Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen.
<h4>Background</h4>The bovine rumen maintains a diverse microbial community that serves to break down indigestible plant substrates. However, those bacteria specifically adapted to degrade cellulose, the major structural component of plant biomass, represent a fraction of the rumen micro...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2011-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22043282/pdf/?tool=EBI |
| _version_ | 1818573600670613504 |
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| author | Jennifer M Brulc Carl J Yeoman Melissa K Wilson Margret E Berg Miller Patricio Jeraldo Sadanari Jindou Nigel Goldenfeld Harry J Flint Raphael Lamed Ilya Borovok Maša Vodovnik Karen E Nelson Edward A Bayer Bryan A White |
| author_facet | Jennifer M Brulc Carl J Yeoman Melissa K Wilson Margret E Berg Miller Patricio Jeraldo Sadanari Jindou Nigel Goldenfeld Harry J Flint Raphael Lamed Ilya Borovok Maša Vodovnik Karen E Nelson Edward A Bayer Bryan A White |
| author_sort | Jennifer M Brulc |
| collection | DOAJ |
| description | <h4>Background</h4>The bovine rumen maintains a diverse microbial community that serves to break down indigestible plant substrates. However, those bacteria specifically adapted to degrade cellulose, the major structural component of plant biomass, represent a fraction of the rumen microbiome. Previously, we proposed scaC as a candidate for phylotyping Ruminococcus flavefaciens, one of three major cellulolytic bacterial species isolated from the rumen. In the present report we examine the dynamics and diversity of scaC-types both within and between cattle temporally, following a dietary switch from corn-silage to grass-legume hay. These results were placed in the context of the overall bacterial population dynamics measured using the 16S rRNA.<h4>Principal findings</h4>As many as 117 scaC-types were estimated, although just nineteen were detected in each of three rumens tested, and these collectively accounted for the majority of all types present. Variation in scaC populations was observed between cattle, between planktonic and fiber-associated fractions and temporally over the six-week survey, and appeared related to scaC phylogeny. However, by the sixth week no significant separation of scaC populations was seen between animals, suggesting enrichment of a constrained set of scaC-types. Comparing the amino-acid translation of each scaC-type revealed sequence variation within part of the predicted dockerin module but strong conservation in the N-terminus, where the cohesin module is located.<h4>Conclusions</h4>The R. flavefaciens species comprises a multiplicity of scaC-types in-vivo. Enrichment of particular scaC-types temporally, following a dietary switch, and between fractions along with the phylogenetic congruence suggests that functional differences exist between types. Observed differences in dockerin modules suggest at least part of the functional heterogeneity may be conferred by scaC. The polymorphic nature of scaC enables the relative distribution of R. flavefaciens strains to be examined and represents a gene-centric approach to investigating the intraspecific adaptation of an important specialist population. |
| first_indexed | 2024-12-15T00:13:31Z |
| format | Article |
| id | doaj.art-9982268a55b44bcba9e701007484da16 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-15T00:13:31Z |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-9982268a55b44bcba9e701007484da162022-12-21T22:42:30ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-01610e2532910.1371/journal.pone.0025329Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen.Jennifer M BrulcCarl J YeomanMelissa K WilsonMargret E Berg MillerPatricio JeraldoSadanari JindouNigel GoldenfeldHarry J FlintRaphael LamedIlya BorovokMaša VodovnikKaren E NelsonEdward A BayerBryan A White<h4>Background</h4>The bovine rumen maintains a diverse microbial community that serves to break down indigestible plant substrates. However, those bacteria specifically adapted to degrade cellulose, the major structural component of plant biomass, represent a fraction of the rumen microbiome. Previously, we proposed scaC as a candidate for phylotyping Ruminococcus flavefaciens, one of three major cellulolytic bacterial species isolated from the rumen. In the present report we examine the dynamics and diversity of scaC-types both within and between cattle temporally, following a dietary switch from corn-silage to grass-legume hay. These results were placed in the context of the overall bacterial population dynamics measured using the 16S rRNA.<h4>Principal findings</h4>As many as 117 scaC-types were estimated, although just nineteen were detected in each of three rumens tested, and these collectively accounted for the majority of all types present. Variation in scaC populations was observed between cattle, between planktonic and fiber-associated fractions and temporally over the six-week survey, and appeared related to scaC phylogeny. However, by the sixth week no significant separation of scaC populations was seen between animals, suggesting enrichment of a constrained set of scaC-types. Comparing the amino-acid translation of each scaC-type revealed sequence variation within part of the predicted dockerin module but strong conservation in the N-terminus, where the cohesin module is located.<h4>Conclusions</h4>The R. flavefaciens species comprises a multiplicity of scaC-types in-vivo. Enrichment of particular scaC-types temporally, following a dietary switch, and between fractions along with the phylogenetic congruence suggests that functional differences exist between types. Observed differences in dockerin modules suggest at least part of the functional heterogeneity may be conferred by scaC. The polymorphic nature of scaC enables the relative distribution of R. flavefaciens strains to be examined and represents a gene-centric approach to investigating the intraspecific adaptation of an important specialist population.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22043282/pdf/?tool=EBI |
| spellingShingle | Jennifer M Brulc Carl J Yeoman Melissa K Wilson Margret E Berg Miller Patricio Jeraldo Sadanari Jindou Nigel Goldenfeld Harry J Flint Raphael Lamed Ilya Borovok Maša Vodovnik Karen E Nelson Edward A Bayer Bryan A White Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen. PLoS ONE |
| title | Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen. |
| title_full | Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen. |
| title_fullStr | Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen. |
| title_full_unstemmed | Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen. |
| title_short | Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen. |
| title_sort | cellulosomics a gene centric approach to investigating the intraspecific diversity and adaptation of ruminococcus flavefaciens within the rumen |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22043282/pdf/?tool=EBI |
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