16S rDNA library-based analysis of ruminal bacterial diversity

Edwards, Joan E.; McEwan, Neil R.; Travis, Anthony J.; Wallace, Robert John

doi:10.1023/b:anto.0000047942.69033.24

Cited by 224 publications

(191 citation statements)

References 47 publications

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“…Similar to other ecosystems, the number of microbial species isolated and characterised from the rumen is low. It is estimated that less than 15% of rumen bacteria can be cultured using standard techniques (Teather, 2001;Edwards et al, 2004), highlighting the importance of molecular biology approaches to sidestep this limitation and study the rumen system in toto. The huge diversity of species in the rumen means that cultivation-based methods are simply not suited to follow changes in community structure, even if all the species could be cultured.…”

Section: The Ruminant Superorganismmentioning

confidence: 99%

Rumen microbial (meta)genomics and its application to ruminant production

Morgavi

Kelly

Janssen

et al. 2013

Animal

209

163

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Meat and milk produced by ruminants are important agricultural products and are major sources of protein for humans. Ruminant production is of considerable economic value and underpins food security in many regions of the world. However, the sector faces major challenges because of diminishing natural resources and ensuing increases in production costs, and also because of the increased awareness of the environmental impact of farming ruminants. The digestion of feed and the production of enteric methane are key functions that could be manipulated by having a thorough understanding of the rumen microbiome. Advances in DNA sequencing technologies and bioinformatics are transforming our understanding of complex microbial ecosystems, including the gastrointestinal tract of mammals. The application of these techniques to the rumen ecosystem has allowed the study of the microbial diversity under different dietary and production conditions. Furthermore, the sequencing of genomes from several cultured rumen bacterial and archaeal species is providing detailed information about their physiology. More recently, metagenomics, mainly aimed at understanding the enzymatic machinery involved in the degradation of plant structural polysaccharides, is starting to produce new insights by allowing access to the total community and sidestepping the limitations imposed by cultivation. These advances highlight the promise of these approaches for characterising the rumen microbial community structure and linking this with the functions of the rumen microbiota. Initial results using high-throughput culture-independent technologies have also shown that the rumen microbiome is far more complex and diverse than the human caecum. Therefore, cataloguing its genes will require a considerable sequencing and bioinformatic effort. Nevertheless, the construction of a rumen microbial gene catalogue through metagenomics and genomic sequencing of key populations is an attainable goal. A rumen microbial gene catalogue is necessary to understand the function of the microbiome and its interaction with the host animal and feeds, and it will provide a basis for integrative microbiome–host models and inform strategies promoting less-polluting, more robust and efficient ruminants.

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Section: The Ruminant Superorganismmentioning

confidence: 99%

Rumen microbial (meta)genomics and its application to ruminant production

Morgavi

Kelly

Janssen

et al. 2013

Animal

209

163

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“…The diversity of these microbial taxa is only now becoming truly acknowledged, due to the application of cultivation-independent techniques (28)(29)(30)(31)(32) . However, it is with this complex microbial population that the source of ruminal inefficiencies in feed use lies.…”

Section: Ruminants As a Source Of Environmental Pollutantsmentioning

confidence: 99%

Plant-based strategies towards minimising ‘livestock's long shadow’

et al. 2010

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Ruminant farming is an important component of the human food chain. Ruminants can use offtake from land unsuitable for cereal crop cultivation via interaction with the diverse microbial population in their rumens. The rumen is a continuous flow fermenter for the digestion of ligno-cellulose, with microbial protein and fermentation end-products incorporated by the animal directly or during post-ruminal digestion. However, ruminal fermentation is inefficient in capturing the nutrient resource presented, resulting in environmental pollution and generation of greenhouse gases. Methane is generated as a consequence of ruminal fermentation and poor retention of ingested forage nitrogen causes nitrogenous pollution of water and land and contributes to the generation of nitrous oxide. One possible cause is the imbalanced provision of dietary substrates to the rumen micro-organisms. Deamination of amino acids by ammonia-producing bacteria liberates ammonia which can be assimilated by the rumen bacteria and used for microbial protein synthesis. However, when carbohydrate is limiting, microbial growth is slow, meaning low demand for ammonia for microbial protein synthesis and excretion of the excess. Protein utilisation can therefore be improved by increasing the availability of readily fermentable sugars in forage or by making protein unavailable for proteolysis through complexing with plant secondary products. Alternatively, realisation that grazing cattle ingest living cells has led to the discovery that plant cells undergo endogenous, stress-mediated protein degradation due to the exposure to rumen conditions. This presents the opportunity to decrease the environmental impact of livestock farming by using decreased proteolysis as a selection tool for the development of improved pasture grass varieties. Ruminant: Protein: Nitrogen: Methane: Grass: Clover: Forage Making assessments of the impact and value of livestock farming is complex. The rearing of domestic livestock is important in food production, although there are conflicts between the use of land for production of animal feed as opposed to producing grain for human consumption (1) . The livestock sector is economically valuable. Livestock contributes 1 . 4 % of global gross domestic product providing employment for 20% of the global population in both developed and developing countries (1) . Livestock products can provide an important addition to diet especially in the developing world, providing key vitamins and nutrients. Indeed, the consumption of meat has been linked to both physical and mental development in children (2) , but in the developed world over-consumption of meat has been linked to development of serious health problems (3) . Current projections estimate that the global demand for meat and milk will have doubled by 2050 compared with that at the onset of the 21st century (4) . This is being driven by demographic changes, (the emergence of a larger, but older population) and economic growth (1) . Increased demand for livestock products comes mostl...

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“…These studies illustrated similar principles. Edwards et al (2004) drew all the sequence information then present in public-access databases, formulated the sequences together in a single phylogenetic tree and concluded that the number of phylotypes in the rumen was rather similar to the number determined by Eckburg et al (2005) in humans. A total of 341 phylotypes was identified, once again with the majority being Firmicutes at 54% of the total.…”

Section: Microbial Diversity In the Human Intestine And The Rumenmentioning

confidence: 99%

“…Ruminococcus albus and Ruminococcus flavefaciens are the two most common cellulolytic ruminococci. They are phylogenetically much more similar to the majority of ruminal bacteria, being central in the Firmicutes phylum (Edwards et al, 2004).…”

Section: Microbial Diversity In the Human Intestine And The Rumenmentioning

confidence: 99%

Gut microbiology – broad genetic diversity, yet specific metabolic niches

Wallace¹

2008

Animal

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Analysis of 16S ribosomal RNA (rRNA)-encoding gene sequences from gut microbial ecosystems reveals bewildering genetic diversity. Some metabolic functions, such as glucose utilisation, are fairly widespread throughout the genetic spectrum. Others, however, are not. Despite so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, particularly the final step of biohydrogenation of C18 fatty acids, stearate formation, is achieved only by a small sub-group of bacteria related to Butyrivibrio fibrisolvens. Individuals who lack Oxalobacter formigenes fail to metabolise oxalate and suffer kidney stones composed of calcium oxalate. Perhaps the most celebrated example of the difference a single species can make is the 'mimosine story' in ruminants. Mimosine is a toxic amino acid found in the leguminous plant, Leucaena leucocephala. Mimosine can cause thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were toxic to ruminants in some countries but not others led to the discovery of Synergistes jonesii, which metabolises 3-hydroxy-4(1H)-pyridone and protects animals from toxicity. Thus, despite the complexities indicated by molecular microbial ecology and genomics, it should never be forgotten that gut communities contain important metabolic niches inhabited by species with highly specific metabolic capability.

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16S rDNA library-based analysis of ruminal bacterial diversity

Cited by 224 publications

References 47 publications

Rumen microbial (meta)genomics and its application to ruminant production

Rumen microbial (meta)genomics and its application to ruminant production

Plant-based strategies towards minimising ‘livestock's long shadow’

Gut microbiology – broad genetic diversity, yet specific metabolic niches

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