This week, we have broken down a research paper written in January 2026: 'Complete Extruded Diet: How does Equine fecal microbiota change during intake adaptation? ' (Franzan et al.) So that you can stay up to recent research on gut microbiota and the practical applications for your own horses.
Background & Objectives
With a combination of climate change and decreased land available for grazing affecting forage availability, plus storage difficulties associated with bulk buying preserved forage for many horses, alternative dietary strategies are becoming increasingly common.
Low fibre intakes combined with high starch and sugar grain-based diets are known to have adverse effects for the gut microbiota, along many other aspects of gastro-intestinal health and wellbeing. With that in mind, many companies have created high-fibre concentrates to meet daily nutritional requirements. A Complete Extruded Diet (CED) is defined by the National Research Council as “the combination of all nutrients to supply the nutritional category requirements in a single product, except water”.
Such feeds have been used for a long time in specific situations such as supporting weight gain in weaned foals, improving nutritional intake in horse with dental issues or following clinical events related to gastro-intestinal disorders. While there has been a lot of research in recent years exploring the links between the diet and gut microbiota, the specific effects of a CED on the gut microbiota haven’t yet been explored in detail.
What they did
A group of twelve geldings, averaging 4.4 years old and all weighing approximately 370kgs, were split into two groups.
Group one had a diet of hay only, while the second group had the same hay for the first 30 days, then 70% hay and 30% concentrate from days 7-14, 40% hay and 60% concentrate from day 14 to day 21, and lastly 100% CED from day 21 until the end of the trial on day 28. Both groups were offered 2.5% of their bodyweight per day on a dry matter basis.
At the end of each 7-day period, faecal samples were taken from each horse. The bacteria were extracted and identified so that the researchers could compare their abundance and diversity to build a picture of how the gut microbial community adapted as the diet changed.
The bacteria from the faecal material was also put into test tubes with either the hay of CED for 48 hours to measure gas production during that time, and at the end the pH (acidity) and how much of each feed’s dry matter and organic matter had broken down. This was to get an indication of how well the bacteria from each group could ferment the different feeds.
The CED was given in three equal amounts at 6am, midday, and 6pm.
None of the horses were reported to have any gastro-intestinal issues during the trial, although nothing is mentioned about whether the consistency of the horse’s droppings changed in any way during the trial. The researchers didn’t mention whether the horses all finished their hay and/or feeds.
What they found
The microbiota changed as the diet changed in the CED group, although the biggest change was only noted in the final week when hay was completely removed from the diet. Some bacterial groups, including Fibrobacteres decreased when hay was removed completely during the last week of the test, while others, including Verrucomicrobia and Synergistetes decreased. However, we don’t yet know enough about the microbiota to comment on whether those changes are likely to have any health implications for the horses.
The results from the lab fermentation studies, bacteria taken from the hay only group showed greater fermentation capacity when hay was tested, and the bacteria from the CED fed group showed the same. The researchers concluded that the changes observed in the microbiota suggested a shift towards a microbial community more specialised towards the type of feed the horses were having, which mirrors previous research. After the 48 hour testing period the pH of the test tubes was measured, and those with the bacteria from the CED group showed a drop in pH after 14 days. However, it should be mentioned that this result was from the lab study, the pH of the horses’ hindgut was not measured directly.
Practical takeaways
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Maintaining a source of forage in the diet – The biggest microbial shifts were seen once hay was completely removed from the diet, so maintaining a source of forage even if, technically, the horse is receiving all of it’s nutrients from a complete feed is still important.
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When changing feeds, forage types, or introducing more feeds that are marketed as partial forage replacers (as many of us might have to do this winter) it’s important to make the changes slowly. Don’t wait until the hay barn is already empty before swapping to a new forage source; thinking ahead and introducing new bucket feeds will help make the hay last longer, and is likely to benefit the horse’s hindgut as well.
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We need to consider what we’re putting into the horse, but also how that affects fermentation. This was a short study, only 28 days, so it’s important to keep an eye on droppings and signs of hindgut health such as bloating or discomfort as the diet changes.
Reviewers Comments
The findings of this study are broadly consistent with our existing understanding of how the gut microbiota adapts to, and specialises in response to, the diet.
Although the most substantial changes in microbial composition were observed when hay was completely removed from the complete extruded diet (CED) group, I would be cautious about drawing firm conclusions from this finding alone. It would have been valuable to investigate how the microbiota responded if the horses had remained on the 40% hay and 60% CED diet for a longer period. One week may not be sufficient for the full effects of a dietary change to become apparent. Therefore, it would be premature to conclude that the observed changes occurred specifically as a result of the complete removal of hay. It is possible that similar changes might have emerged had the horses remained on the 40:60 diet for longer, as the microbial community continued to adapt.
A further consideration is that, although the authors state that the CED was offered at 06:00, 12:00 and 18:00, they do not report how long the horses took to consume each meal. Hay was provided ad libitum, but the time required to consume the CED could have influenced the horses' overall feeding behaviour and the duration of periods without feed intake. If the CED was consumed within one or two hours of being offered, horses may still have experienced extended periods overnight without anything available to chew, even while hay remained part of the ration. This is relevant because chewing stimulates saliva production, which helps buffer gastric acid. Prolonged periods without eating can therefore increase the risk of gastric ulceration and may have wider implications for gastrointestinal health. Furthermore, previous research has demonstrated that replacing a high-fibre diet with one containing greater amounts of non-fibre carbohydrates can contribute to a more acidic hindgut environment, which was the case with the nutritional content of the CED compared to the hay.
Consequently, it is difficult to determine whether the changes in microbial composition and the differences in pH observed during the laboratory fermentation experiments resulted primarily from the increased proportion of non-fibre carbohydrates in the CED, the complete removal of hay during the final week, or differences in feeding patterns and the duration of periods without feed intake. These factors may have interacted, and the study design does not allow their individual contributions to be distinguished confidently. Further investigation, including a longer adaptation period at the 40:60 hay-to-CED ratio and more detailed monitoring of feed intake and feeding behaviour, would help clarify these relationships.
Conclusion
Given that many UK horse owners are likely to need to think about partial forage replacers this winter due to the poor harvest, this paper does give some pointers of things to think about. Overall, it reinforces the idea that we need to think about making dietary changes gradually, so in the context of the likely hay shortage this winter, we need to have contingency plans in place while we still have hay available. We also need to think about what we’re using as complete or partial forage replacers, to ensure that the horse is still receiving an adequate fibre intake, and also the time it takes to eat that forage replacer as we don’t want to leave horses for long periods of time overnight without anything to chew on due to the risk of ulcers and other potential gastrointestinal upsets.
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