Bacteria, Fungi, and Protozoa of the Rumen

Hespell, Robert B.; Akin, Danny E.; Dehority, Burk A.

doi:10.1007/978-1-4757-0322-1_3

Cited by 81 publications

(77 citation statements)

References 341 publications

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“…Phenotypically, the genus Ruminococcus includes several isolates from gastrointestinal environments (Hespell et al, 1997). In the rumen R. albus and R. flavefaciens are usually the predominant species, while R. brornii, R.…”

Section: Discussionmentioning

confidence: 99%

16S rDNA sequencing of Ruminococcus albus and Ruminococcus flavefaciens: design of a signature probe and its application in adult sheep

et al. 1999

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The ruminococci are an important group of fibrolytic bacteria inhabiting the rumen. Seventeen strains of presumptively identified Ruminococcus were evaluated by a combination of nearly complete and partial 165 rDNA sequence that identified all strains as either Ruminococcus albus or Ruminococcus flavefaciens. All sequences fell into cluster IV of the clostridia, while other species of ruminococci (eg. Ruminococcus obeum, Ruminococcus gnaws, Ruminococcus lactaris) fall into cluster XlVa of the clostridia. Ruminococcus cluster IV sequences were used to design a 165 rRNA oligonucleotide probe to assess the relative abundance of target populations in a stable ruminal environment. A stable population (animals fed eight times per day) was established in sheep so that statistically robust comparisons could be made in the absence of variation due to diurnal rumen fluctuations. The steady state populations were sampled six times over a 24 d period and direct microscopic counts (DC), total culturable counts (TCC), and total cellulolytic counts (CEL) were determined. DC and culturable data (TCC and CEL) were compared with relative abundance estimates of Ruminococcus IV and Fibrobacter succinogenes. A combination of the Ruminococcus and i. succinogenes probes accounted for 4 9 *!o of the bacterial population and cellulolytic bacteria (measured by most-probable numbers) were 5 2 % of the total culturable count. These data suggest that a major portion of the Ruminococcus and Fibmbacter diversity has been cultured and is represented by available sequences. Steady state populations were measured over several days in three sheep and an estimate of variation in DC, TCC, CEL and 16s-based data were obtained. These variance estimates could be used to determine the theoretical sample sizes required to obtain statistically significant differences under different experimental conditions.

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Section: Discussionmentioning

confidence: 99%

16S rDNA sequencing of Ruminococcus albus and Ruminococcus flavefaciens: design of a signature probe and its application in adult sheep

et al. 1999

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“…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).…”

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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.

651

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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“…M. elsdenii strains carrying tet(OWO) genes exhibited the highest tetracycline MICs (128 to >256 g/ml), suggesting that tet(O)-tet(W) mosaic genes provide the selective advantage of greater tetracycline resistance for this species. Seven tet genotypes are now known for M. elsdenii, an archetype commensal anaerobe and model for tet gene evolution in the mammalian intestinal tract.Megasphaera elsdenii is a commensal (mutualist) species in the gastrointestinal tracts of ruminant and nonruminant mammals, including humans (7,25,26). This anaerobic bacterium contributes to the overall metabolism that takes place in those microbial ecosystems (2,5,13,15).…”

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“…Megasphaera elsdenii is a commensal (mutualist) species in the gastrointestinal tracts of ruminant and nonruminant mammals, including humans (7,25,26). This anaerobic bacterium contributes to the overall metabolism that takes place in those microbial ecosystems (2,5,13,15).…”

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Diverse Tetracycline Resistance Genotypes of Megasphaera elsdenii Strains Selectively Cultured from Swine Feces

Stanton

McDowall

Rasmussen

2004

Appl Environ Microbiol

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A total of 30 Megasphaera elsdenii strains, selectively isolated from the feces of organically raised swine by using Me109 M medium, and one bovine strain were analyzed for tetracycline resistance genotypic and phenotypic traits. Tetracycline-resistant strains carried tet(O), tet(W), or a tet gene mosaic of tet(O) and tet(W). M. elsdenii strains carrying tet(OWO) genes exhibited the highest tetracycline MICs (128 to >256 g/ml), suggesting that tet(O)-tet(W) mosaic genes provide the selective advantage of greater tetracycline resistance for this species. Seven tet genotypes are now known for M. elsdenii, an archetype commensal anaerobe and model for tet gene evolution in the mammalian intestinal tract.Megasphaera elsdenii is a commensal (mutualist) species in the gastrointestinal tracts of ruminant and nonruminant mammals, including humans (7,25,26). This anaerobic bacterium contributes to the overall metabolism that takes place in those microbial ecosystems (2,5,13,15). M. elsdenii has been the focus of both prebiotic and probiotic applications for improving animal health (10,12,19,27).In a recent study of intestinal bacteria resistant to tetracycline, we detected resistant M. elsdenii strains at high population levels (approximately 10 7 CFU/g) in cecal samples from healthy swine (24). Eight strains were isolated and characterized. The M. elsdenii strains are highly resistant to chlortetracycline (MIC ϭ 256 to Ͼ256 g/ml) and carry one of two "tet(OWO)" genes for tetracycline resistance. [Throughout the manuscript, "tet(OW)" and "tet(OWO)" are used as convenient, practical terms for describing M. elsdenii recombinant tet genes and genotypes. As noted previously (24), these designations are not recognized under present tet classification guidelines (14). It is our hope that future guidelines will be developed to accommodate these novel interclass hybrid genes.] These tet genes are interclass mosaic genes apparently formed by doublecrossover recombinations between tet(O) and tet(W) genes.Our previous study used a nutritionally complex medium with high concentrations of chlortetracycline and, thus, was biased to select tetracycline-resistant M. elsdenii strains. In this study, Me109M medium was developed and used to select M. elsdenii strains without using chlortetracycline. The goals were twofold: first, to obtain tetracycline-sensitive strains of M. elsdenii useful both for investigating tet gene transfer and for probiotic applications, and second, to discover whether or not M. elsdenii strains have additional tet genotypes.Selective isolation of M. elsdenii-Me109M medium. On the basis of previous studies (4-6, 9, 14, 16, 17, 19-21) and preliminary experiments in our laboratory, Me109M medium was developed to selectively culture M. elsdenii. Me109M contained (per liter): tryptone-peptone, 4 g; yeast extract, 2 g; salts solution A (6 g of K 2 HPO 4 /liter of water), 40 ml; salts solution B [6 g of KH 2 PO 4 , 12 g of (NH 4 ) 2 SO 4 , 12 g of NaCl, 1.2 g of MgSO 4 -7H 2 O, 0.6 g of CaCl 2 /liter of water], 40 ml; ...

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Bacteria, Fungi, and Protozoa of the Rumen

Cited by 81 publications

References 341 publications

16S rDNA sequencing of Ruminococcus albus and Ruminococcus flavefaciens: design of a signature probe and its application in adult sheep

16S rDNA sequencing of Ruminococcus albus and Ruminococcus flavefaciens: design of a signature probe and its application in adult sheep

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

Diverse Tetracycline Resistance Genotypes of Megasphaera elsdenii Strains Selectively Cultured from Swine Feces

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