Change the bugs, change everything.

That’s the bottom-line premise and potential of relatively new, rapidly expanding microbiome research that will likely transform how veterinarians and medical doctors diagnose and treat disease in the not-so-distant future.

Buckle up. A little baking is needed in order to get the pie.

You’ve heard the term, but for the record the microbiome—a fuzzy term sometimes called the microbiota in the gut of animals—is the community of microorganisms that live in or on an individual animal. Depending on whom you ask, it can also include microorganisms living around an individual animal. Think here of microorganisms like bacteria, viruses, fungi and protozoa. For our purposes we’ll focus on bacteria, and specifically it’s the DNA within these microorganisms that make up the microbiome.

Speaking more broadly, an animal’s microbiome is comprised of collections of communities (ecosystems) of microorganisms.

How these microorganisms interact with the host and each other influences everything from how a host’s genes are expressed to whether resident pathogens can cause disease.

“When you were in animal science 101, you were taught that phenotype was the consequence of the genotype plus the environment. My question was always, what’s the environment?” says Keith Belk, holder of the Ken and Myra Monfort Endowed Chair in meat Science at Colorado State University (CSU). “It turns out that a big chunk of the environment is this feature of bacterial communities influencing the genetics of the organisms they happen to be in contact with. That’s the reason clones can perform differently.”

The concept is not new. At least as far back as the 1950’s, Nobel Laureate Joshua Lederberg helped prove bacteria can share genetic information between strains and contribute to antibiotic resistance. For at least as long, scientists have explored rumen microbiology. Technology in recent years, however, enabled rapid exploration and understanding of microbiome specifics.

Jessica Metcalf, a microbiome scientist who is part of the CSU Microbiome Network explains: “Microbiome science, as the high-throughput study of microbial communities, using DNA sequencing, took off about a decade ago with advances in next-generation sequencing. The widespread use of it results from both advances in sequencing and bioinformatics.”

For perspective, Belk notes the Human Genome Project took more than 13 years and about $3 billion to sequence 3 billion gene base pairs. Today, he can sequence 8 billion base pairs in an afternoon for about $600.

Now for the pie.

“So, if the whole animal, what we call the core in this concept of ecological genomics, is influenced by all of these peripheral genomics available to them in the microbiome, in various niches of communities of bacteria, then it seems to us like we ought to be able to modify these peripheral niches of bacteria and their genetics, and therefore modify the host,” Belk says.

In other words, the idea is modify the microbiome to eliminate specific pathogens or better withstand them. Do that, and there’s less need for treatment with antibiotics, for example. Maybe you can even rid cattle of bacteria resistant to the most medically important antibiotics.

This is the exact journey CSU began a few years ago. The first target is liver abscesses in feedlot cattle. Based on National Beef Quality Audits (NBQA) over time, the incidence of liver abscesses and the cost associated with them is a growing problem. For perspective, according to the most recent NBQA, 44.6% of livers were condemned in 2016, versus 30.8% in 1994.

The primary strategy to prevent and treat these abscesses is adding Tylosin or chlortetracyclines to rations while cattle are on feed. Given the precautionary environment of regulatory agencies, the end to that practice is likely nearer than further away.

“Our first goal has been to figure out ways to modify the microbiome in such a fashion that we don’t injure performance of the cattle while they’re in the feedlot, but at the same time reduce the need for cattle to be treated with antibiotics,” Belk says.

They are using two approaches. In the first he explains, "We are able to screen various compounds and combinations in vitro (in a lab-based environment) in order to decide whether it is worth considering. We’re looking to see if we can shift the flora of the rumen or lower gut in a manner that addresses the likelihood of infection, while at the same time not hurting performance, or even improving performance.”

Once identified, the next step is conducting large trials with the compounds in the feedlot. Results thus far are more than promising. CSU is testing compounds for several private companies.

Belk says he wouldn’t be surprised to see these compounds available for commercial use within the next year or two. But he adds, “It’s likely that the same compounds or combinations that work in one feedyard in one part of the country won’t work the same way in other parts of the country. The community of bacteria in the gut of the cattle being fed in Cactus, Texas, won’t be the same as cattle being fed in Greely, Colorado.”

The second approach CSU is exploring utilizes gene-editing technology to target and kill antibiotic-resistant pathogens.

You’ve likely heard about CRISPR-Cas9. For purposes here think of it as RNA-guided molecular scissors that snip the double strand of nucleotides in a DNA molecule at a specific spot. Such breakages occur naturally all of the time. Mother Nature abhors them. Nature guesses at how to splice the DNA back together, which can result in a mutated gene or one that doesn’t function. Or, in the case of gene-editing, you direct the repair with donor nucleic acid.

Belk and his team snip the DNA and allow the cell of interest to die. They’ve already done it in lab conditions.

“Our idea is to first kill the pathogens, then kill bacteria with genes resistant to antibiotics, leaving a community of bacteria that is healthy for the organisms, animals and humans,” Belk says.

Rather than kill all of these bacteria, the goal is to kill enough of them to shift the population of bacteria. They’re going to use a phage delivery system, by which a virus carrying the guide RNA and gene splicing shears invades the targeted bacteria. In practical terms, this could be as simple as a feed additive.

Belk explains the approach also could be used to rid the microbiome of all genes resistant to, say, the 15-20 most medically important antibiotics, in order to preserve their use.

“This is truly paradigm shifting,” Belk says. “You have to start thinking about ecologies instead of individual organisms.”

What was previously thought to be the target becomes something else.

“E. coli 0157:H7 isn’t a problem,” Belk explains. “The problem is the genes within that organism that produce proteins that make people sick.”

No antibiotic-resistant genes found in beef

Along the way, CSU efforts are also aimed at documenting to what degree, if any, beef from cattle receiving antibiotics could contribute to antibiotic resistance in humans.

In a first-of-its-kind study completed in 2016, called Resistome Diversity in Cattle, Colorado State University meat scientist Keith Belk and Paul Morley, a CSU veterinary internal medicine specialist and epidemiologist, along with other CSU researchers, began tracking antibiotic resistance through the beef production process by looking at transmission through meat products and environmental effluents.

In sum, they found antimicrobial resistant (AMR) genes in the feedlot (in feces) where cattle were fed, on the trucks that hauled them, in water of holding pens and at the packing house.

However Belk explains, “In this particular study, with the sensitivity available to us, we couldn’t find a single, solitary AMR gene in the meat product leaving the packing plant, going to consumers.”

That’s not saying there are none. It does suggest that meat from cattle receiving antibiotics, as a conduit to passing along resistance to humans, is negligible.

“Where we do believe it could be a problem is how we disseminate those genetics into the environment,” Belk says. “When we look at the genetics for microbial resistance in feedyards, we’ll always find tetracycline at a predominant level.”

Did cattle feeders create tetracycline resistance in treating to reduce those liver abscesses referenced in the main story?

"That’s absolutely not what happened. What happened was that a tetracycline-resistant gene occurred in a mutation eons ago, but because we selected for it over time with long periods of treatment, it ended up becoming the predominant microbiological genome,” Belk says.

By the same token, in other research antimicrobial resistance in cattle administered metaphylaxis was no different 26 days later than before treatment.