Dataset Information

Insights Into Culturomics of the Rumen Microbiome.

ABSTRACT: Cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. In this study, we aimed to discover the potential of culturomics for characterizing the rumen microbiome and for identifying factors, specifically sample dilution and media type, which affect microbial richness on agar plates. Our cultivation experiment captured 23% of all operational taxonomic units (OTUs) found in the rumen microbiome in this study. The use of different media increased the number of cultured OTUs by up to 40%. Sample dilution had the strongest effect on increasing richness on the plates, while abundance and phylogeny were the main factors determining cultivability of rumen microbes. Our findings from phylogenetic analysis of cultured OTUs on the lower branches of the phylogenetic tree suggest that multifactorial traits govern cultivability. Interestingly, most of our cultured OTUs belonged to the rare rumen biosphere. These cultured OTUs could not be detected in the rumen microbiome, even when we surveyed it across a 38 rumen microbiome samples. These findings add another unique dimension to the complexity of the rumen microbiome and suggest that a large number of different organisms can be cultured in a single cultivation effort.

SUBMITTER: Zehavi T

PROVIDER: S-EPMC6123358 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Insights Into Culturomics of the Rumen Microbiome.

Zehavi Tamar T Probst Maraike M Mizrahi Itzhak I

Frontiers in microbiology 20180829

Cultivation of undescribed rumen microorganisms is one of the most important tasks in rumen microbiology. In this study, we aimed to discover the potential of culturomics for characterizing the rumen microbiome and for identifying factors, specifically sample dilution and media type, which affect microbial richness on agar plates. Our cultivation experiment captured 23% of all operational taxonomic units (OTUs) found in the rumen microbiome in this study. The use of different media increased the ...[more]

PMID: 30210474

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Project description:The standardization of collection and processing methods for rumen samples is crucial to reduce the level of errors that may affect the analysis and interpretation of the data. The aim of this study was to compare two processing methods and their impacts on the microbial community composition analysis, from material that was either immediately frozen or samples that were stored as cell pellets after removing the supernatant prior to freezing. Eight rumen-fistulated Brahman steers received chloroform as an antimethanogenic compound for 21 days. Rumen fluid samples (60 mL per animal) were collected using a probe covered with two layers of cheesecloth at 3 h post feeding at day 0 prior-treatment (control period) and day 21 of treatment. One sub-set of samples were placed in dry ice and stored at -80°C (Method 1) for subsequent DNA extraction, while a second subset of samples was centrifuged, the supernatant removed and the microbial pellet and rumen contents placed in dry ice and stored at -80°C (Method 2) prior to DNA extractions. Phylogenetic based methods (Illumina Miseq) targeting the 16S rRNA gene were used to characterize the bacterial and archaeal communities from both collection methods for the control and treatment periods. The results from this study showed that the chloroform treatment was significantly different for all beta diversity measures regardless of the processing method used. Significant differences in the relative abundances of some bacteria and archaea, such as Elusimicrobia, Fibrobacteres, Lentisphaerae, Spirochaetes, and Verrucomicrobia and Methanomassiliicoccaceae, were observed at higher levels in the Method 2. These microbial populations are known to have fragile cell wall structures and are susceptible to cell lysis. Regardless of the processing method used, both identified the key microbial groups and can be used to compare the relative shifts in the rumen microbiome between treatments. However, immediately freezing samples might alter the abundance of material from species that are more readily lysed and will not be suitable for studies that aim to assign absolute abundance values to these species within the rumen.

Dataset Information

Insights Into Culturomics of the Rumen Microbiome.

Publications

Insights Into Culturomics of the Rumen Microbiome.

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