Harnessing the Microbiome to Increase Animal Feed Efficiency

A major advance in food production has been the gradual improvement in animal feed efficiency seen over the last decades. Using an example from the poultry industry, modern commercial broilers require half as much feed for the same gain in weight as they did in the 1950s.1 This feed efficiency increase is primarily from animal breeding programs designed to select for animals with low maintenance energy needs. More recently, the microbiome has been identified as a novel target for improving animal feed efficiency.

Feed efficiency is an important factor in both the profitability and sustainability of livestock production facilities. When feed conversion is high, animals require less feed to put on weight, or produce eggs or milk. Feed costs are a large part of costs for farmers, so improving feed conversion directly improves financials for farmers. Better feed conversion also means that animals produce less waste and the environmental “footprint” is reduced. 

The gut microbiome of livestock plays a crucial role in feed conversion. Gut microbial fermentation converts feed to nutrients that are used by the animal. The fermentation products are influenced by the type of microbes present, the type of feed, and factors such as genetics and the age of the animal. There are also indirect effects related to improved immunity: healthy animals put on weight efficiently. What do we know now about how the microbiome affects feed conversion and how to boost feed efficiency for livestock?


The cornerstone of efficient feed conversion in cattle, sheep and other ruminants is the rumen. As the primary organ responsible for the conversion of feed to nutrients that the animal can use, there is considerable focus on rumen fermentation to increase yields and feed efficiency. Feed costs are the largest variable cost in beef production. New genomics techniques present an opportunity to understand better how the ruminant microbiome contributes to feed conversion so that it can be steered towards higher yields.

In one extensive study that investigated differences in the rumen microbiome of beef cattle in the context of feed conversion efficiency and weight gain, several interesting differences were found between high-yielding and low-yielding groups.2 In particular, animals with a higher daily bodyweight gain had a significantly higher proportion of Firmicutes phylum bacteria. Interestingly, a higher relative abundance of Firmicutes in humans is associated with obesity, a result of more efficient production of short chain fatty acids from dietary fibre, which increases the available energy content of the diet.3 Firmicutes was also positively associated with weight gain in meat goats.4 Similar results were found in a study of dairy cattle: milk fat content increased in animals with a higher proportion of Firmicutes, therefore increasing milk yield.5 Changing the macronutrient composition of the ruminant diet was able to favourably change the composition of the rumen microbiota towards a higher Firmicutes content,6 showing that it is plausible to modulate the rumen microbiome towards a more energy efficient profile.


In swine, microbial fermentation in the hindgut is less important than enzymatic hydrolysis in the stomach and small intestine for the release of nutrients from feed. However, the gut microbiota does play an important role in maintaining the health of the gut, and some nutrients are made available from undigested food in the cecum and large intestine by the microbiota. Feed efficiency can therefore be approached from two angles in swine: firstly, but maintaining the health of the gastrointestinal tract to avoid illnesses such as diarrhoea that wastes feed, and secondly by modifying the hindgut microbiota to increase its efficiency in releasing nutrients from feed.

The gut microbiome is a key requirement for the normal development of gut immune function, as pigs grown in a sterile environment develop atypical gut morphology and functions.7An important phase of development in piglets is weaning: profound changes to the gut microbiota occur as the animals transition from milk to solid food. This is also a time when feed efficiency can be negatively impacted by diarrhoea caused by gut microbial dysbiosis, and piglets are at risk of higher mortality around the time of weaning.8 Certain characteristic changes occur in piglets that develop diarrhoea. Prevotella, Sutterella, Campylobacter, and Fusobacteriaceae increase, while Firmicutes decreases in diarrhoeic piglets.8 Functional changes include a reduction in genes for carbohydrate metabolism and related to gut function. Several interventions that modify the gut microbiota have been shown to reduce diarrhoea and promote gut health in piglets, thereby improving feed efficiency in the early post-weaning period. For example, fermentation of feed with lactic acid bacteria reduces the pH of feed and increases Lactobacillus in the faeces of piglets.9 Inoculation of piglets with the gut microbiota of mature, healthy pigs promotes the healthy development of the post-weaning piglet microbiome.10 Careful analysis of microbiome changes in weaning piglets can identify novel interventions to reduce diarrhoeal incidence during this critical phase of development, thereby improving feed efficiency.

There are several ways that the gut microbiome can directly affect the amount of energy and nutrients that can be extracted from food by swine. Enzymes in the porcine hindgut degrade the otherwise undigestible cell wall of plants and convert to short chain fatty acids, which are used as an energy source. The microbes themselves can also be a source of amino acids, which are also required for optimal pig growth. Several studies in pigs have found differences in the microbiome of high-efficiency compared to low-efficiency animals within the same group. For example, Lactobacillus and Ruminococcus are more prevalent in animals with high feed efficiency.11 While Lactobacilli are more likely to assist in feed efficiency by maintaining a healthy gut and preventing diarrhoea, Ruminococci can efficiently convert dietary fibre to short chain fatty acids, increasing the overall accessible energy content of the diet. Further research is needed to establish how to modulate the gut microbiota to enhance feed efficiency in pigs.


Commercial broiler breeds have arisen from extensive breeding programs to produce highly feed-efficient birds with traits that are amenable to intensive production. Interestingly, this genetic selection has produced several anatomical and physiological changes in the chickens’ digestive tracts. Their upper gut is more developed, with a heavier gizzard and proventriculus, while the intestines are shorter. The retention time of feed in the upper digestive tract is longer, allowing a greater amount of time for the food to be ground to finer particles, for digestive enzymes to break down feed and for nutrients to be absorbed. In contrast to breeding work, the microbiome is currently a relatively unexplored area of research into feed conversion efficiency in poultry.

The gut microbiome of poultry potentially contributes to feed efficiency through several mechanisms. These include improvements in the health of the bird, and allowing the inclusion of feed ingredients that are lower cost but can be metabolised by the gut microbiome to improve nutrient availability. Chickens, in contrast to ruminants and swine, are fed a fairly refined diet that contains easily accessible nutrients. Historically, crude fibre intakes above 3% were considered to reduce voluntary feed intakes and reduce the feed’s digestibility.12 However, crude fibre is an inexpensive ingredient, and certain types have favourable effects on the gut microbiota that results in improvements in overall feed efficiency. The chicken microbiome could potentially be modified to increase the production of short chain fatty acids by gut bacteria, thereby increasing the harvestable energy of the feed.13

In a feeding study using a combination of a probiotic and prebiotic (Bifidobacterium animalis ssp. animalis, Lactobacillus salivarius ssp. salivarius, and Enterococcus faecium, together with fructooligosaccharides), birds treated from hatching with the synbiotic showed lower mortality and improved feed conversion. Foot pad mortality, which affects animal welfare, food intake and thus weight gain, and selling price of the chickens, was reduced.14 Characteristic changes were seen the chicken microbiome that are associated with the production of short chain fatty acids in the gut, thereby increasing harvestable energy intake and modifying the gut pH to prevent diarrheal disease.


Currently, we have some good indications that there are differences in the microbiota of high-yielding and low-yielding animals. Certain host and environmental factors can steer the microbial profile towards better feed conversion. Feed efficiency is made up of multiple components that contribute to weight gain and improvements in extracting and using the nutrients in food, therefore there are a number of potential targets for modulating the microbiome to improve the feed conversion ratio. Careful analysis of the microbiome can help identify both species and functional pathways associated with feed efficiency. During an intervention that is targeted towards the microbiome, it is essential to monitor changes in the gut microbiota of animals to establish that changes are taking place. Since the vast improvements in feed efficiency obtained over the past decades have reached a plateau, the microbiome could be the next area for optimisation in livestock production.


Experts Meeting on Microbiome & Animal Health and Performace

On Thursday October 29 BaseClear organises an online experts meeting on Microbiome & Animal Performance and Health, At this meeting industry experts from DSM Animal Nutrition & Health, BaseClear, Olmix, Alltech, Phileo by Lesaffre and Biomin will discuss animal microbiome studies and regulatory aspects. This meeting has 2 sessions of 1,5 hours themed “Microbiome link to animal health” and “Modulating the animal microbiome”. Registration is free of charge!

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