Abstract
BackgroundIntestinal microbiota plays a key role in nutrient digestion and utilization with a profound impact on feed efficiency of livestock animals. However, the intestinal microbes that are critically involved in feed efficiency remain elusive.MethodsTo identify intestinal bacteria associated with residual feed intake (RFI) in chickens, male Cobb broiler chicks were individually housed from day 14 to day 35. Individual RFI values were calculated for 56 chickens. Luminal contents were collected from the ileum, cecum, and cloaca of each animal on day 35. Bacterial DNA was isolated and subjected to 16S rRNA gene sequencing. Intestinal microbiota was classified to the feature level using Deblur and QIIME 2. High and low RFI groups were formed by selecting 15 and 17 chickens with the most extreme RFI values for subsequent LEfSe comparison of the difference in the microbiota. Spearman correlation analysis was further performed to identify correlations between the intestinal microbiota composition and RFI.ResultsNo significant difference in evenness, richness, and overall diversity of the microbiota in the ileum, cecum, or cloaca was observed between high and low RFI chickens. However, LEfSe analysis revealed a number of bacterial features being differentially enriched in either high or low RFI chickens. Spearman correlation analysis further identified many differentially enriched bacterial features to be significantly correlated with RFI (P < 0.05). Importantly, not all short-chain fatty acid (SCFA) producers showed a positive association with RFI. While two novel members of Oscillibacter and Butyricicoccus were more abundant in low-RFI, high-efficiency chickens, several other SCFA producers such as Subdoligranulum variabile and two related Peptostreptococcaceae members were negatively associated with feed efficiency. Moreover, a few closely-related Lachnospiraceae family members showed a positive correlation with feed efficiency, while others of the same family displayed an opposite relationship.ConclusionsOur results highlight the complexity of the intestinal microbiota and a need to differentiate the bacteria to the species, subspecies, and even strain levels in order to reveal their true association with feed efficiency. Identification of RFI-associated bacteria provides important leads to manipulate the intestinal microbiota for improving production efficiency, profitability, and sustainability of poultry production.
Highlights
Feed accounts for up to 70% of the costs in broiler production [1]
Sixteen animals were excluded because of subtle health issues or our inability to extract a sufficient quantity or quality of bacterial DNA for sequencing. Those 56 chickens that were retained displayed a large variation in feed efficiency with the residual feed intake (RFI) values ranging from − 379.9 to 483.1 (Fig. 1a)
Sequences were further denoised by Deblur, and the reads present in < 5% of samples were removed, resulting in a total of 551 bacterial features
Summary
Feed accounts for up to 70% of the costs in broiler production [1]. Maximizing feed efficiency is paramount to ensuring the profitability and sustainability of the industry. In livestock production, feed efficiency is generally measured by feed conversion ratio (FCR) or residual feed intake (RFI). FCR is defined as the ratio of feed intake to weight gain, with lower FCR values indicating higher efficiency. RFI is defined as the difference between actual measured feed intake and expected feed intake of an animal accounting for its maintenance requirement, where expected feed intake is calculated based on average feed intake and weight grain of a group of animals [2, 3]. Similar to FCR, a lower RFI value indicates higher efficiency. Unlike FCR, which measures the ratio of two biological traits (feed intake and growth rate), RFI measures feed efficiency independent of body weight, mature size, or growth rate [2, 4]. The intestinal microbes that are critically involved in feed efficiency remain elusive
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