1
|
Al Makishah NH, Elfarash AE. Molecular characterization of cellulase genes in Pseudomonas stutzeri. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
2
|
Hart EH, Christofides SR, Davies TE, Rees Stevens P, Creevey CJ, Müller CT, Rogers HJ, Kingston-Smith AH. Forage grass growth under future climate change scenarios affects fermentation and ruminant efficiency. Sci Rep 2022; 12:4454. [PMID: 35292703 PMCID: PMC8924208 DOI: 10.1038/s41598-022-08309-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 02/21/2022] [Indexed: 11/25/2022] Open
Abstract
With an increasing human population access to ruminant products is an important factor in global food supply. While ruminants contribute to climate change, climate change could also affect ruminant production. Here we investigated how the plant response to climate change affects forage quality and subsequent rumen fermentation. Models of near future climate change (2050) predict increases in temperature, CO2, precipitation and altered weather systems which will produce stress responses in field crops. We hypothesised that pre-exposure to altered climate conditions causes compositional changes and also primes plant cells such that their post-ingestion metabolic response to the rumen is altered. This “stress memory” effect was investigated by screening ten forage grass varieties in five differing climate scenarios, including current climate (2020), future climate (2050), or future climate plus flooding, drought or heat shock. While varietal differences in fermentation were detected in terms of gas production, there was little effect of elevated temperature or CO2 compared with controls (2020). All varieties consistently showed decreased digestibility linked to decreased methane production as a result of drought or an acute flood treatment. These results indicate that efforts to breed future forage varieties should target tolerance of acute stress rather than long term climate.
Collapse
Affiliation(s)
- Elizabeth H Hart
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3FG, UK
| | - Sarah R Christofides
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Teri E Davies
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3FG, UK
| | - Pauline Rees Stevens
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3FG, UK
| | | | - Carsten T Müller
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Hilary J Rogers
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, Wales, SY23 3FG, UK.
| |
Collapse
|
3
|
Theoretical Methane Emission Estimation from Volatile Fatty Acids in Bovine Rumen Fluid. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11167730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Methane production from livestock farming is recognized as an important contributor to global GHGs. Volatile fatty acids (VFAs) found in bovine rumen may be utilized as a substrate for methanogens to form CH4, and thus improvement of quantitative VFA measurements can help facilitate greater understanding and mitigation of CH4 production. This study aims to contribute to the development of more accurate methods for the quantification and specification of VFAs in bovine rumen. The VFAs were analyzed using the conventional method and an alternative catalytic esterification reaction (CER) method. Substantial differences in the detected concentrations of the C3+ VFAs (chain length ≥ 3) were observed between both methods, especially for butyric acid. Evaluation of the sensitivity of both methods to detecting the VFA concentrations in standard solutions confirmed that the values resulting from the CER method were closer to the known concentrations of the standard solution than those from the conventional method. The results of this study provide the first quantitative proof to show the improved accuracy of the measurements of C3+ VFAs when using the CER method compared with the conventional method. Therefore, the CER method can be recommended to analyze the VFAs found in rumen, especially butyric acid and other C3+ VFAs.
Collapse
|
4
|
Huws SA, Edwards JE, Lin W, Rubino F, Alston M, Swarbreck D, Caim S, Stevens PR, Pachebat J, Won MY, Oyama LB, Creevey CJ, Kingston-Smith AH. Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches. MICROBIOME 2021; 9:143. [PMID: 34154659 PMCID: PMC8215763 DOI: 10.1186/s40168-021-01087-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/02/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. RESULTS Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be 'cheating' in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. CONCLUSIONS In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants. Video Abstract.
Collapse
Affiliation(s)
- Sharon A Huws
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland, UK.
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK.
| | - Joan E Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK
- Laboratory of Microbiology, Wageningen University & Research, 6708, Wageningen, WE, Netherlands
- Current work address: Palital Feed Additives, Velddriel, Netherlands
| | - Wanchang Lin
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK
| | - Francesco Rubino
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland, UK
| | | | | | | | - Pauline Rees Stevens
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK
| | - Justin Pachebat
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK
| | - Mi-Young Won
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland, UK
| | - Linda B Oyama
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland, UK
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK
| | - Christopher J Creevey
- Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, Northern Ireland, UK
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3FG, UK
| |
Collapse
|
5
|
Patel M, Patel HM, Vohra N, Dave S. Complete genome sequencing and comparative genome characterization of the lignocellulosic biomass degrading bacterium Pseudomonas stutzeri MP4687 from cattle rumen. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00530. [PMID: 32983925 PMCID: PMC7498857 DOI: 10.1016/j.btre.2020.e00530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 11/18/2022]
Abstract
We report the complete genome sequencing of novel Pseudomonas stutzeri strain MP4687 isolated from cattle rumen. Various strains of P. stutzeri have been reported from different environmental samples including oil-contaminated sites, crop roots, air, and human clinical samples, but not from rumen samples, which is being reported here for the first time. The genome of P. stutzeri MP4687 has a single replicon, 4.75 Mb chromosome and a G + C content of 63.45%. The genome encodes for 4,790 protein coding genes including 164 CAZymes and 345 carbohydrate processing genes. The isolate MP4687 harbors LCB hydrolyzing potential through endoglucanase (4.5 U/mL), xylanase (3.1 U/mL), β-glucosidase (3.3 U/mL) and β-xylosidase (1.9 U/mL) activities. The pangenome analysis further revealed that MP4687 has a very high number of unique genes (>2100) compared to other P. stutzeri genomes, which might have an important role in rumen functioning.
Collapse
Affiliation(s)
- Maulik Patel
- Department of Biotechnology, Hemchandracharya North Gujarat University, Patan, 384265, Gujarat, India
- Laboratory of Renewable Resources Engineering and Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, 47906, IN, United States
- Corresponding author at: Laboratory of Renewable Resources Engineering and Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, 47906, IN, United States
| | - Hiral M. Patel
- P.G. Department of Biosciences, Vadtal Road, Sardar Patel University, Bakrol, 388315, Anand, Gujarat, India
| | - Nasim Vohra
- Anand Agricultural University, Anand, 388110, Gujarat, India
| | - Sanjay Dave
- Department of Biotechnology, Hemchandracharya North Gujarat University, Patan, 384265, Gujarat, India
| |
Collapse
|
6
|
Kamau S, Belanche A, Davies T, Rees Stevens P, Humphreys M, Kingston‐Smith AH. A route to decreasing N pollution from livestock: Use of Festulolium hybrids improves efficiency of N flows in rumen simulation fermenters. Food Energy Secur 2020; 9:e209. [PMID: 32999716 PMCID: PMC7507801 DOI: 10.1002/fes3.209] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/12/2020] [Accepted: 04/29/2020] [Indexed: 11/30/2022] Open
Abstract
Ruminant agriculture suffers from inefficient capture of forage protein and consequential release of N pollutants to land. This is due to proteolysis in the rumen catalyzed by both microbial but initially endogenous plant proteases. Plant breeding-based solutions are sought to minimize these negative environmental impacts. The aim of this study was to perform an integrated study of rumen N metabolism using semi-continuous rumen simulation fermenters (Rusitec) to explore the extent to which swards containing Festulolium populations (interspecific hybrids between Lolium and Festuca grass species) with decreased rates of endogenous protein degradation conferred advantageous protein utilization in comparison with a National Listed perennial ryegrass. An in vitro experiment was conducted using three Festulolium hybrids (Lolium perenne × Festuca arundinacea var. glaucescens, LpFg; Lolium perenne × Festuca mairei, LpFm; and Lolium multiflorum × Festuca arundinacea var. glaucescens, LmFg) and a Lolium perenne, Lp control. LpFm and LmFg demonstrated significantly lower plant-mediated proteolysis than the control. Fresh forage was incubated in Rusitec with rumen fluid from four donor cows. Feed disappearance and production of gas, methane, and volatile fatty acids were similar across cultivars. Whereas no differences in microbial protein synthesis were noted across treatments during early fermentation (0-6 hr after feeding), an increased microbial N flow in LpFm (+30%) and LmFg hybrids (+41%) was observed during late fermentation (6-24 hr after feeding), with higher overall microbial N flows (+13.5% and + 20.2%, respectively) compared with the control (Lp). We propose an underpinning mechanism involving the partitioning of amino acid catabolism toward branched-chain amino acids and microbial protein synthesis in grasses with slow plant-mediated proteolysis instead of accumulation of rumen ammonia in grasses with fast plant-mediated proteolysis. These observations indicate the potential of Festulolium hybrids with a slow plant-mediated proteolysis trait to improve the efficiency of capture of forage protein and decrease the release of N pollutants onto the land.
Collapse
Affiliation(s)
- Stephen Kamau
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Alejandro Belanche
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
- Estacion Experimental del Zaidín (CSIC)GranadaSpain
| | - Teri Davies
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Pauline Rees Stevens
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Mike Humphreys
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Alison H. Kingston‐Smith
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| |
Collapse
|
7
|
Huws SA, Creevey CJ, Oyama LB, Mizrahi I, Denman SE, Popova M, Muñoz-Tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan SJ, Yáñez-Ruiz DR, Belanche A, Guan L, Gruninger RJ, McAllister TA, Newbold CJ, Roehe R, Dewhurst RJ, Snelling TJ, Watson M, Suen G, Hart EH, Kingston-Smith AH, Scollan ND, do Prado RM, Pilau EJ, Mantovani HC, Attwood GT, Edwards JE, McEwan NR, Morrisson S, Mayorga OL, Elliott C, Morgavi DP. Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future. Front Microbiol 2018; 9:2161. [PMID: 30319557 PMCID: PMC6167468 DOI: 10.3389/fmicb.2018.02161] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/23/2018] [Indexed: 12/24/2022] Open
Abstract
The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in “omic” data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.
Collapse
Affiliation(s)
- Sharon A Huws
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Linda B Oyama
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Milka Popova
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Rafael Muñoz-Tamayo
- UMR Modélisation Systémique Appliquée aux Ruminants, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Evelyne Forano
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sinead M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Grange, Ireland
| | - Matthias Hess
- College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Ilma Tapio
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Hauke Smidt
- Department of Agrotechnology and Food Sciences, Wageningen, Netherlands
| | - Sophie J Krizsan
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - David R Yáñez-Ruiz
- Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Alejandro Belanche
- Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Leluo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Robert J Gruninger
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Tim A McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | - Rainer Roehe
- Scotland's Rural College, Edinburgh, United Kingdom
| | | | - Tim J Snelling
- The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Mick Watson
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies (R(D)SVS), University of Edinburgh, Edinburgh, United Kingdom
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Elizabeth H Hart
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Nigel D Scollan
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Rodolpho M do Prado
- Laboratório de Biomoléculas e Espectrometria de Massas-Labiomass, Departamento de Química, Universidade Estadual de Maringá, Maringá, Brazil
| | - Eduardo J Pilau
- Laboratório de Biomoléculas e Espectrometria de Massas-Labiomass, Departamento de Química, Universidade Estadual de Maringá, Maringá, Brazil
| | | | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Joan E Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Neil R McEwan
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Steven Morrisson
- Sustainable Livestock, Agri-Food and Bio-Sciences Institute, Hillsborough, United Kingdom
| | - Olga L Mayorga
- Colombian Agricultural Research Corporation, Mosquera, Colombia
| | - Christopher Elliott
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Diego P Morgavi
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| |
Collapse
|
8
|
Hart EH, Creevey CJ, Hitch T, Kingston-Smith AH. Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria. Sci Rep 2018; 8:10504. [PMID: 30002438 PMCID: PMC6043501 DOI: 10.1038/s41598-018-28827-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/29/2018] [Indexed: 11/17/2022] Open
Abstract
The rumen is a complex ecosystem. It is the primary site for microbial fermentation of ingested feed allowing conversion of a low nutritional feed source into high quality meat and milk products. However, digestive inefficiencies lead to production of high amounts of environmental pollutants; methane and nitrogenous waste. These inefficiencies could be overcome by development of forages which better match the requirements of the rumen microbial population. Although challenging, the application of meta-proteomics has potential for a more complete understanding of the rumen ecosystem than sequencing approaches alone. Here, we have implemented a meta-proteomic approach to determine the association between taxonomies of microbial sources of the most abundant proteins in the rumens of forage-fed dairy cows, with taxonomic abundances typical of those previously described by metagenomics. Reproducible proteome profiles were generated from rumen samples. The most highly abundant taxonomic phyla in the proteome were Bacteriodetes, Firmicutes and Proteobacteria, which corresponded with the most abundant taxonomic phyla determined from 16S rRNA studies. Meta-proteome data indicated differentiation between metabolic pathways of the most abundant phyla, which is in agreement with the concept of diversified niches within the rumen microbiota.
Collapse
Affiliation(s)
- E H Hart
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3FG, UK
| | - C J Creevey
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3FG, UK
| | - T Hitch
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3FG, UK
| | - A H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3FG, UK.
| |
Collapse
|
9
|
Belanche A, Newbold CJ, Lin W, Rees Stevens P, Kingston-Smith AH. A Systems Biology Approach Reveals Differences in the Dynamics of Colonization and Degradation of Grass vs. Hay by Rumen Microbes with Minor Effects of Vitamin E Supplementation. Front Microbiol 2017; 8:1456. [PMID: 28824585 PMCID: PMC5541034 DOI: 10.3389/fmicb.2017.01456] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/18/2017] [Indexed: 11/29/2022] Open
Abstract
Increasing the efficiency of utilization of fresh and preserved forage is a key target for ruminant science. Vitamin E is often used as additive to improve product quality but its impact of the rumen function is unknown. This study investigated the successional microbial colonization of ryegrass (GRA) vs. ryegrass hay (HAY) in presence of zero or 50 IU/d supplementary vitamin E, using a rumen simulation technique. A holistic approach was used to link the dynamics of feed degradation with the structure of the liquid-associated (LAB) and solid-associated bacteria (SAB). Results showed that forage colonization by SAB was a tri-phasic process highly affected by the forage conservation method: Early colonization (0-2 h after feeding) by rumen microbes was 2× faster for GRA than HAY diets and dominated by Lactobacillus and Prevotella which promoted increased levels of lactate (+56%) and ammonia (+18%). HAY diets had lower DM degradation (-72%) during this interval being Streptococcus particularly abundant. During secondary colonization (4-8 h) the SAB community increased in size and decreased in diversity as the secondary colonizers took over (Pseudobutyrivibrio) promoting the biggest differences in the metabolomics profile between diets. Secondary colonization was 3× slower for HAY vs. GRA diets, but this delay was compensated by a greater bacterial diversity (+197 OTUs) and network complexity resulting in similar feed degradations. Tertiary colonization (>8 h) consisted of a slowdown in the colonization process and simplification of the bacterial network. This slowdown was less evident for HAY diets which had higher levels of tertiary colonizers (Butyrivibrio and Ruminococcus) and may explain the higher DM degradation (+52%) during this interval. The LAB community was particularly active during the early fermentation of GRA and during the late fermentation for HAY diets indicating that the availability of nutrients in the liquid phase reflects the dynamics of feed degradation. Vitamin E supplementation had minor effects but promoted a simplification of the LAB community and a slight acceleration in the SAB colonization sequence which could explain the higher DM degradation during the secondary colonization. Our findings suggest that when possible, grass should be fed instead of hay, in order to accelerate feed utilization by rumen microbes.
Collapse
Affiliation(s)
- Alejandro Belanche
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
- Estacion Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Charles J. Newbold
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Wanchang Lin
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Pauline Rees Stevens
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Alison H. Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| |
Collapse
|
10
|
Mayorga OL, Kingston-Smith AH, Kim EJ, Allison GG, Wilkinson TJ, Hegarty MJ, Theodorou MK, Newbold CJ, Huws SA. Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria. Front Microbiol 2016; 7:1854. [PMID: 27917166 PMCID: PMC5114307 DOI: 10.3389/fmicb.2016.01854] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/03/2016] [Indexed: 11/24/2022] Open
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.
Collapse
Affiliation(s)
- Olga L Mayorga
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Eun J Kim
- Department of Animal Science, Kyungpook National University Sangju, Korea
| | - Gordon G Allison
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Toby J Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Matthew J Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Michael K Theodorou
- Department of Animal Production, Welfare and Veterinary Sciences, Harper Adams University Newport, UK
| | - Charles J Newbold
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| | - Sharon A Huws
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University Aberystwyth, UK
| |
Collapse
|
11
|
Hart EH, Onime LA, Davies TE, Morphew RM, Kingston-Smith AH. The effects of PPO activity on the proteome of ingested red clover and implications for improving the nutrition of grazing cattle. J Proteomics 2016; 141:67-76. [PMID: 27109346 PMCID: PMC4881418 DOI: 10.1016/j.jprot.2016.04.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/24/2016] [Accepted: 04/15/2016] [Indexed: 12/16/2022]
Abstract
UNLABELLED Increasing the rumen-stable protein content of feed would lead to improved nitrogen utilisation in cattle, and less nitrogenous waste. Red clover (Trifolium pratense L.) is a high protein ruminant feed containing high polyphenol oxidase (PPO) activity. PPO mediated protein-quinone binding has been linked to protecting plant proteins from proteolysis. To explore the mechanism underlying the effect of PPO on protein protection in fresh forage feeds, proteomic components of feed down-boli produced from wild-type red clover and a low PPO mutant, at point of ingestion and after 4h in vitro incubation with rumen inoculum were analysed. Significant differences in proteomic profiles between wild-type and mutant red clover were determined after 4h incubation, with over 50% less spots in mutant than wild-type proteomes, indicating decreased proteolysis in the latter. Protein identifications revealed preferentially retained proteins localised within the chloroplast, suggesting that PPO mediated protection in the wild-type operates due to the proximity of target proteins to the enzyme and substrates, either diffusing into this compartment from the vacuole or are present in the chloroplast. This increased understanding of protein targets of PPO indicates that wider exploitation of the trait could contribute to increased protein use efficiency in grazing cattle. BIOLOGICAL SIGNIFICANCE One of the main challenges for sustainable livestock farming is improving capture of dietary nitrogen by ruminants. Typically up to 70% of ingested protein-N is excreted representing a loss of productivity potential and a serious environmental problem in terms of nitrogenous pollution of lands and water. Identification of key characteristics of rumen-protected protein will deliver target traits for selection in forage breeding programmes. The chloroplastic enzyme PPO catalyzes the oxidation of phenols to quinones, which react with protein. Little is currently known about the intracellular protein targets of the products of PPO activity or the mechanism underlying protein complexing, including whether there is any specificity to the reaction. Here we have determined significant differences in the proteomes of freshly ingested down boli corresponding to the presence or absence of active PPO. These results show that in the presence of PPO the forage protein is less amenable to proteolysis and provide the novel information that the protected proteins are putatively chloroplastically located. These data also contribute to a growing evidence base that a chloroplastic PPO substrate exists in red clover in addition to the currently known vacuolar substrates.
Collapse
Affiliation(s)
- E H Hart
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK
| | - L A Onime
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK
| | - T E Davies
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK
| | - R M Morphew
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK
| | - A H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK.
| |
Collapse
|
12
|
Huws SA, Edwards JE, Creevey CJ, Rees Stevens P, Lin W, Girdwood SE, Pachebat JA, Kingston-Smith AH. Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass. FEMS Microbiol Ecol 2015; 92:fiv137. [PMID: 26542074 DOI: 10.1093/femsec/fiv137] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2015] [Indexed: 01/21/2023] Open
Abstract
This study investigated successional colonization of fresh perennial ryegrass (PRG) by the rumen microbiota over time. Fresh PRG was incubated in sacco in the rumens of three Holstein × Friesian cows over a period of 8 h, with samples recovered at various times. The diversity of attached bacteria was assessed using 454 pyrosequencing of 16S rRNA (cDNA). Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following rumen incubation, and that temporal colonization of the PRG by the rumen bacteria was biphasic with primary (1 and 2 h) and secondary (4-8 h) events evident with the transition period being with 2-4 h. A decrease in sequence reads pertaining to Succinivibrio spp. and increases in Pseudobutyrivibrio, Roseburia and Ruminococcus spp. (the latter all order Clostridiales) were evident during secondary colonization. Irrespective of temporal changes, the continually high abundances of Butyrivibrio, Fibrobacter, Olsenella and Prevotella suggest that they play a major role in the degradation of the plant. It is clear that a temporal understanding of the functional roles of these microbiota within the rumen is now required to unravel the role of these bacteria in the ruminal degradation of fresh PRG.
Collapse
Affiliation(s)
- Sharon A Huws
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Joan E Edwards
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Christopher J Creevey
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Pauline Rees Stevens
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Wanchang Lin
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Susan E Girdwood
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Justin A Pachebat
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| | - Alison H Kingston-Smith
- Animal and Microbial Sciences, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth SY23 3FG, UK
| |
Collapse
|
13
|
Firkins JL, Yu Z. RUMINANT NUTRITION SYMPOSIUM: How to use data on the rumen microbiome to improve our understanding of ruminant nutrition1,2. J Anim Sci 2015; 93:1450-70. [DOI: 10.2527/jas.2014-8754] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- J. L. Firkins
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| | - Z. Yu
- Department of Animal Sciences, The Ohio State University, Columbus 43210
| |
Collapse
|
14
|
Creevey CJ, Kelly WJ, Henderson G, Leahy SC. Determining the culturability of the rumen bacterial microbiome. Microb Biotechnol 2014; 7:467-79. [PMID: 24986151 PMCID: PMC4229327 DOI: 10.1111/1751-7915.12141] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/14/2014] [Accepted: 06/02/2014] [Indexed: 11/25/2022] Open
Abstract
The goal of the Hungate1000 project is to generate a reference set of rumen microbial genome sequences. Toward this goal we have carried out a meta-analysis using information from culture collections, scientific literature, and the NCBI and RDP databases and linked this with a comparative study of several rumen 16S rRNA gene-based surveys. In this way we have attempted to capture a snapshot of rumen bacterial diversity to examine the culturable fraction of the rumen bacterial microbiome. Our analyses have revealed that for cultured rumen bacteria, there are many genera without a reference genome sequence. Our examination of culture-independent studies highlights that there are few novel but many uncultured taxa within the rumen bacterial microbiome. Taken together these results have allowed us to compile a list of cultured rumen isolates that are representative of abundant, novel and core bacterial species in the rumen. In addition, we have identified taxa, particularly within the phylum Bacteroidetes, where further cultivation efforts are clearly required. This information is being used to guide the isolation efforts and selection of bacteria from the rumen microbiota for sequencing through the Hungate1000.
Collapse
Affiliation(s)
- Christopher J Creevey
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland; Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | | | | | | |
Collapse
|