Move Over Genetic Engineering, Here Comes Microbiome Engineering

NSFL (Not Safe For Lunchtime. Perhaps.)

Thirteen years ago The New Yorker published what has since become that magazine’s most reproduced cartoon.

It shows two dogs, the first sitting in front of a computer, speaking to the other, who is down on the floor.

Dog 1 says: “On the Internet, nobody knows you’re a dog.”

Cartoonist Peter Steiner is reported to have earned over $50,000 from reprintings.

I mention this as it may have occurred to you (well, you never know) to ask yourself if, in microbiome testing, “Nobody knows you’re a dog.”

Perhaps disappointingly, the truth is the opposite.

Canine and human microbiomes are pretty different.

But this of course raises the whole issue of non-human microbiomes, and like many of our weekly microbiological meanderings here at uBiome, this one will take us on an illuminating journey, particularly when it comes to animal health.

You see, just about every creature—from the weightiest whale to the most miniature mosquito—carries its own ecosystem of bacteria, often supporting life, but sometimes also being associated with disease.

People with pets have almost certainly seen their furry or scaly friends eating poop—either their own, or the product of other creatures.

While undeniably an off-putting spectacle, there’s often method behind their apparent madness.

Termed “coprophagia,” many animals spontaneously engage in this unpleasant but instinctive practice.

Veterinarians have taken notice, and some treat sick animals with deliberate therapies that build on this behavior.

Just as fecal microbiota transplants have been used experimentally (but often surprisingly effectively) to clear up C. difficile infections in humans, some animals are treated with what’s termed microbiome restorative therapy, where fecal matter is transferred from a healthy donor animal to a sick recipient creature.

For example, a veterinarian in Massachusetts has carried out hundreds of such procedures, posting online “how-to” videos that show both oral and rectal administration of mashed-up fecal matter.

I know, right? Apologies if you happen to be reading this over lunch.

A study this year from researchers at Justus-Liebig University in Germany, and Texas A&M University, reports that although evidence for this kind of therapy is scarce and tends to be anecdotal, there have certainly been reports of chronic diarrhea in dogs being immediately resolved through healthy donor stool material administered via enema.

Actually, farmers have long known the value of transferring digestive material from a healthy animal to a sick one, even though they almost certainly had no idea of why it worked originally.

In the 1700s, cattle farmers were known to transfer cud (partly-digested and regurgitated food) between the mouths of healthy and sick cows.

300 years ago there would probably have been no awareness of bacteria in the farming community, even though Dutch “citizen scientist” Antonie van Leeuwenhoek had become the first human to actually see them in the late 1670s.

Things are different now, of course, and the “re-seeding” of cows’ stomachs is done more knowledgeably and routinely.

Rather extraordinarily, a process called transfaunation involves healthy donor cattle being fitted with what amounts to trapdoors in their sides, covering a tube that goes directly to one of their four stomachs.

From this, around 10 litres at a time of a fluid called “rumen liquor” can be extracted, then transferred via an oral tube directly into the stomach of a sick cow.

A 2015 study from UC Davis showed this to be common practice in dairy farming, speeding up recovery and improving milk production in sick animals.

The surgical insertion of the “rumen fistula” (the tubeway to the stomach) is said to cause no ill-effect to the healthy cow, and involves a routine procedure that apparently takes only 90 minutes.

While it may lead to no discomfort to the cow, however, some of us may feel distinctly uneasy about such a practice.

However it’s pretty certain that so called “microbiome engineering,” to enhance animal and plant performance is only in its infancy.

This too may sound unpleasant, but aren’t we already doing this to some degree to ourselves (or at least intending to) every time we swallow a probiotic supplement?

Further reading

Benefits of rumen fluid after DA surgery

Collection of rumen fluid

Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing

Eat Sh*t & Live – Micro-Biome Restorative Therapy

Engineering Microbiomes to Improve Plant and Animal Health

Holey Cow—The Wonderful World of a Fistulated Cow

On the Internet, nobody knows you’re a dog

The functionality of the gastrointestinal microbiome in non-human animals

Treating dairy cow indigestion with rumen transfaunation

Understanding the canine intestinal microbiota and its modification by pro-, pre- and synbiotics – what is the evidence?

When medicine is crap—Fecal transplants in veterinary medicine