Findings by U of A microbial ecologist Jens Walter and his colleagues suggest differences in our microbial makeup likely depend on when we acquire our first micro-organisms after birth — and the order they arrive in our gut has a lasting impact on how the microbiome looks when we grow up.

The discovery sheds new light on how these microbiomes, which are as personal as fingerprints, establish themselves and what drives their unique nature. That’s key to figuring out how to change our microbiomes for the better, said Walter.

“Each of us harbours a microbiome that is vastly distinct, even for identical twins. Microbiomes are important for our health, but they appear to be shaped by many unknown factors, so it’s hugely important to understand why we are all different,” he said.

Studies have already shown that a person’s genetics, diet, environment, lifestyle and physiological state all make small contributions to the variation of the gut microbiome. But those factors account for less than 30 per cent of the variation, noted Walter.

In the study, researchers introduced distinct microbial communities, collected one at a time, from adult mice into the gastrointestinal tracts of young, genetically identical mice. The results showed that the microbiome in the adults was more similar to the microbiome introduced first. Even using a cocktail of four different bacteria, the researchers repeatedly found that the first microbes showed the highest level of persistence and the strongest influence on how the gut microbiome developed.

The discovery about timing brings scientists one step closer to understanding how microbiomes might become disrupted — for example, through caesarean section birth or antibiotic use — which is then more likely to predispose us to chronic diseases, and how to potentially address that.

Poor gut health has been linked to obesity, Type 2 diabetes, heart disease, inflammatory bowel disease, colon cancer, neurological disorders, autism and allergies.

“If we know what drives specific microbiomes in specific people, we can have a much more rational approach to potentially altering the microbiome, and developing strategies to address those diseases,” Walter said.

“Having long-term persistence of microbes when they colonize in the gut early in life means that a health-promoting biome could potentially be established by introducing beneficial bacteria straight after birth.”

Baby formulas fortified with probiotics already do this to a degree, but knowing more about how probiotics affect other members of the gut’s microbial community could take it to the next level, he said.

“We could be a lot more systematic. I think in 30 or 40 years we’ll be able to colonize infants with specific bacteria we know are health promoting and shape the microbiome in a beneficial way.”

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While there is no silver bullet lying in wait to replace antibiotic growth promotants, a thoughtful mix of improved husbandry and antibiotic alternatives can prove as effective, University of Manitoba animal science professor, Martin Nyachoti told a department seminar last week.

Those with doubts can look to Scandinavian countries for guidance, he said.

“Really, the first step was taken in 1986 when Sweden became the first country to outlaw the use of antibiotics in livestock diets,” he said. “After that a few other Scandinavian countries followed suit.”

In 2006 the European Union banned the use of antibiotics as feed additives, and now the United States and Canada are also moving in that direction, albeit through voluntary changes to product labelling.

“To put things in context, there have been questions for a very long time — right since the 1960s — as to whether or not we should be using antibiotics in animal or livestock feed,” said Nyachoti. “This has been going on for a long, long time.”

That long history gives Manitoba’s producers a lot of good information to base production decisions on.

For example, when Scandinavian countries moved away from antibiotics by incorporating zinc oxide into piglet feed, the result was fewer enteric diseases, including post-weaning diarrhea. But Nyachoti notes Canadian producers won’t be able to replicate that transition because of Canadian restriction on the use of zinc — it can still be used in pig feed in Canada, but not at levels high enough to be effective on its own.

Alternatives

However, Nyachoti said there are other elements that can also be incorporated, including probiotics and prebiotics, the effects of which he is continuing to study.

“There has been a lot of interest in using the probiotics and prebiotics together to create a potential benefit, rather that using either one of them independently,” he said, adding that they can also be combined with feed enzymes, which can then assist in creating the short-chain carbohydrates pigs need to grow.

Egg yolk antibodies, cornstarch, lysozyme and organic acids have also proven beneficial, as have more controversial feed additives, such as blood plasma.

“Spray-dried plasma was in the news quite a bit last year, but it is actually one ingredient that we know works, and has been shown to work in baby pigs, it improves performance, it improves feed intake, and it does help prevent diarrhea problems in the piglets,” he said, but added, the additive was also implicated in the first cases of porcine epidemic diarrhea (PED).

“But that is something to talk about on another day,” said Nyachoti.

Many of these alternative feed additives are already in use in Manitoba, such as starch.

“Since we published that first paper on potato starch, there has been a lot of people who use that in the swine industry,” he said. “The industry realizes that they can actually get a benefit by including this product in baby pig diets.”

Other methods of improving piglet health and lessening the occurrence of gastrointestinal disease include low-protein diets and fermented feed.

“Fermented products do have high levels of organic acids and they can have a benefit to gut health,” Nyachoti said.

Husbandry

But to achieve good piglet health, and raise healthy pigs, husbandry methods also have to be re-examined.

“I think if we took the approach that you start clean and you stay clean, you can already go a long way in helping these pigs stay healthy, then they do not have to need this intervention,” he said.

One production method that made Nyachoti’s list of possible changes was outdoor pork production, although he acknowledges that isn’t likely to become a solution for Manitoba producers.

“For us, one of our biggest problems obviously is the weather, so outdoor production is probably not the way to go, but I think if we took the approach that you start clean and you stay clean, you can already go a long way in helping these pigs stay healthy, then they do not have to need this intervention,” he said.

But while he advised greater attention to husbandry methods, he didn’t go so far as to say less intensive methods were needed to prevent disease.

“Right now the way it is, there is the code of practice that says each animal needs to get so much space, and that, I think, is based on good information,” he said. “But having said that though, it’s also good to know that restriction in space does lead to stress and that can also compromise the health of an animal, but I think that what the industry is using, the code of practice, is determined as being sufficient.”

In the end, producers will likely need to use a combination of alternative feed additives, in addition to re-evaluating husbandry practices, to completely move away from the use of antibiotics as growth promotants.

“Yes the cost of production might go up a little bit,” he said. “But you can still competitively produce livestock.”

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While prebiotics have a similar intention to probiotics they do not contain the actual micro-organisms, rather substances which have been extracted from fermentation vats where selected microbes have been grown. They are indicated to help “feed” the beneficial intestinal microflora. Although the mechanism of action for probiotics and prebiotics is poorly described, it is thought they support or enrich the populations of beneficial microbes in the horse’s hind gut and thus improve digestive health.

The health of horses is highly dependent upon a thriving population of essential microbes in the hind gut that produce enzymes necessary to digest or break down plant fibre. Their presence is absolutely crucial to the horse, as horses themselves lack these vital enzymes.

Byproducts of the fermentation process provide the horse with energy and micronutrients. When in good numbers, these microbes provide as much as 70 per cent of the horse’s energy and synthesize enough B vitamins and vitamin K to meet the horse’s needs. In exchange for this energetic and nutritional advantage billions of bacteria, yeast and protozoa are housed in the warm, moist confines of the horse’s hind gut and are provided with a steady supply of fibrous “plant food.”

It is important to understand that grass and hay are the most important prebiotics for horses as plant fibre is the ideal food source for hind gut microbes. Any departure from a steady influx of an all-forage diet is detrimental to beneficial populations of microbes and thus the health of the horse. The health of these essential microbes is ultimately dependent upon this very specific food source.

Many events in the life of a domestic horse can upset the delicate balance of the hind gut. These include an abrupt change in feed, high-grain diets, processed feeds, weaning, vaccination, deworming, stress from training and travel, changing companions, or a course of antibiotics. Illnesses such as colic, laminitis, inappetence, diarrhea, fatigue, ill-thrift, skin and hoof problems, behavioural and performance changes are often rooted in feeding and management practices which are detrimental to the health of a horse’s hind gut.

Each horse develops a highly individualized microbial population specific to their own diet, their own environment and their own biochemistry. They are virtually “supplemented” with a variety of micro-organisms while ingesting their feedstuff. Simply adding more of the ‘good’ bacteria, even if we knew for sure which ones these were, will be limited by the health of the hind gut first and foremost.

When hind gut health is not optimal the application of probiotics and prebiotics may offer temporary benefit until hind gut health is restored. If a horse is healthy, and has a healthy lifestyle, they will have a healthy hind gut and will inherently be able to support their own population of vibrant microbes.

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Researchers were looking for alternatives to antibiotics for reducing pathogens in the intestines of young pigs following the EU’s ban on using antibiotics as growth promotors in 2006.

“We found a clear reduction of E. coli strains possessing typical genes for extra-intestinal pathogenic E. coli (ExPEC),” said researcher Carmen Bednorz of Freie Universitat Berlin, Germany. The reduction was particularly noticeable in strains that adhere to the intestinal mucosa (and less so in the feces), which was “very interesting,” she says, because “ExPEC typically harbour a lot of adhesion genes that promote colonization of the mucosa.

“Our data suggest that the feeding of probiotics could substitute for antimicrobials as growth promoters,” says Bednorz. “This could help to reduce the burden of antimicrobial resistance,” she adds.

The study was published ahead of print in the journal Applied and Environmental Microbiology.

In the study, Bednorz and her collaborators compared piglets fed with E. faecium to those in a control group. They collected more than 1,400 samples of E. coli from piglets of different ages, and from different parts of the intestine.

The results suggest that E. faecium inhibits pathogenic E. coli from becoming attached to the intestinal mucosa.

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