Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host.

Autor: Hess MK; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand. melanie.k.hess@gmail.com., Hodgkinson HE; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand., Hess AS; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.; Agriculture, Veterinary & Rangeland Sciences, University of Nevada-Reno, 1664 N. Virginia St. Mail stop 202, Reno, NV, 89557, USA., Zetouni L; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.; Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, The Netherlands., Budel JCC; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.; Graduate Program in Animal Science, Universidade Federal do Pará (UFPa), Castanhal, Brazil., Henry H; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand., Donaldson A; NSW Department of Primary Industries, University of New England, Armidale, 2351, Australia., Bilton TP; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand., van Stijn TC; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand., Kirk MR; AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand., Dodds KG; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand., Brauning R; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand., McCulloch AF; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand., Hickey SM; AgResearch Ltd., Ruakura Research Centre, Private Bag 3115, Hamilton, 3214, New Zealand., Johnson PL; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand., Jonker A; AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand., Morton N; Te Pūnaha Matatini, University of Auckland, Auckland, 1010, New Zealand., Hendy S; Te Pūnaha Matatini, University of Auckland, Auckland, 1010, New Zealand., Oddy VH; NSW Department of Primary Industries, University of New England, Armidale, 2351, Australia., Janssen PH; AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand., McEwan JC; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand., Rowe SJ; AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2023 Sep 18; Vol. 24 (1), pp. 551. Date of Electronic Publication: 2023 Sep 18.
DOI: 10.1186/s12864-023-09660-3
Abstrakt: Background: Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible.
Results: Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets.
Conclusions: Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual's future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.
(© 2023. BioMed Central Ltd., part of Springer Nature.)
Databáze: MEDLINE
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