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Kuster R, Staton M. Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches. BMC Bioinformatics 2024; 25:191. [PMID: 38750423 PMCID: PMC11095026 DOI: 10.1186/s12859-024-05809-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/10/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND The application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and whole metagenome sequencing approaches but has not been widely adopted as a technique. A major barrier to adoption is the lack of read simulation software built to handle characteristic features of these novel approaches. Reduced metagenomic sequencing (RMS) produces unique patterns of fragmentation per genome that are sensitive to restriction enzyme choice, and the non-uniform size selection of these fragments may introduce novel challenges to taxonomic assignment as well as relative abundance estimates. RESULTS Through the development and application of simulation software, readsynth, we compare simulated metagenomic sequencing libraries with existing RMS data to assess the influence of multiple library preparation and sequencing steps on downstream analytical results. Based on read depth per position, readsynth achieved 0.79 Pearson's correlation and 0.94 Spearman's correlation to these benchmarks. Application of a novel estimation approach, fixed length taxonomic ratios, improved quantification accuracy of simulated human gut microbial communities when compared to estimates of mean or median coverage. CONCLUSIONS We investigate the possible strengths and weaknesses of applying the RMS technique to profiling microbial communities via simulations with readsynth. The choice of restriction enzymes and size selection steps in library prep are non-trivial decisions that bias downstream profiling and quantification. The simulations investigated in this study illustrate the possible limits of preparing metagenomic libraries with a reduced representation sequencing approach, but also allow for the development of strategies for producing and handling the sequence data produced by this promising application.
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Affiliation(s)
- Ryan Kuster
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA.
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
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da Silva ÉBR, da Silva JAR, da Silva WC, Belo TS, Sousa CEL, dos Santos MRP, Neves KAL, Rodrigues TCGDC, Camargo-Júnior RNC, Lourenço-Júnior JDB. A Review of the Rumen Microbiota and the Different Molecular Techniques Used to Identify Microorganisms Found in the Rumen Fluid of Ruminants. Animals (Basel) 2024; 14:1448. [PMID: 38791665 PMCID: PMC11117383 DOI: 10.3390/ani14101448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 05/26/2024] Open
Abstract
Variations in environments, including climate, diet, and agricultural practices, significantly impact the composition and microbial activity. A profound understanding of these adaptations allows for the improvement of nutrition and ruminant production. Therefore, this review aims to compile data from the literature on the rumen microbiota and molecular techniques for identifying the different types of microorganisms from the rumen fluid of ruminants. Analyzing the literature on rumen microbiology in different ruminants is complex due to microbial interactions, influenced by the environment and nutrition of these animals. In addition, it is worth noting that the genera of protozoa and fungi most evident in the studies used in this review on the microbiology of rumen fluid were Entodinium spp. and Aspergillus spp., respectively, and Fibrobacter spp. for bacteria. About the techniques used, it can be seen that DNA extraction, amplification, and sequencing were the most cited in the studies evaluated. Therefore, this review describes what is present in the literature and provides an overview of the main microbial agents in the rumen and the molecular techniques used.
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Affiliation(s)
- Éder Bruno Rebelo da Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
| | | | - Welligton Conceição da Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
| | - Tatiane Silva Belo
- Department of Veterinary Medicine, University Center of the Amazon (UNAMA), Santarém 68010-200, Brazil; (T.S.B.); (C.E.L.S.)
| | - Carlos Eduardo Lima Sousa
- Department of Veterinary Medicine, University Center of the Amazon (UNAMA), Santarém 68010-200, Brazil; (T.S.B.); (C.E.L.S.)
| | | | | | - Thomaz Cyro Guimarães de Carvalho Rodrigues
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
| | - Raimundo Nonato Colares Camargo-Júnior
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
| | - José de Brito Lourenço-Júnior
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Federal University of Para (UFPA), Castanhal 68746-360, Brazil; (W.C.d.S.); (T.C.G.d.C.R.); (R.N.C.C.-J.); (J.d.B.L.-J.)
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Noronha GN, Hess MK, Dodds KG, Silva AGME, de Souza SM, da Silva JAR, Graças DAD, de Carvalho Rodrigues TCG, da Silva WC, da Silva ÉBR, Janssen PH, Henry HM, Rowe SJ, de Castro VCG, Lourenço-Júnior JDB. Characterization of the Ruminal Microbiome of Water Buffaloes (Bubalus bubalis) Kept in Different Ecosystems in the Eastern Amazon. Animals (Basel) 2023; 13:3858. [PMID: 38136895 PMCID: PMC10740732 DOI: 10.3390/ani13243858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/18/2023] [Accepted: 11/06/2023] [Indexed: 12/24/2023] Open
Abstract
Increasing the efficiency of rumen fermentation is one of the main ways to maximize the production of ruminants. It is therefore important to understand the ruminal microbiome, as well as environmental influences on that community. However, there are no studies that describe the ruminal microbiota in buffaloes in the Amazon. The objective of this study was to characterize the rumen microbiome of the water buffalo (Bubalus bubalis) in the eastern Amazon in the dry and rainy seasons in three grazing ecosystems: Baixo Amazonas (BA), Continente do Pará (CP), Ilha do Marajó (IM), and in a confinement system: Tomé-Açu (TA). Seventy-one crossbred male buffaloes (Murrah × Mediterranean) were used, aged between 24 and 36 months, with an average weight of 432 kg in the rainy season and 409 kg in the dry season, and fed on native or cultivated pastures. In the confinement system, the feed consisted of sorghum silage, soybean meal, wet sorghum premix, and commercial feed. Samples of the diet from each ecosystem were collected for bromatological analysis. The collections of ruminal content were carried out in slaughterhouses, with the rumen completely emptied and homogenized, the solid and liquid fractions separated, and the ruminal pH measured. DNA was extracted from the rumen samples, then sequenced using Restriction Enzyme Reduced Representation Sequencing. The taxonomic composition was largely similar between ecosystems. All 61 genera in the reference database were recognized, including members of the domains Bacteria and Archaea. The abundance of 23 bacterial genera differed significantly (p < 0.01) between the Tomé-Açu confinement and other ecosystems. Bacillus, Ruminococcus, and Bacteroides had lower abundance in samples from the Tomé-Açu system. Among the Archaea, the genus Methanomicrobium was less abundant in Tomé-Açu, while Methanosarcina was more abundant. There was a difference caused by all evaluated factors, but the diet (available or offered) was what most influenced the ruminal microbiota.
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Affiliation(s)
- Gerlane Nunes Noronha
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Melanie K. Hess
- Invermay Agriculture Centre, AgResearch, Mosgiel 9053, New Zealand; (M.K.H.); (K.G.D.); (H.M.H.); (S.J.R.)
| | - Ken G. Dodds
- Invermay Agriculture Centre, AgResearch, Mosgiel 9053, New Zealand; (M.K.H.); (K.G.D.); (H.M.H.); (S.J.R.)
| | - André Guimarães Maciel e Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Shirley Motta de Souza
- Federal Institute of Education, Science and Technology, South of Minas Gerais, Pouso Alegre 37550-000, Brazil;
| | | | - Diego Assis das Graças
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belem 66075-750, Brazil;
| | - Thomaz Cyro Guimarães de Carvalho Rodrigues
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Welligton Conceição da Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Éder Bruno Rebelo da Silva
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - Peter H. Janssen
- Grasslands Research Centre, AgResearch, Palmerston North 4410, New Zealand;
| | - Hannah M. Henry
- Invermay Agriculture Centre, AgResearch, Mosgiel 9053, New Zealand; (M.K.H.); (K.G.D.); (H.M.H.); (S.J.R.)
| | - Suzanne J. Rowe
- Invermay Agriculture Centre, AgResearch, Mosgiel 9053, New Zealand; (M.K.H.); (K.G.D.); (H.M.H.); (S.J.R.)
| | - Vinicius Costa Gomes de Castro
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
| | - José de Brito Lourenço-Júnior
- Postgraduate Program in Animal Science (PPGCAN), Institute of Veterinary Medicine, Brazilian Agricultural Research Corporation (EMBRAPA), Castanhal 68746-360, Brazil; (G.N.N.); (A.G.M.e.S.); (T.C.G.d.C.R.); (É.B.R.d.S.); (V.C.G.d.C.); (J.d.B.L.-J.)
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Hess MK, Hodgkinson HE, Hess AS, Zetouni L, Budel JCC, Henry H, Donaldson A, Bilton TP, van Stijn TC, Kirk MR, Dodds KG, Brauning R, McCulloch AF, Hickey SM, Johnson PL, Jonker A, Morton N, Hendy S, Oddy VH, Janssen PH, McEwan JC, Rowe SJ. 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. BMC Genomics 2023; 24:551. [PMID: 37723422 PMCID: PMC10506323 DOI: 10.1186/s12864-023-09660-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 09/07/2023] [Indexed: 09/20/2023] Open
Abstract
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.
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Affiliation(s)
- Melanie K Hess
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand.
| | - Hannah E Hodgkinson
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Andrew S Hess
- 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
| | - Larissa Zetouni
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
- Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, The Netherlands
| | - Juliana C C Budel
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
- Graduate Program in Animal Science, Universidade Federal do Pará (UFPa), Castanhal, Brazil
| | - Hannah Henry
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Alistair Donaldson
- NSW Department of Primary Industries, University of New England, Armidale, 2351, Australia
| | - Timothy P Bilton
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Tracey C van Stijn
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Michelle R Kirk
- AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand
| | - Ken G Dodds
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Alan F McCulloch
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Sharon M Hickey
- AgResearch Ltd., Ruakura Research Centre, Private Bag 3115, Hamilton, 3214, New Zealand
| | - Patricia L Johnson
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Arjan Jonker
- AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand
| | - Nickolas Morton
- Te Pūnaha Matatini, University of Auckland, Auckland, 1010, New Zealand
| | - Shaun Hendy
- Te Pūnaha Matatini, University of Auckland, Auckland, 1010, New Zealand
| | - V Hutton Oddy
- NSW Department of Primary Industries, University of New England, Armidale, 2351, Australia
| | - Peter H Janssen
- AgResearch Ltd., Grasslands Research Centre, Private Bag 11,008, Palmerston North, 4410, New Zealand
| | - John C McEwan
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Suzanne J Rowe
- AgResearch Ltd., Invermay Agricultural Centre, Private Bag 50034, Mosgiel, 9053, New Zealand
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5
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Boggio GM, Christensen OF, Legarra A, Meynadier A, Marie-Etancelin C. Microbiability of milk composition and genetic control of microbiota effects in sheep. J Dairy Sci 2023; 106:6288-6298. [PMID: 37474364 DOI: 10.3168/jds.2022-22948] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/28/2023] [Indexed: 07/22/2023]
Abstract
Recently, high-dimensional omics data are becoming available in larger quantities, and models have been developed that integrate them with genomics to understand in finer detail the relationship between genotype and phenotype, and thus improve the performance of genetic evaluations. Our objectives are to quantify the effect of the inclusion of microbiome data in the genetic evaluation for dairy traits in sheep, through the estimation of the heritability, microbiability, and how the microbiome effect on dairy traits decomposes into genetic and nongenetic parts. In this study we analyzed milk and rumen samples of 795 Lacaune dairy ewes. We included, as phenotype, dairy traits and milk fatty acids and proteins composition; as omics measurements, 16S rRNA rumen bacterial abundances; and as genotyping, 54K SNP chip for all ewes. Two nested genomic models were used: a first model to predict the individual contributions of the genetic and microbial abundances to phenotypes, and a second model to predict the additive genetic effect of the microbial community. In addition, microbiome-wide association studies for all dairy traits were applied using the 2,059 rumen bacterial abundances, and the genetic correlations between microbiome principal components and dairy traits were estimated. Results showed that in general the inclusion of both genetic and microbiome effect did not improve the fit of the model compared with the model with the genetic effect only. In addition, for all dairy traits the total heritability was equal to the direct heritability after fitting microbiota effects, due to a microbiability being almost zero for most dairy traits and heritability of the microbial community was very close to zero. Microbiome-wide association studies did not show operational taxonomic units with major effect for any of the dairy traits evaluated, and the genetic correlations between the first 5 principal components and dairy traits were low to moderate. So far, we can conclude that, using a substantial data set of 795 Lacaune dairy ewes, rumen bacterial abundances do not provide improved genetic evaluation for dairy traits in sheep.
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Affiliation(s)
- G Martinez Boggio
- GenPhySE, Université de Toulouse, INRAE-ENVT, 31326, Castanet-Tolosan, France.
| | - O F Christensen
- Center for Quantitative Genetics and Genomics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - A Legarra
- GenPhySE, Université de Toulouse, INRAE-ENVT, 31326, Castanet-Tolosan, France
| | - A Meynadier
- GenPhySE, Université de Toulouse, INRAE-ENVT, 31326, Castanet-Tolosan, France
| | - C Marie-Etancelin
- GenPhySE, Université de Toulouse, INRAE-ENVT, 31326, Castanet-Tolosan, France.
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Hess MK, Zetouni L, Hess AS, Budel J, Dodds KG, Henry HM, Brauning R, McCulloch AF, Hickey SM, Johnson PL, Elmes S, Wing J, Bryson B, Knowler K, Hyndman D, Baird H, McRae KM, Jonker A, Janssen PH, McEwan JC, Rowe SJ. Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits. Genet Sel Evol 2023; 55:53. [PMID: 37491204 PMCID: PMC10367317 DOI: 10.1186/s12711-023-00822-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/03/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA sequencing to predict performance traits or traits related to environmental impact, such as enteric methane emissions. Metagenome profiles were generated from 3139 rumen samples, collected from 1200 dual purpose ewes, using restriction enzyme-reduced representation sequencing (RE-RRS). Phenotypes were available for methane (CH4) and carbon dioxide (CO2) emissions, the ratio of CH4 to CH4 plus CO2 (CH4Ratio), feed efficiency (residual feed intake: RFI), liveweight at the time of methane collection (LW), liveweight at 8 months (LW8), fleece weight at 12 months (FW12) and parasite resistance measured by faecal egg count (FEC1). We estimated the proportion of phenotypic variance explained by host genetics and the rumen microbiome, as well as prediction accuracies for each of these traits. RESULTS Incorporating metagenome profiles increased the variance explained and prediction accuracy compared to fitting only genomics for all traits except for CO2 emissions when animals were on a grass diet. Combining the metagenome profile with host genotype from lambs explained more than 70% of the variation in methane emissions and residual feed intake. Predictions were generally more accurate when incorporating metagenome profiles compared to genetics alone, even when considering profiles collected at different ages (lamb vs adult), or on different feeds (grass vs lucerne pellet). A reference-free approach to metagenome profiling performed better than metagenome profiles that were restricted to capturing genera from a reference database. We hypothesise that our reference-free approach is likely to outperform other reference-based approaches such as 16S rRNA gene sequencing for use in prediction of individual animal performance. CONCLUSIONS This paper shows the potential of using RE-RRS as a low-cost, high-throughput approach for generating metagenome profiles on thousands of animals for improved prediction of economically and environmentally important traits. A reference-free approach using a microbial relationship matrix from log10 proportions of each tag normalized within cohort (i.e., the group of animals sampled at the same time) is recommended for future predictions using RE-RRS metagenome profiles.
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Affiliation(s)
- Melanie K Hess
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand.
- University of Nebraska-Lincoln, Institute of Agriculture and Natural Resources, 300 Agricultural Hall, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
| | - Larissa Zetouni
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
- Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Andrew S Hess
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
- University of Nevada, Reno, Agriculture, Veterinary & Rangeland Sciences, 1664 N. Virginia St., Mail Stop 202, Reno, NV, 89557, USA
| | - Juliana Budel
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
- Graduate Program in Animal Science, Universidade Federal do Pará (UFPa), Castanhal, Brazil
| | - Ken G Dodds
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Hannah M Henry
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Rudiger Brauning
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Alan F McCulloch
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Sharon M Hickey
- Ruakura Research Centre, AgResearch Ltd., Private Bag 3115, Hamilton, 3240, New Zealand
| | - Patricia L Johnson
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Sara Elmes
- Deer Industry New Zealand, PO Box 10702, Wellington, 6140, New Zealand
| | - Janine Wing
- Pāmu, Landcorp Farming Ltd, PO Box 5349, Wellington, 6011, New Zealand
| | - Brooke Bryson
- Woodlands Research Farm, AgResearch Ltd., 204 Woodlands-Morton Mains Road, Woodlands, 9871, New Zealand
| | - Kevin Knowler
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Dianne Hyndman
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Hayley Baird
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Kathryn M McRae
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Arjan Jonker
- Grasslands Research Centre, AgResearch Ltd., Private Bag 11008, Palmerston North, 4410, New Zealand
| | - Peter H Janssen
- Grasslands Research Centre, AgResearch Ltd., Private Bag 11008, Palmerston North, 4410, New Zealand
| | - John C McEwan
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Suzanne J Rowe
- University Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
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7
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Le Graverand Q, Marie-Etancelin C, Meynadier A, Weisbecker JL, Marcon D, Tortereau F. Predicting feed efficiency traits in growing lambs from their ruminal microbiota. Animal 2023; 17:100824. [PMID: 37224614 DOI: 10.1016/j.animal.2023.100824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/26/2023] Open
Abstract
Selecting feed-efficient sheep could improve the sustainability of this livestock production. However, most sheep breeding companies cannot afford to record feed intake to select feed-efficient animals. Past studies underlined the potential of omics data, including microbiota metabarcoding data, as proxies for feed efficiency. The study involved 277 Romane lambs from two lines divergently selected for residual feed intake (RFI). There were two objectives: check the consequences of selecting for feed efficiency over the rumen microbiota, and assess the predictive ability of the rumen microbiota for host traits. The study assessed two contrasting diets (concentrate diet and mixed diet) and two microbial groups (prokaryotes and eukaryotes). Discriminant analyses did not highlight any significant effect of sheep selection for residual feed intake on the rumen microbiota composition. Indeed, prokaryotic and eukaryotic microbiota compositions poorly discriminated the RFI lines, with averaged balanced error rates ranging from 45% to 55%. Correlations between host traits (feed efficiency and production traits) and their predictions from microbiota data varied between -0.07 and 0.56, depending on the trait, diet and sequencing. Feed intake was the most accurately predicted trait. However, predictions from fixed effects and BW were more accurate than or as accurate as predictions from the microbiota. Environmental effects can greatly affect the variability of microbiota compositions. Considering batch and environmental effects should be paramount when the predictive ability of the microbiota is assessed. This study argues why metabarcoding the rumen microbiota is not the best way to predict meat sheep production traits: fixed effects and BW were more cost-effective proxies and they led to similar or better predictive accuracies than microbiota metabarcoding (16S and 18S sequencing).
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Affiliation(s)
- Q Le Graverand
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France.
| | - C Marie-Etancelin
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France
| | - A Meynadier
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France
| | - J-L Weisbecker
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France
| | - D Marcon
- INRAE, Unité Expérimentale P3R, Domaine de la Sapinière, F-18390 Osmoy, France
| | - F Tortereau
- GenPhySE, Université de Toulouse, INRAE, ENVT, 24 Chemin de Borde-Rouge-Auzeville CS 52627, F-31326 Castanet-Tolosan, France
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8
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Effects of Dietary Nonfibrous Carbohydrate/Neutral Detergent Fiber Ratio on Methanogenic Archaea and Cellulose-Degrading Bacteria in the Rumen of Karakul Sheep: a 16S rRNA Gene Sequencing Study. Appl Environ Microbiol 2023; 89:e0129122. [PMID: 36541769 PMCID: PMC9888294 DOI: 10.1128/aem.01291-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The study was conducted to investigate the effects of dietary nonfibrous carbohydrate (NFC)/neutral detergent fiber (NDF) ratio on methanogenic archaea and cellulose-degrading bacteria in Karakul sheep by 16S rRNA gene sequencing. Twelve Karakul sheep were randomly divided into four groups, each group with three replicates, and they were fed with four dietary NFC/NDF ratios at 0.54, 0.96, 1.37, and 1.90 as groups 1, 2, 3, and 4, respectively. The experiment lasted for four periods: I (1 to 18 days), II (19 to 36 days), III (37 to 54 days), and IV (55 to 72 days); during each period, rumen contents were collected before morning feeding to investigate on methanogenic archaea and cellulose-degrading bacteria. The results showed that with an increase in dietary NFC/NDF ratio, the number of rumen archaea operational taxonomic units and the diversity of archaea decrease. The most dominant methanogens did not change with dietary NFC/NDF ratio and prolongation of experimental periods. Methanobrevibacter was the most dominant genus. At the species level, the relative abundance of Methanobrevibacter ruminantium first increased and then decreased when the NFC/NDF ratio increased. When the dietary NFC/NDF ratio was 0.96, the structure of archaea was largely changed, and the relative abundance of Fibrobacter sp. strain UWCM, Ruminococcus flavefaciens, and Ruminococcus albus were the highest. When the dietary NFC/NDF ratio was 1.37, the relative abundance of Butyrivibrio fibrisolvens was higher than for other groups. Based on all the data, we concluded that a dietary NFC/NDF ratio of ca. 0.96 to 1.37 was a suitable ratio to support optimal sheep production. IMPORTANCE CH4 produced by ruminants aggravates the greenhouse effect and cause wastage of feed energy, and CH4 emissions are related to methanogens. According to the current literature, there is a symbiotic relationship between methanogens and cellulolytic bacteria, so reducing methane will inevitably affect the degradation of fiber materials. This experiment used 16S rRNA gene high-throughput sequencing technology to explore the balance relationship between methanogens and cellulolytic bacteria for the first time through a long-term feeding period. The findings provide fundamental data, supporting for the diet structures with potential to reduce CH4 emission.
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9
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Genomic insights into the physiology of Quinella, an iconic uncultured rumen bacterium. Nat Commun 2022; 13:6240. [PMID: 36266280 PMCID: PMC9585023 DOI: 10.1038/s41467-022-34013-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/11/2022] [Indexed: 12/25/2022] Open
Abstract
Quinella is a genus of iconic rumen bacteria first reported in 1913. There are no cultures of these bacteria, and information on their physiology is scarce and contradictory. Increased abundance of Quinella was previously found in the rumens of some sheep that emit low amounts of methane (CH4) relative to their feed intake, but whether Quinella contributes to low CH4 emissions is not known. Here, we concentrate Quinella cells from sheep rumen contents, extract and sequence DNA, and reconstruct Quinella genomes that are >90% complete with as little as 0.20% contamination. Bioinformatic analyses of the encoded proteins indicate that lactate and propionate formation are major fermentation pathways. The presence of a gene encoding a potential uptake hydrogenase suggests that Quinella might be able to use free hydrogen (H2). None of the inferred metabolic pathways is predicted to produce H2, a major precursor of CH4, which is consistent with the lower CH4 emissions from those sheep with high abundances of this bacterium.
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10
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Marshall C, Beck M, Garrett K, Castillo A, Barrell G, Al-Marashdeh O, Gregorini P. The effect of feeding a mix of condensed and hydrolyzable tannins to heifers on rumen fermentation patterns, blood urea nitrogen, and amino acid profile. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Ross EM, Hayes BJ. Metagenomic Predictions: A Review 10 years on. Front Genet 2022; 13:865765. [PMID: 35938022 PMCID: PMC9348756 DOI: 10.3389/fgene.2022.865765] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Metagenomic predictions use variation in the metagenome (microbiome profile) to predict the unknown phenotype of the associated host. Metagenomic predictions were first developed 10 years ago, where they were used to predict which cattle would produce high or low levels of enteric methane. Since then, the approach has been applied to several traits and species including residual feed intake in cattle, and carcass traits, body mass index and disease state in pigs. Additionally, the method has been extended to include predictions based on other multi-dimensional data such as the metabolome, as well to combine genomic and metagenomic information. While there is still substantial optimisation required, the use of metagenomic predictions is expanding as DNA sequencing costs continue to fall and shows great promise particularly for traits heavily influenced by the microbiome such as feed efficiency and methane emissions.
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12
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Budel JCC, Hess MK, Bilton TP, Henry H, Dodds KG, Janssen PH, McEwan JC, Rowe SJ. Low-cost sample preservation methods for high-throughput processing of rumen microbiomes. Anim Microbiome 2022; 4:39. [PMID: 35668514 PMCID: PMC9171989 DOI: 10.1186/s42523-022-00190-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background The use of rumen microbial community (RMC) profiles to predict methane emissions has driven interest in ruminal DNA preservation and extraction protocols that can be processed cheaply while also maintaining or improving DNA quality for RMC profiling. Our standard approach for preserving rumen samples, as defined in the Global Rumen Census (GRC), requires time-consuming pre-processing steps of freeze drying and grinding prior to international transportation and DNA extraction. This impedes researchers unable to access sufficient funding or infrastructure. To circumvent these pre-processing steps, we investigated three methods of preserving rumen samples for subsequent DNA extraction, based on existing lysis buffers Tris-NaCl-EDTA-SDS (TNx2) and guanidine hydrochloride (GHx2), or 100% ethanol. Results Rumen samples were collected via stomach intubation from 151 sheep at two time-points 2 weeks apart. Each sample was separated into four subsamples and preserved using the three preservation methods and the GRC method (n = 4 × 302). DNA was extracted and sequenced using Restriction Enzyme-Reduced Representation Sequencing to generate RMC profiles. Differences in DNA yield, quality and integrity, and sequencing metrics were observed across the methods (p < 0.0001). Ethanol exhibited poorer quality DNA (A260/A230 < 2) and more failed samples compared to the other methods. Samples preserved using the GRC method had smaller relative abundances in gram-negative genera Anaerovibrio, Bacteroides, Prevotella, Selenomonas, and Succiniclasticum, but larger relative abundances in the majority of 56 additional genera compared to TNx2 and GHx2. However, log10 relative abundances across all genera and time-points for TNx2 and GHx2 were on average consistent (R2 > 0.99) but slightly more variable compared to the GRC method. Relative abundances were moderately to highly correlated (0.68 ± 0.13) between methods for samples collected within a time-point, which was greater than the average correlation (0.17 ± 0.11) between time-points within a preservation method. Conclusions The two modified lysis buffers solutions (TNx2 and GHx2) proposed in this study were shown to be viable alternatives to the GRC method for RMC profiling in sheep. Use of these preservative solutions reduces cost and improves throughput associated with processing and sequencing ruminal samples. This development could significantly advance implementation of RMC profiles as a tool for breeding ruminant livestock. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00190-z.
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Affiliation(s)
- Juliana C C Budel
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand.,Graduate Program in Animal Science, Federal University of Pará, UFPA, Castanhal, 68740-970, Brazil
| | - Melanie K Hess
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Timothy P Bilton
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand.
| | - Hannah Henry
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Ken G Dodds
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Peter H Janssen
- Grasslands Research Centre, AgResearch Ltd., Private Bag 11008, Palmerston North, 4410, New Zealand
| | - John C McEwan
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
| | - Suzanne J Rowe
- Invermay Agricultural Centre, AgResearch Ltd., Private Bag 50034, Mosgiel, 9053, New Zealand
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13
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Sun Z, Huang S, Zhu P, Tzehau L, Zhao H, Lv J, Zhang R, Zhou L, Niu Q, Wang X, Zhang M, Jing G, Bao Z, Liu J, Wang S, Xu J. Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M. Genome Biol 2022; 23:36. [PMID: 35078506 PMCID: PMC8789378 DOI: 10.1186/s13059-021-02576-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
Abstract
AbstractMicrobiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based or whole-metagenome sequencing approaches. Here, we introduce 2bRAD-M, a highly reduced and cost-effective strategy which only sequences ~ 1% of metagenome and can simultaneously produce species-level bacterial, archaeal, and fungal profiles. 2bRAD-M can accurately generate species-level taxonomic profiles for otherwise hard-to-sequence samples with merely 1 pg of total DNA, high host DNA contamination, or severely fragmented DNA from degraded samples. Tests of 2bRAD-M on various stool, skin, environmental, and clinical FFPE samples suggest a successful reconstruction of comprehensive, high-resolution microbial profiles.
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14
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Asselstine V, Lam S, Miglior F, Brito LF, Sweett H, Guan L, Waters SM, Plastow G, Cánovas A. The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies. J Anim Sci 2021; 99:6377879. [PMID: 34586400 PMCID: PMC8480417 DOI: 10.1093/jas/skab193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Ruminant supply chains contribute 5.7 gigatons of CO2-eq per annum, which represents approximately 80% of the livestock sector emissions. One of the largest sources of emission in the ruminant sector is methane (CH4), accounting for approximately 40% of the sectors total emissions. With climate change being a growing concern, emphasis is being put on reducing greenhouse gas emissions, including those from ruminant production. Various genetic and environmental factors influence cattle CH4 production, such as breed, genetic makeup, diet, management practices, and physiological status of the host. The influence of genetic variability on CH4 yield in ruminants indicates that genomic selection for reduced CH4 emissions is possible. Although the microbiology of CH4 production has been studied, further research is needed to identify key differences in the host and microbiome genomes and how they interact with one another. The advancement of “-omics” technologies, such as metabolomics and metagenomics, may provide valuable information in this regard. Improved understanding of genetic mechanisms associated with CH4 production and the interaction between the microbiome profile and host genetics will increase the rate of genetic progress for reduced CH4 emissions. Through a systems biology approach, various “-omics” technologies can be combined to unravel genomic regions and genetic markers associated with CH4 production, which can then be used in selective breeding programs. This comprehensive review discusses current challenges in applying genomic selection for reduced CH4 emissions, and the potential for “-omics” technologies, especially metabolomics and metagenomics, to minimize such challenges. The integration and evaluation of different levels of biological information using a systems biology approach is also discussed, which can assist in understanding the underlying genetic mechanisms and biology of CH4 production traits in ruminants and aid in reducing agriculture’s overall environmental footprint.
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Affiliation(s)
- Victoria Asselstine
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Stephanie Lam
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.,Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Hannah Sweett
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Leluo Guan
- Livestock Gentec, Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, T6G 2C8, Canada
| | - Sinead M Waters
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, T6G 2C8, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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15
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Snipen L, Angell IL, Rognes T, Rudi K. Reduced metagenome sequencing for strain-resolution taxonomic profiles. MICROBIOME 2021; 9:79. [PMID: 33781324 PMCID: PMC8008692 DOI: 10.1186/s40168-021-01019-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/02/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. RESULTS We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. CONCLUSION We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS . Video abstract.
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Affiliation(s)
- Lars Snipen
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Inga-Leena Angell
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, P.O. Box 1080, Blindern, NO-0316 Oslo, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
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Knap PW, Doeschl-Wilson A. Why breed disease-resilient livestock, and how? Genet Sel Evol 2020; 52:60. [PMID: 33054713 PMCID: PMC7557066 DOI: 10.1186/s12711-020-00580-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Fighting and controlling epidemic and endemic diseases represents a considerable cost to livestock production. Much research is dedicated to breeding disease resilient livestock, but this is not yet a common objective in practical breeding programs. In this paper, we investigate how future breeding programs may benefit from recent research on disease resilience. MAIN BODY We define disease resilience in terms of its component traits resistance (R: the ability of a host animal to limit within-host pathogen load (PL)) and tolerance (T: the ability of an infected host to limit the damage caused by a given PL), and model the host's production performance as a reaction norm on PL, depending on R and T. Based on this, we derive equations for the economic values of resilience and its component traits. A case study on porcine respiratory and reproductive syndrome (PRRS) in pigs illustrates that the economic value of increasing production in infectious conditions through selection for R and T can be more than three times higher than by selection for production in disease-free conditions. Although this reaction norm model of resilience is helpful for quantifying its relationship to its component traits, its parameters are difficult and expensive to quantify. We consider the consequences of ignoring R and T in breeding programs that measure resilience as production in infectious conditions with unknown PL-particularly, the risk that the genetic correlation between R and T is unfavourable (antagonistic) and that a trade-off between them neutralizes the resilience improvement. We describe four approaches to avoid such antagonisms: (1) by producing sufficient PL records to estimate this correlation and check for antagonisms-if found, continue routine PL recording, and if not found, shift to cheaper proxies for PL; (2) by selection on quantitative trait loci (QTL) known to influence both R and T in favourable ways; (3) by rapidly modifying towards near-complete resistance or tolerance, (4) by re-defining resilience as the animal's capacity to resist (or recover from) the perturbation caused by an infection, measured as temporal deviations of production traits in within-host longitudinal data series. CONCLUSIONS All four alternatives offer promising options for genetic improvement of disease resilience, and most rely on technological and methodological developments and innovation in automated data generation.
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Affiliation(s)
| | - Andrea Doeschl-Wilson
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush Estate, Edinburgh, EH25 9RG Scotland, UK
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17
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Brito LF, Oliveira HR, McConn BR, Schinckel AP, Arrazola A, Marchant-Forde JN, Johnson JS. Large-Scale Phenotyping of Livestock Welfare in Commercial Production Systems: A New Frontier in Animal Breeding. Front Genet 2020; 11:793. [PMID: 32849798 PMCID: PMC7411239 DOI: 10.3389/fgene.2020.00793] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Genomic breeding programs have been paramount in improving the rates of genetic progress of productive efficiency traits in livestock. Such improvement has been accompanied by the intensification of production systems, use of a wider range of precision technologies in routine management practices, and high-throughput phenotyping. Simultaneously, a greater public awareness of animal welfare has influenced livestock producers to place more emphasis on welfare relative to production traits. Therefore, management practices and breeding technologies in livestock have been developed in recent years to enhance animal welfare. In particular, genomic selection can be used to improve livestock social behavior, resilience to disease and other stress factors, and ease habituation to production system changes. The main requirements for including novel behavioral and welfare traits in genomic breeding schemes are: (1) to identify traits that represent the biological mechanisms of the industry breeding goals; (2) the availability of individual phenotypic records measured on a large number of animals (ideally with genomic information); (3) the derived traits are heritable, biologically meaningful, repeatable, and (ideally) not highly correlated with other traits already included in the selection indexes; and (4) genomic information is available for a large number of individuals (or genetically close individuals) with phenotypic records. In this review, we (1) describe a potential route for development of novel welfare indicator traits (using ideal phenotypes) for both genetic and genomic selection schemes; (2) summarize key indicator variables of livestock behavior and welfare, including a detailed assessment of thermal stress in livestock; (3) describe the primary statistical and bioinformatic methods available for large-scale data analyses of animal welfare; and (4) identify major advancements, challenges, and opportunities to generate high-throughput and large-scale datasets to enable genetic and genomic selection for improved welfare in livestock. A wide variety of novel welfare indicator traits can be derived from information captured by modern technology such as sensors, automatic feeding systems, milking robots, activity monitors, video cameras, and indirect biomarkers at the cellular and physiological levels. The development of novel traits coupled with genomic selection schemes for improved welfare in livestock can be feasible and optimized based on recently developed (or developing) technologies. Efficient implementation of genetic and genomic selection for improved animal welfare also requires the integration of a multitude of scientific fields such as cell and molecular biology, neuroscience, immunology, stress physiology, computer science, engineering, quantitative genomics, and bioinformatics.
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Affiliation(s)
- Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Betty R. McConn
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Allan P. Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Aitor Arrazola
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | | | - Jay S. Johnson
- USDA-ARS Livestock Behavior Research Unit, West Lafayette, IN, United States
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