Temporal metagenomic and metabolomic characterization of fresh perennial ryegrass degradation by rumen bacteria

Olga L Mayorga, Alison H Kingston-Smith, Eun J Kim, Gordon G Allison, Toby J Wilkinson, Matthew J Hegarty, Michael K Theodorou, Charles J Newbold, Sharon A Huws

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Abstract

Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR). Metagenomic Rapid Annotation using Subsystem Technology (MG-RAST) taxonomical analysis of shotgun metagenomic sequences showed that the genera Butyrivibrio, Clostridium, Eubacterium, Prevotella, and Selenomonas dominated the attached microbiome irrespective of time. MG-RAST also showed that Acidaminococcus, Bacillus, Butyrivibrio, and Prevotella rDNA increased in read abundance during secondary colonization, whilst Blautia decreased in read abundance. MG-RAST Clusters of Orthologous Groups (COG) functional analysis also showed that the primary function of the attached microbiome was categorized broadly within "metabolism;" predominantly amino acid, carbohydrate, and lipid metabolism and transport. Most sequence read abundances (51.6, 43.8, and 50.0% of COG families pertaining to amino acid, carbohydrate and lipid metabolism, respectively) within these categories were higher in abundance during secondary colonization. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis confirmed that the PRG-attached microbiota present at 1 and 4 h of rumen incubation possess a similar functional capacity, with only a few pathways being uniquely found in only one incubation time point only. FT-IR data for the plant residues also showed that the main changes in plant chemistry between primary and secondary colonization was due to increased carbohydrate, amino acid, and lipid metabolism. This study confirmed primary and secondary colonization events and supported the hypothesis that functional changes occurred as a consequence of taxonomical changes. Sequences within the carbohydrate metabolism COG families contained only 3.2% of cellulose activities, on average across both incubation times (1 and 4 h), suggesting that degradation of the plant cell walls may be a key rate-limiting factor in ensuring the bioavailability of intra-plant nutrients in a timely manner to the microbes and ultimately the animal. This suggests that a future focus for improving ruminant nutrient use efficiency should be altering the recalcitrant plant cell wall components and/or improving the cellulolytic capacity of the rumen microbiota.

Original languageEnglish
Article number1854
JournalFrontiers in Microbiology
Volume7
DOIs
Publication statusPrint publication - Nov 2016
Externally publishedYes

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Metagenomics
Lolium
Metabolomics
Microbiota
Rumen
Bacteria
Carbohydrate Metabolism
Butyrivibrio
Lipid Metabolism
Prevotella
Firearms
Plant Cells
Ruminants
Technology
Amino Acids
Food
Cell Wall
Acidaminococcus
Selenomonas
Encyclopedias

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Mayorga, O. L., Kingston-Smith, A. H., Kim, E. J., Allison, G. G., Wilkinson, T. J., Hegarty, M. J., ... Huws, S. A. (2016). Temporal metagenomic and metabolomic characterization of fresh perennial ryegrass degradation by rumen bacteria. Frontiers in Microbiology, 7, [1854]. https://doi.org/10.3389/fmicb.2016.01854
Mayorga, Olga L ; Kingston-Smith, Alison H ; Kim, Eun J ; Allison, Gordon G ; Wilkinson, Toby J ; Hegarty, Matthew J ; Theodorou, Michael K ; Newbold, Charles J ; Huws, Sharon A. / Temporal metagenomic and metabolomic characterization of fresh perennial ryegrass degradation by rumen bacteria. In: Frontiers in Microbiology. 2016 ; Vol. 7.
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Mayorga, OL, Kingston-Smith, AH, Kim, EJ, Allison, GG, Wilkinson, TJ, Hegarty, MJ, Theodorou, MK, Newbold, CJ & Huws, SA 2016, 'Temporal metagenomic and metabolomic characterization of fresh perennial ryegrass degradation by rumen bacteria', Frontiers in Microbiology, vol. 7, 1854. https://doi.org/10.3389/fmicb.2016.01854

Temporal metagenomic and metabolomic characterization of fresh perennial ryegrass degradation by rumen bacteria. / Mayorga, Olga L; Kingston-Smith, Alison H; Kim, Eun J; Allison, Gordon G; Wilkinson, Toby J; Hegarty, Matthew J; Theodorou, Michael K; Newbold, Charles J; Huws, Sharon A.

In: Frontiers in Microbiology, Vol. 7, 1854, 11.2016.

Research output: Contribution to journalArticle

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AU - Mayorga, Olga L

AU - Kingston-Smith, Alison H

AU - Kim, Eun J

AU - Allison, Gordon G

AU - Wilkinson, Toby J

AU - Hegarty, Matthew J

AU - Theodorou, Michael K

AU - Newbold, Charles J

AU - Huws, Sharon A

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AB - Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR). Metagenomic Rapid Annotation using Subsystem Technology (MG-RAST) taxonomical analysis of shotgun metagenomic sequences showed that the genera Butyrivibrio, Clostridium, Eubacterium, Prevotella, and Selenomonas dominated the attached microbiome irrespective of time. MG-RAST also showed that Acidaminococcus, Bacillus, Butyrivibrio, and Prevotella rDNA increased in read abundance during secondary colonization, whilst Blautia decreased in read abundance. MG-RAST Clusters of Orthologous Groups (COG) functional analysis also showed that the primary function of the attached microbiome was categorized broadly within "metabolism;" predominantly amino acid, carbohydrate, and lipid metabolism and transport. Most sequence read abundances (51.6, 43.8, and 50.0% of COG families pertaining to amino acid, carbohydrate and lipid metabolism, respectively) within these categories were higher in abundance during secondary colonization. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis confirmed that the PRG-attached microbiota present at 1 and 4 h of rumen incubation possess a similar functional capacity, with only a few pathways being uniquely found in only one incubation time point only. FT-IR data for the plant residues also showed that the main changes in plant chemistry between primary and secondary colonization was due to increased carbohydrate, amino acid, and lipid metabolism. This study confirmed primary and secondary colonization events and supported the hypothesis that functional changes occurred as a consequence of taxonomical changes. Sequences within the carbohydrate metabolism COG families contained only 3.2% of cellulose activities, on average across both incubation times (1 and 4 h), suggesting that degradation of the plant cell walls may be a key rate-limiting factor in ensuring the bioavailability of intra-plant nutrients in a timely manner to the microbes and ultimately the animal. This suggests that a future focus for improving ruminant nutrient use efficiency should be altering the recalcitrant plant cell wall components and/or improving the cellulolytic capacity of the rumen microbiota.

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