Use of DNA probes to monitor nutritional effects on ruminal prokaryotes and Fibrobacter succinogenes S852

Sl, Briesacher; T, May; Kn, Grigsby; Ms, Kerley; Rv, Anthony; Ja, Paterson

doi:10.2527/1992.701289x

Cited by 48 publications

(31 citation statements)

References 5 publications

(5 reference statements)

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“…S4). SSU 16S rRNA gene sequences matching the genus Ruminococcus, a fibrolytic rumen bacterium, were rare in all libraries (e.g., 7 SSU rRNA gene pyrosequences total), which agrees with previous molecular studies of the rumen (4,8,11,13,32,35,36). Additionally, the distribution of EGTs from the Bacteria …”

Section: Resultssupporting

confidence: 76%

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

Brulc

Antonopoulos

Miller

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

645

563

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The complex microbiome of the rumen functions as an effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels. The rumen and gastrointestinal tract harbor a dense and complex microbiome. To gain a greater understanding of the ecology and metabolic potential of this microbiome, we used comparative metagenomics (phylotype analysis and SEED subsystems-based annotations) to examine randomly sampled pyrosequence data from 3 fiber-adherent microbiomes and 1 pooled liquid sample (a mixture of the liquid microbiome fractions from the same bovine rumens). Even though the 3 animals were fed the same diet, the community structure, predicted phylotype, and metabolic potentials in the rumen were markedly different with respect to nutrient utilization. A comparison of the glycoside hydrolase and cellulosome functional genes revealed that in the rumen microbiome, initial colonization of fiber appears to be by organisms possessing enzymes that attack the easily available side chains of complex plant polysaccharides and not the more recalcitrant main chains, especially cellulose. Furthermore, when compared with the termite hindgut microbiome, there are fundamental differences in the glycoside hydrolase content that appear to be diet driven for either the bovine rumen (forages and legumes) or the termite hindgut (wood).CAZymes ͉ cellulases ͉ plant cell wall ͉ pyrosequencing H erbivores carry out a foregut fermentation that digests plant cell wall materials by a complex and efficient microbial process. The microbiome inhabiting the rumen is characterized by its high population density, wide diversity, and complexity of interactions. Bacteria predominate the rumen, with a variety of anaerobic protozoa and fungi (1), and the associated occurrence of bacteriophage is well documented (2). The use of small subunit (SSU) rRNA sequence analysis has allowed for a more complete description of the rumen microbiome and these inventories have demonstrated that a large microbial component remains uncultured (3)(4)(5)(6)(7)(8)(9)(10)(11)(12) and that a high proportion of the fibrolytic population has not been thoroughly described (7,8,13,14). The rumen habitat contains a consortium of microbes that harbor the complex lignocellulosic degradation system for the microbial attachment and digestion of plant biomass. However, the complex chemical processes required to break down the plant cell wall are rarely carried out by a single species. Evidence also suggests that the most important organisms and gene sets involved in the most efficient hydrolysis of plant cell walls are associated with the fiber portion of the rumen digesta (15). Because we continue to investigate the community structure of the rumen, it is also clear that the system is not fully characterized with respect to the metabolic potential, especially as the system relates to plant...

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Section: Resultssupporting

confidence: 76%

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

Brulc

Antonopoulos

Miller

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

645

563

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“…In agreement with this, the relative proportions of the different cellulolytic bacterial species, determined with the oligonucleotide probes, remain fairly constant at several times after feeding for steers fed orchardgrass [2] or for sheep fed a diet containing 60% barley [16]. Concerning the effect of the diet on the relative population size of the cellulolytic bacterial community, only one study dealing with this aspect is available in the literature [29].…”

Section: Cellulolytic Bacterial Community In the Sabmentioning

confidence: 92%

Cereal supplementation modified the fibrolytic activity but not the structure of the cellulolytic bacterial community associated with rumen solid digesta

et al. 2001

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-4 ruminally cannulated cows were fed a forage diet (93% hay + 7% straw) and a mixed diet (33 % hay + 7% straw + 40% barley) in a 2 ¥ 2 crossover experimental design. In sacco degradation of forage, fibrolytic activities (polysaccharidases and glycosidases) of the solid-associated bacteria (SAB), and distribution of the 3 main cellulolytic bacterial species (Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens) were determined for both diets. Barley supplementation decreased the hay degradation rate and mainly the polysaccharidase activities of the SAB (30% on average). The sum of rRNA of the 3 cellulolytic bacterial species represented on average 17% of the total bacterial signal and R. albus was the dominant cellulolytic bacterial species of the 3 studied. Barley supplementation did not modify the proportion of the 3 cellulolytic bacteria attached to plant particles. The negative effect of barley on the ruminal hay degradation rate is due to a decrease in fibrolytic activity of the SAB, and not to a modification of the balance of the three cellulolytic bacterial species examined. fibrolytic activity / oligonucleotide probe / cellulolytic bacteria / cereal supplementation / rumen Résumé -La supplémentation en céréale modifie l'activité fibrolytique mais pas la structure de la communauté bactérienne cellulolytique associée à la phase solide du contenu ruminal. 4 vaches, canulées du rumen, ont été alimentées avec un régime fourrage (93 % foin + 7 % paille) et un régime mixte (33 % foin + 7 % paille + 60 % orge) dans un schéma croisé 2 ¥ 2. La dégradation Reprod. Nutr. Dev. 41 (2001) 413-424 413

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“…F. succinogenes has been denoted as one of the most widespread cellulolytic bacteria in the rumen, contributing ca. 5 to 6% of total prokaryotic 16S rRNA in the rumen contents of cattle (3). Given the fibrolytic activity of this species, we would have anticipated its abundance to be lower for animals on the LF diet due to the lower fiber content.…”

Section: Figmentioning

confidence: 99%

Effect of Phenotypic Residual Feed Intake and Dietary Forage Content on the Rumen Microbial Community of Beef Cattle

Carberry

Kenny

Han

et al. 2012

Appl Environ Microbiol

256

224

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ABSTRACTFeed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations ofEntodiniumspp., protozoa,Fibrobacter succinogenes,Ruminococcus flavefaciens,Ruminococcus albus,Prevotella brevis, the genusPrevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed thatPrevotellaabundance was higher (P< 0.0001) in inefficient animals. A higher (P< 0.0001) abundance ofEntodiniumandPrevotellaspp. and a lower (P< 0.0001) abundance ofFibrobacter succinogeneswere observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered.

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Use of DNA probes to monitor nutritional effects on ruminal prokaryotes and Fibrobacter succinogenes S852

Cited by 48 publications

References 5 publications

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases

Cereal supplementation modified the fibrolytic activity but not the structure of the cellulolytic bacterial community associated with rumen solid digesta

Effect of Phenotypic Residual Feed Intake and Dietary Forage Content on the Rumen Microbial Community of Beef Cattle

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