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Wang RF, Cao WW, Cerniglia CE. PCR detection of Ruminococcus spp. in human and animal faecal samples. Mol Cell Probes 1997; 11:259-65. [PMID: 9281411 DOI: 10.1006/mcpr.1997.0111] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Polymerase chain reaction (PCR) procedures for Ruminococcus spp. were developed and used for the detection of Ruminococcus spp. in human and animal faeces. The PCR specificity was established for Ruminococcus albus, R. bromii, R. obeum, R. callidus and R. flavefaciens. The PCR sensitivity ranged from 4 to 100 cells of the pure cultures, depending on the species. Ruminococcus albus, R. bromii, R. obeum and R. callidus were detected in human faeces. R. bromii, R. albus and R. obeum were also detected in animal faeces. R. flavefaciens was not detected in most of the samples tested, except for a weak positive in monkey faecal specimens. The PCR appears to be a specific and efficient method for the detection of Ruminococcus spp. in faecal specimens.
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Affiliation(s)
- R F Wang
- Microbiology Division, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
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52
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Schofield P, Pell AN, Krause DO. Molecular beacons: trial of a fluorescence-based solution hybridization technique for ecological studies with ruminal bacteria. Appl Environ Microbiol 1997; 63:1143-7. [PMID: 9055429 PMCID: PMC168404 DOI: 10.1128/aem.63.3.1143-1147.1997] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Molecular beacons are fluorescent probes developed for solution rather than membrane hybridization. We have investigated the utility of these probes to study rumen microbial ecology. Two cellulolytic species, Ruminococcus albus and Fibrobacter succinogenes, were tested. Membrane and solution hybridizations gave similar results in competition experiments with cocultures of R. albus 8 and F. succinogenes S85.
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Affiliation(s)
- P Schofield
- Department of Animal Science, Cornell University, Ithaca, New York 14853, USA
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53
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Shi Y, Odt CL, Weimer PJ. Competition for cellulose among three predominant ruminal cellulolytic bacteria under substrate-excess and substrate-limited conditions. Appl Environ Microbiol 1997; 63:734-42. [PMID: 9023950 PMCID: PMC168362 DOI: 10.1128/aem.63.2.734-742.1997] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Three predominant ruminal cellulolytic bacteria (Fibrobacter succinogenes S85, Ruminococcus flavefaciens FD-1, and Ruminococcus albus 7) were grown in different binary combinations to determine the outcome of competition in either cellulose-excess batch culture or in cellulose-limited continuous culture. Relative populations of each species were estimated by using signature membrane-associated fatty acids and/or 16S rRNA-targeted oligonucleotide probes. Both F. succinogenes and R. flavefaciens coexisted in cellulose-excess batch culture with similar population sizes (58 and 42%, respectively; standard error, 12%). By contrast, under cellulose limitation R. flavefaciens predominated (> 96% of total cell mass) in coculture with F. succinogenes, regardless of whether the two strains were inoculated simultaneously or whether R. flavefaciens was inoculated into an established culture of F. succinogenes. The predominance of R. flavefaciens over F. succinogenes under cellulose limitation is in accord with the former's more rapid adherence to cellulose and its higher affinity for cellodextrin products of cellulose hydrolysis. In batch cocultures of F. succinogenes and R. albus, the populations of the two species were similar. However, under cellulose limitation, F. succinogenes was the predominant strain (approximately 80% of cell mass) in cultures simultaneously coinoculated with R. albus. The results from batch cocultures of R. flavefaciens and R. albus were not consistent within or among trials: some experiments yielded monocultures of R. albus (suggesting production of an inhibitory agent by R. albus), while others contained substantial populations of both species. Under cellulose limitation, R. flavefaciens predominated over R. albus (85 and 15%, respectively), as would be expected by the former's greater adherence to cellulose. The retention of R. albus in the cellulose-limited coculture may result from a combination of its ability to utilize glucose (which is not utilizable by R. flavefaciens), its demonstrated ability to adapt under selective pressure in the chemostat to utilization of lower concentrations of cellobiose, a major product of cellulose hydrolysis, and its possible production of an inhibitory agent.
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Affiliation(s)
- Y Shi
- Department of Dairy Science, University of Wisconsin-Madison 53706, USA
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54
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Kalmokoff ML, Teather RM. Isolation and characterization of a bacteriocin (Butyrivibriocin AR10) from the ruminal anaerobe Butyrivibrio fibrisolvens AR10: evidence in support of the widespread occurrence of bacteriocin-like activity among ruminal isolates of B. fibrisolvens. Appl Environ Microbiol 1997; 63:394-402. [PMID: 9023920 PMCID: PMC168332 DOI: 10.1128/aem.63.2.394-402.1997] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Forty-nine isolates of Butyrivibrio fibrisolvens and a single isolate of Butyrivibrio crossotus were screened for the production of inhibitors by a deferred plating procedure. Twenty-five isolates produced factors which, to various degrees, inhibited the growth of the other Butyrivibrio isolates. None of the inhibitory activity was due to bacteriophages. The inhibitory products from 18 of the producing strains were sensitive to protease digestion. Differences in the ranges of activity among the Butyrivibrio isolates and protease sensitivity profiles suggest that a number of different inhibitory compounds are produced. These findings suggest that the production of bacteriocin-like inhibitors may be a widespread characteristic throughout the genus Butyrivibrio. The bacteriocin-like activity from one isolate, B. fibrisolvens AR10, was purified and confirmed to reside in a single peptide. Crude bacteriocin extracts were prepared by ammonium sulfate and methanol precipitation of spent culture supernatants, followed by dialysis and high-speed centrifugation. The active component was isolated from the semicrude extract by reverse-phase chromatography. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis confirmed that the peptide was purified to homogeneity, having an estimated molecular mass of approximately 4,000 Da. The N terminus of the peptide was blocked. A cyanogen bromide cleavage fragment of the native peptide yielded a sequence of 20 amino acids [(M)GIQLAPAXYQDIVNXVAAG]. No homology with previously reported bacteriocins was found. Butyrivibriocin AR10 represents the first bacteriocin isolated from a ruminal anaerobe.
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Affiliation(s)
- M L Kalmokoff
- Centre for Food and Animal Research, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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55
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Shi Y, Weimer PJ. Competition for cellobiose among three predominant ruminal cellulolytic bacteria under substrate-excess and substrate-limited conditions. Appl Environ Microbiol 1997; 63:743-8. [PMID: 9023951 PMCID: PMC168363 DOI: 10.1128/aem.63.2.743-748.1997] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The ruminal cellulolytic bacteria Ruminococcus flavefaciens FD-1 and Fibrobacter succinogenes S85 coexisted in substrate-excess coculture with about equal population size, but R. flavefaciens outcompeted F. succinogenes for cellobiose in the substrate-limited cocultures whether the two strains were coinoculated or a steady-state culture of F. succinogenes was challenged by R. flavefaciens. This outcome of competition between these two strains is due to a classical pure and simple competition mechanism based on affinity for cellobiose. Although the population size of F. succinogenes was much higher (> 70%) than that of another cellulolytic species, Ruminococcus albus 7 in substrate-excess coculture, F. succinogenes was replaced by a population of R. albus in the substrate-limited coculture in both coinoculation and challenge experiments. R albus outcompeted F. succinogenes, apparently due to selection in the chemostat of a population of R. albus with a higher affinity for cellobiose. R. albus also outcompeted R. flavefaciens under substrate-limited conditions.
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Affiliation(s)
- Y Shi
- Department of Dairy Science, University of Wisconsin-Madison 53706, USA
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56
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Abstract
The production of toxic compounds or antibiotics is a common component of intermicrobial competitive interactions, and many of these toxins have been adopted and adapted for the control of microbial populations. One class of these toxins, the bacteriocins, is a heterogeneous group of proteinaceous antibiotics that often display a high degree of target specificity, although many have a very wide spectrum of activity. To date, only limited information is available concerning the occurrence of bacteriocins among ruminal isolates or the sensitivity of ruminal microorganisms to exogenous bacteriocins. A survey of 50 strains of Butyrivibrio spp. isolated from a variety of sources (sheep, deer, and cattle) for bacteriocin production indicated a high incidence of bacteriocin-like activity (50%). Many of these inhibitory compounds appear to have a broad spectrum of activity, which suggests that bacteriocins may have a significant impact on both the competitive fitness of individual microbial strains within the rumen and on the overall structure of the microbial population within the rumen. Selected bacteriocins from lactic acid bacteria also were shown to have activity against Butyrivibrio spp. and may have application in ruminant systems. Bacteriocins may provide an alternative group of antibiotics for the manipulation of ruminal microbial populations. Bacteriocins have significant advantages over other antibiotics in target specificity, susceptibility to proteolytic digestion, possibility of genetic transfer and manipulation, and, in the case of some bacteriocins derived from lactic acid bacteria, a long history of safe use.
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Affiliation(s)
- M L Kalmokoff
- Centre for Food and Animal Research, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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57
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Piwonka EJ, Firkins JL. Effect of glucose fermentation on fiber digestion by ruminal microorganisms in vitro. J Dairy Sci 1996; 79:2196-206. [PMID: 9029358 DOI: 10.3168/jds.s0022-0302(96)76596-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Two in vitro digestion trials were performed to determine whether the negative effect on fiber digestion when pH was maintained at > 6.2 was attributable to glucose alone or to end products of glucose fermentation. In some treatments, glucose was depleted by a previous 6-h incubation; the supernatant from this incubation was used as the buffer source for treatments using the fermented glucose medium. In trial 1, mixed cultures were grown on cellulose, soybean hulls, and corn bran in fresh media with 0 (control) or 25 mM glucose, in media previously fermented for 6 h with 0 (control) or 25 mM glucose, or in fermented control medium plus 25 mM lactic acid. The rate of NDF digestion was decreased with fermented glucose medium but not with fresh glucose medium or lactic acid medium. Concentrations of lactate, propionate, and butyrate did not appear to affect NDF digestion directly. In trial 2, six treatment media were used: control and glucose media that were either fresh or previously fermented for 6 h and fermented control and glucose media treated with a protease. Rate of NDF digestion was slower in cultures with fermented glucose medium that was treated with protease than in fermented control medium without protease. When treated with protease, rate of NDF digestion was not different between the fermented control medium and the fermented glucose medium. Thus, the negative effect on fiber digestion appeared to be attributable partially to a proteinaceous inhibitor that was produced in culture media containing a rapidly fermented sugar.
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Affiliation(s)
- E J Piwonka
- Department of Animal Sciences, Ohio State University, Columbus 43210, USA
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58
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Abstract
This paper discusses the reasons and current evidence for gene transfer between ruminal bacteria and other bacteria in the environment, possible routes for genetic exchange, and candidate genes. Gene transfer between ruminal bacteria has been demonstrated in vitro; however, success has been only minimal in obtaining plasmids and other self-transmissible genetic material from ruminal bacteria. The application of molecular biology techniques with ruminal microorganisms should permit the opportunity for an in vivo assessment of gene transfer. Studies that could provide pertinent information for ruminal microbiologists and dairy nutritionists are outlined.
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Affiliation(s)
- M Morrison
- Department of Animal Science and School of Biological Sciences, University of Nebraska, Lincoln 68583, USA
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59
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Li S, Cullen D, Hjort M, Spear R, Andrews JH. Development of an oligonucleotide probe for Aureobasidium pullulans based on the small-subunit rRNA gene. Appl Environ Microbiol 1996; 62:1514-8. [PMID: 8633850 PMCID: PMC167926 DOI: 10.1128/aem.62.5.1514-1518.1996] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Aureobasidium pullulans, a cosmopolitan yeast-like fungus, colonizes leaf surfaces and has potential as a biocontrol agent of pathogens. To assess the feasibility of rRNA as a target for A. pullulans-specific oligonucleotide probes, we compared the nucleotide sequences of the small-subunit rRNA (18S) genes of 12 geographically diverse A. pullulans strains. Extreme sequence conservation was observed. The consensus A. pullulans sequence was compared with other fungal sequences to identify potential probes. A 21-mer probe which hybridized to the 12 A. pullulans strains but not to 98 other fungi, including 82 isolates from the phylloplane, was identified. A 17-mer highly specific for Cladosporium herbarum was also identified. These probes have potential in monitoring and quantifying fungi in leaf surface and other microbial communities.
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Affiliation(s)
- S Li
- Department of Plant Pathology, University of Wisconsin-Madison 53706, USA
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60
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Shi Y, Weimer PJ. Utilization of individual cellodextrins by three predominant ruminal cellulolytic bacteria. Appl Environ Microbiol 1996; 62:1084-8. [PMID: 8975600 PMCID: PMC167871 DOI: 10.1128/aem.62.3.1084-1088.1996] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Growth of the ruminal bacteria Fibrobacter succinogenes S85, Ruminococcus flavefaciens FD-1, and R. albus 7 followed Monod kinetics with respect to concentrations of individual pure cellodextrins (cellobiose, cellotriose, cellotetraose, cellopentaose, and cellohexaose). Under the conditions tested, R. flavefaciens FD-1 possesses the greatest capacity to compete for low concentrations of these cellodextrins.
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Affiliation(s)
- Y Shi
- Department of Dairy Science, University of Wisconsin-Madison, USA
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61
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James GA, Beaudette L, Costerton JW. Interspecies bacterial interactions in biofilms. ACTA ACUST UNITED AC 1995. [DOI: 10.1007/bf01569978] [Citation(s) in RCA: 93] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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62
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Odenyo AA, Mackie RI, Stahl DA, White BA. The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: pure-culture studies with cellulose and alkaline peroxide-treated wheat straw. Appl Environ Microbiol 1994; 60:3697-703. [PMID: 7527202 PMCID: PMC201875 DOI: 10.1128/aem.60.10.3697-3703.1994] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Specific oligonucleotide probes targeted to sites on the 16S rRNA of Ruminococcus albus 8, Ruminococcus flavefaciens FD-1, and Fibrobacter succinogenes S85 and a domain Bacteria probe were used to study bacterial interactions during the fermentation of cellulose and alkaline hydrogen peroxide-treated wheat straw in monocultures, dicultures, and tricultures. Results showed that R. albus 8 inhibited the growth of R. flavefaciens FD-1 when grown as a diculture with cellulose or alkaline hydrogen peroxide-treated wheat straw as the carbon source. In dicultures containing R. albus 8 and F. succinogenes S85 grown on cellulose or alkaline hydrogen peroxide-treated wheat straw, competition was not detected. R. flavefaciens FD-1 outcompeted F. succinogenes S85 when cellulose was used as the carbon source. In tricultures with cellulose as the carbon source, R. flavefaciens FD-1 was inhibited, R. albus 8 appeared to dominate during the early phase of degradation (12 to 48 h), while F. succinogenes S85 became predominant during the later phase of degradation (60 to 70 h). When alkaline hydrogen peroxide-treated wheat straw was used as a growth substrate, F. succinogenes S85 showed better growth than either R. albus 8 or R. flavefaciens FD-1. However, R. flavefaciens FD-1 was present in small numbers throughout the incubation period, unlike the growth patterns when cellulose was the carbon source.
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Affiliation(s)
- A A Odenyo
- Department of Animal Sciences, University of Illinois at Urbana-Champaign 61801
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