Linkage between the intestinal microbiota and residual feed intake in broiler chickens

Abstract Background Intestinal 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. Methods To 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. Results No 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. Conclusions Our 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.

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Exploring a Possible Link between the Intestinal Microbiota and Feed Efficiency in Pigs

Applied and Environmental Microbiology ◽

10.1128/aem.00380-17 ◽

2017 ◽

Vol 83 (15) ◽

Cited By ~ 116

Author(s):

Ursula M. McCormack ◽

Tânia Curião ◽

Stefan G. Buzoianu ◽

Maria L. Prieto ◽

Tomas Ryan ◽

...

Keyword(s):

Microbial Diversity ◽

Intestinal Microbiota ◽

Feed Intake ◽

Feed Efficiency ◽

Residual Feed Intake ◽

Production Costs ◽

Microbiota Composition ◽

Content Type ◽

Intestinal Microbes ◽

Pig Production

ABSTRACT Feed efficiency (FE) is critical in pig production for both economic and environmental reasons. As the intestinal microbiota plays an important role in energy harvest, it is likely to influence FE. Therefore, our aim was to characterize the intestinal microbiota of pigs ranked as low, medium, and high residual feed intake ([RFI] a metric for FE), where genetic, nutritional, and management effects were minimized, to explore a possible link between the intestinal microbiota and FE. Eighty-one pigs were ranked according to RFI between weaning and day 126 postweaning, and 32 were selected as the extremes in RFI (12 low, 10 medium, and 10 high). Intestinal microbiota diversity, composition, and predicted functionality were assessed by 16S rRNA gene sequencing. Although no differences in microbial diversity were found, some RFI-associated compositional differences were revealed, principally among members of Firmicutes, predominantly in feces at slaughter (albeit mainly for low-abundance taxa). In particular, microbes associated with a leaner and healthier host (e.g., Christensenellaceae, Oscillibacter, and Cellulosilyticum) were enriched in low RFI (more feed-efficient) pigs. Differences were also observed in the ileum of low RFI pigs; most notably, Nocardiaceae (Rhodococcus) were less abundant. Predictive functional analysis suggested improved metabolic capabilities in these animals, especially within the ileal microbiota. Higher ileal isobutyric acid concentrations were also found in low RFI pigs. Overall, the differences observed within the intestinal microbiota of low RFI pigs compared with that of their high RFI counterparts, albeit relatively subtle, suggest a possible link between the intestinal microbiota and FE in pigs. IMPORTANCE This study is one of the first to show that differences in intestinal microbiota composition, albeit subtle, may partly explain improved feed efficiency (FE) in low residual feed intake (RFI) pigs. One of the main findings is that, although microbial diversity did not differ among animals of varying FE, specific intestinal microbes could potentially be linked with porcine FE. However, as the factors impacting FE are still not fully understood, intestinal microbiota composition may not be a major factor determining differences in FE. Nonetheless, this work has provided a potential set of microbial biomarkers for FE in pigs. Although culturability could be a limiting factor and intervention studies are required, these taxa could potentially be targeted in the future to manipulate the intestinal microbiome so as to improve FE in pigs. If successful, this has the potential to reduce both production costs and the environmental impact of pig production.

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Porcine Feed Efficiency-Associated Intestinal Microbiota and Physiological Traits: Finding Consistent Cross-Locational Biomarkers for Residual Feed Intake

mSystems ◽

10.1128/msystems.00324-18 ◽

2019 ◽

Vol 4 (4) ◽

Cited By ~ 10

Author(s):

Ursula M. McCormack ◽

Tânia Curião ◽

Barbara U. Metzler-Zebeli ◽

Elizabeth Magowan ◽

Donagh P. Berry ◽

...

Keyword(s):

Intestinal Microbiota ◽

Feed Intake ◽

Feed Efficiency ◽

Sampling Site ◽

Geographic Location ◽

Residual Feed Intake ◽

Physiological Traits ◽

Associated Bacteria ◽

Geographic Locations ◽

Rearing Environment

ABSTRACT Optimal feed efficiency (FE) in pigs is important for economic and environmental reasons. Previous research identified FE-associated bacterial taxa within the intestinal microbiota of growing pigs. This study investigated whether FE-associated bacteria and selected FE-associated physiological traits were consistent across geographic locations (Republic of Ireland [ROI] [two batches of pigs, ROI1 and ROI2], Northern Ireland [NI], and Austria [AT]), where differences in genetic, dietary, and management factors were minimized. Pigs (n = 369) were ranked, within litter, on divergence in residual feed intake (RFI), and 100 extremes were selected (50 with high RFI and 50 with low RFI) across geographic locations for intestinal microbiota analysis using 16S rRNA amplicon sequencing and examination of FE-associated physiological parameters. Microbial diversity varied by geographic location and intestinal sampling site but not by RFI rank, except in ROI2, where more-feed-efficient pigs had greater ileal and cecal diversity. Although none of the 188 RFI-associated taxonomic differences found were common to all locations/batches, Lentisphaerae, Ruminococcaceae, RF16, Mucispirillum, Methanobrevibacter, and two uncultured genera were more abundant within the fecal or cecal microbiota of low-RFI pigs in two geographic locations and/or in both ROI batches. These are major contributors to carbohydrate metabolism, which was reflected in functional predictions. Fecal volatile fatty acids and salivary cortisol were the only physiological parameters that differed between RFI ranks. Despite controlling genetics, diet specification, dietary phases, and management practices in each rearing environment, the rearing environment, encompassing maternal influence, herd health status, as well as other factors, appears to impact intestinal microbiota more than FE. IMPORTANCE Interest in the role of intestinal microbiota in determining FE in pigs has increased in recent years. However, it is not known if the same FE-associated bacteria are found across different rearing environments. In this study, geographic location and intestinal sampling site had a greater influence on the pig gut microbiome than FE. This presents challenges when aiming to identify consistent reliable microbial biomarkers for FE. Nonetheless, seven FE-associated microbial taxa were common across two geographic locations and/or two batches within one location, and these indicated a potentially “healthier” and metabolically more capable microbiota in more-feed-efficient pigs. These taxa could potentially be employed as biomarkers for FE, although bacterial consortia, rather than individual taxa, may be more likely to predict FE. They may also merit consideration for use as probiotics or could be targeted by dietary means as a strategy for improving FE in pigs in the future.

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RAPID COMMUNICATION: Residual feed intake in beef cattle is associated with differences in protein turnover and nutrient transporters in ruminal epithelium

Journal of Animal Science ◽

10.1093/jas/skz080 ◽

2019 ◽

Vol 97 (5) ◽

pp. 2181-2187

Author(s):

Ahmed A Elolimy ◽

Emad Abdel-Hamied ◽

Liangyu Hu ◽

Joshua C McCann ◽

Daniel W Shike ◽

...

Keyword(s):

Amino Acid ◽

Beef Cattle ◽

Protein Degradation ◽

Insulin Signaling ◽

Feed Intake ◽

Feed Efficiency ◽

Protein Turnover ◽

Residual Feed Intake ◽

Ubiquitin Proteasome ◽

Ruminal Epithelium

Abstract Residual feed intake (RFI) is a widely used measure of feed efficiency in cattle. Although the precise biologic mechanisms associated with improved feed efficiency are not well-known, most-efficient steers (i.e., with low RFI coefficient) downregulate abundance of proteins controlling protein degradation in skeletal muscle. Whether cellular mechanisms controlling protein turnover in ruminal tissue differ by RFI classification is unknown. The aim was to investigate associations between RFI and signaling through the mechanistic target of rapamycin (MTOR) and ubiquitin-proteasome pathways in ruminal epithelium. One hundred and forty-nine Red Angus cattle were allocated to 3 contemporary groups according to sex and herd origin. Animals were offered a finishing diet for 70 d to calculate the RFI coefficient for each. Within each group, the 2 most-efficient (n = 6) and least-efficient animals (n = 6) were selected. Compared with least-efficient animals, the most-efficient animals consumed less feed (P < 0.05; 18.36 vs. 23.39 kg/d DMI). At day 70, plasma samples were collected for insulin concentration analysis. Ruminal epithelium was collected immediately after slaughter to determine abundance and phosphorylation status of 29 proteins associated with MTOR, ubiquitin-proteasome, insulin signaling, and glucose and amino acid transport. Among the proteins involved in cellular protein synthesis, most-efficient animals had lower (P ≤ 0.05) abundance of MTOR, p-MTOR, RPS6KB1, EIF2A, EEF2K, AKT1, and RPS6KB1, whereas MAPK3 tended (P = 0.07) to be lower. In contrast, abundance of p-EEF2K, p-EEF2K:EEF2K, and p-EIF2A:EIF2A in most-efficient animals was greater (P ≤ 0.05). Among proteins catalyzing steps required for protein degradation, the abundance of UBA1, NEDD4, and STUB1 was lower (P ≤ 0.05) and MDM2 tended (P = 0.06) to be lower in most-efficient cattle. Plasma insulin and ruminal epithelium insulin signaling proteins did not differ (P > 0.05) between RFI groups. However, abundance of the insulin-responsive glucose transporter SLC2A4 and the amino acid transporters SLC1A3 and SLC1A5 also was lower (P ≤ 0.05) in most-efficient cattle. Overall, the data indicate that differences in signaling mechanisms controlling protein turnover and nutrient transport in ruminal epithelium are components of feed efficiency in beef cattle.

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146 Survey of residual feed intake in Katahdin and Texel lambs in a feedlot environment

Journal of Animal Science ◽

10.1093/jas/skz397.177 ◽

2020 ◽

Vol 98 (Supplement_2) ◽

pp. 75-76

Author(s):

Camren l Maierle ◽

Andrew R Weaver ◽

Eugene Felton ◽

Scott P Greiner ◽

Scott A Bowdridge

Keyword(s):

Feed Intake ◽

Feed Efficiency ◽

Large Scale ◽

Residual Feed Intake ◽

Production Traits ◽

Meaningful Improvement ◽

Average Intake ◽

Test Population ◽

Feeding Trials ◽

Genetic Evaluations

Abstract Residual feed intake (RFI) is quickly becoming the preferred measurement of efficiency in many species due to its inherent independence of most other important production traits. Making meaningful improvement in feed efficiency of sheep will require a consistent methodology to accurately identify efficient individuals. Due to difficulty in measuring this trait efforts must be made to incorporate efficiency data in large-scale genetic evaluations. The aim of this study was to evaluate lambs in a feedlot with large-scale genetic evaluations for feed efficiency calculated by residual feed intake (RFI) utilizing a Growsafe™ system. RFI was calculated by subtracting expected intake from actual intake. Expected intake was determined by regressing metabolic body size of mid-test weight. Regression determined ADG on actual intake for individuals in the population. Texel (n = 58) and Katahdin (n = 118) lambs were placed in a feedlot and fed in separate feeding trials, a complete pellet ad libitum as the sole source of nutrition. In this environment Texel and Katahdin lambs had expected ADG values (0.27 kg/day, 0.32 kg/day respectively) and actual intake data (2154.17 g/day, 1909.33 g/day respectively. After a period of adaptation, Texel average intake was determined over a period of 27 consecutive days and used to calculate individual RFI within the test population. Observable ranges of RFI (-0.62 – +0.62) were seen in the Texel lambs. At the start of the Katahdin trial lambs were separated by sex and FEC treatment. After a period of adaptation, Katahdin average intake was determined over a period of 42 consecutive days and used to calculate individual RFI within the test population. Observable ranges of RFI (-0.53 – +0.50) were seen in the Katahdin lambs as well. In both feeding trials RFI appeared to be normally distributed. Use of this technology may be useful in identifying superior individuals for feed efficiency.

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Genetic parameters and breed differences for feed efficiency, growth, and body composition traits of young beef bulls

Canadian Journal of Animal Science ◽

10.4141/a03-085 ◽

2004 ◽

Vol 84 (2) ◽

pp. 177-185 ◽

Cited By ~ 124

Author(s):

F. S. Schenkel ◽

S. P. Miller ◽

J. W. Wilton

Keyword(s):

Body Composition ◽

Genetic Correlation ◽

Feed Intake ◽

Feed Efficiency ◽

Fixed Effects ◽

Residual Feed Intake ◽

Backfat Thickness ◽

Daily Weight Gain ◽

Feed Conversion ◽

Beef Bulls

Genetic associations between feed efficiency, growth, and live ultrasound measured body composition traits were studied in purebred beef bulls of six breeds in Ontario bull test stations from 1991 to 2000. Feed traits included average daily feed intake (FI), feed conversion ratio (FCR), and residual feed intake [feed intake adjusted for production alone (RFIp) or production and backfat thickness (RFIb)]. Growth traits were average daily weight gain (ADG), mid-test metabolic weight (MW), hip height (HH), and scrotal circumference (SC). Body composition traits included ultrasound backfat thickness (BF), longissimus muscle area (LMA), and predicted percentage of intramuscular fat (IFAT). Bulls were measured every 28 d for weight and individual feed intake, and at the end of test for ultrasound body composition traits. Number of records per trait ranged from 2284 (FI) to 13 319 (ADG). Fixed effects of test group, breed and end of test age (within breed), and random effects of animal and herd of origin were modeled using REML bivariate analyses for all traits. Heritability estimates were moderate for all traits (0.30 to 0.55), except for IFAT (0.14). The genetic correlation between RFIp and RFIb was high (0.99) within breeds, but breeds ranked differently with respect to RFIp and RFIb. Genetic correlations of RFIb with ADG and backfat thickness were essentially zero, which indicate that selection on residual feed intake could be implemented to reduce feed intake and improve feed conversion without compromising growth or changing levels of subcutaneous fat. Key words: Central test, genetic correlation, heritability, residual feed intake

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Claw health and feed efficiency as new selection criteria in the Czech Holstein cattle Krupová Z., Wolfová M., Krupa E., Přibyl J., Zavadilová L.

Czech Journal of Animal Science ◽

10.17221/44/2018-cjas ◽

2018 ◽

Vol 63 (No. 10) ◽

pp. 408-418 ◽

Cited By ~ 1

Author(s):

Z. Krupová ◽

M. Wolfová ◽

E. Krupa ◽

J. Přibyl ◽

L. Zavadilová

Keyword(s):

Feed Intake ◽

Feed Efficiency ◽

Disease Incidence ◽

Selection Index ◽

Residual Feed Intake ◽

Selection Response ◽

Holstein Cattle ◽

Breeding Objective ◽

Economic Weights ◽

The Impact

The objective of this study was to calculate economic weights for ten current breeding objective traits and for four new traits characterising claw health and feed efficiency in Czech Holstein cattle and to investigate the impact of different selection indices on the genetic responses for these traits. Economic weights were estimated using a bio-economic model, while applying actual (2017) and predicted (2025) production and economic circumstances. For the actual situation, the economic weights of claw disease incidence were –100.1 € per case, and those of daily residual feed intake in cows, breeding heifers, and fattened animals were –79.37, –37.16, and –6.33 €/kg dry matter intake per day, respectively. In the predicted situation, the marginal economic weights for claw disease and feed efficiency traits increased on average by 38% and 20%, respectively. The new traits, claw disease incidence and daily residual feed intake, were gradually added to the 17 current Holstein selection index traits to improve the new traits. Constructing a comprehensive index with 21 traits and applying the general principles of the selection index theory, a favourable annual genetic selection response was obtained for the new traits (–0.008 cases of claw disease incidence and –0.006 kg of daily residual feed intake across all cattle categories), keeping the annual selection response of the most important current breeding objective traits at a satisfactory level (e.g., 73 kg of milk yield per lactation, 0.016% of milk fat). Claw health and feed efficiency should be defined as new breeding objectives and new selection index traits of local dairy population.

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Spectral analysis of feeding patterns of steers divergent in residual feed intake

Australian Journal of Experimental Agriculture ◽

10.1071/ea08021 ◽

2008 ◽

Vol 48 (7) ◽

pp. 843 ◽

Cited By ~ 8

Author(s):

Robin Dobos ◽

Robert Herd

Keyword(s):

Spectral Analysis ◽

Feed Intake ◽

Feed Efficiency ◽

Feeding Behaviour ◽

Feeding Rate ◽

Residual Feed Intake ◽

Selection Line ◽

Feeding Patterns ◽

Time Spent Feeding ◽

Efficient Selection

Spectral analysis was used to quantify differences in feeding patterns of Angus steers genetically divergent in residual feed intake (RFI). Forty-two low RFI (more efficient) and 28 high RFI (less efficient) selection line steers were fed a feedlot diet through electronic feeders for 72 days. Mean (±s.e.) daily feed intake was 11.9 ± 0.076 and 12.7 ± 0.095 kg dry matter/day over the 72-day feeding period for low and high RFI steers, respectively. The high RFI steers exhibited different temporal cycles to the low RFI steers in daily feed intake and time spent feeding. However, patterns of number of eating sessions, feeding rate, the time spent eating and the number of eating sessions were similar. Further analysis of daily (24 h) feeding behaviour is required to help improve our understanding of the association between feeding behaviour and feed efficiency.

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