated milk, and the bioavailability when ingested, should be explored. Takeuchi et al. (1998) were able to detect the presence of TSST- 1 in bulk milk tanks, but no one has yet to quantify the amounts of TSST- 1 potentially present in pasteurized milk.

All that being said, what good is this new information? It can be argued that because these infections are chronic and/or subclinical that these strains of S. aureus aren’t very pathogenic, but they’re still causing inflammation. By identifying common serotypes and factors leading to the subclinical infection of a herd, perhaps there are simple management changes that can prevent infection. Milking is an almost sterile procedure, with sanitation of the teats both prior and following milking, wearing gloves, and forestripping; but there could be other tricks that would target risk factors related to the spread of subclinical pathogens, especially those that are specific to a location.



Bulanda M, Zaleska M, Mandel L, Talafantova M, Travnicek J, Kunstmann G, Mauff G, Pulverer G, & Heczko PB (1989). Toxicity of staphylococcal toxic shock syndrome toxin 1 for germ-free and conventional piglets. Reviews of infectious diseases, 11 Suppl 1 PMID: 2928643

Oliveira L, Rodrigues AC, Hulland C, & Ruegg PL (2011). Enterotoxin production, enterotoxin gene distribution, and genetic diversity of Staphylococcus aureus recovered from milk of cows with subclinical mastitis. American journal of veterinary research, 72 (10), 1361-8 PMID: 21962279

Takeuchi, S., Ishiguro, K., Ikegami, M., Kaidoh, T., & Hayakawa, Y. (1998). Production of toxic shock syndrome toxin by Staphylococcus aureus isolated from mastitic cow’s milk and farm bulk milk Veterinary Microbiology, 59 (4), 251-258 DOI: 10.1016/S0378-1135(96)01253-9

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