Characterization of the dynamics of initial bacterial colonization of nonconserved forage in the bovine rumen

Edwards, Joan E.; Huws, Sharon; Kim, Eun Joong; Kingston‐Smith, Alison H.

doi:10.1111/j.1574-6941.2007.00392.x

Cited by 85 publications

(61 citation statements)

References 55 publications

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“…Furthermore, the functional hierarchical classification was illustrated by using SEED subsystem. The sequences were compared using the BLASTX algorithm with an expected cut off of 1 × 10 −5 [26]. …”

Section: Methodsmentioning

confidence: 99%

High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

Singh

Reddy

Patel

et al. 2014

BioMed Research International

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The complex microbiomes of the rumen functions as an effective system for plant cell wall degradation, and biomass utilization provide genetic resource for degrading microbial enzymes that could be used in the production of biofuel. Therefore the buffalo rumen microbiota was surveyed using shot gun sequencing. This metagenomic sequencing generated 3.9 GB of sequences and data were assembled into 137270 contiguous sequences (contigs). We identified potential 2614 contigs encoding biomass degrading enzymes including glycoside hydrolases (GH: 1943 contigs), carbohydrate binding module (CBM: 23 contigs), glycosyl transferase (GT: 373 contigs), carbohydrate esterases (CE: 259 contigs), and polysaccharide lyases (PE: 16 contigs). The hierarchical clustering of buffalo metagenomes demonstrated the similarities and dissimilarity in microbial community structures and functional capacity. This demonstrates that buffalo rumen microbiome was considerably enriched in functional genes involved in polysaccharide degradation with great prospects to obtain new molecules that may be applied in the biofuel industry.

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Section: Methodsmentioning

confidence: 99%

High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

Singh

Reddy

Patel

et al. 2014

BioMed Research International

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Section: Introductionmentioning

confidence: 99%

“…Previous studies have shown temporal changes in bacterial (Edwards et al, 2007; Huws et al, 2013) and fungal (Edwards et al, 2008) populations during ruminal incubation of fresh perennial rye grass ( Lolium perenne ). Specifically, these studies revealed a rapid colonization of the plant material within 5 min of rumen-incubation by both bacterial (Edwards et al, 2007) and fungal populations, followed by a compositional shift in bacterial populations between 2 and 4 h following incubation (Huws et al, 2013). Compositional dynamics may vary among forage types based on observed differences in fiber disappearance and fibrolytic enzyme activities (Bowman and Firkins, 1993) and the observed temporal changes in microbiota may be affected by residual plant metabolism of fresh forages (Huws et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

et al. 2014

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The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H2 was metabolized into CH4 by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome—both microbially facilitated processes with global significance.

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“…In present study, 16S rRNA genes were amplified from plant material and the choice of primer was made to avoid amplification of chloroplast 16S rRNA gene 23,24 . There are a wide variety of other primers available that vary in term of the product length, taxonomic power and usefulness 25,26 .…”

Section: Discussionmentioning

confidence: 99%

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Sanschagrin

Yergeau

2014

JoVE

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One of the major questions in microbial ecology is "who is there?" This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. Traditionally, this was performed by cloning and Sanger (capillary electrophoresis) sequencing of PCR amplicons. The advent of nextgeneration sequencing has tremendously simplified and increased the sequencing depth for 16S rRNA gene sequencing. The introduction of benchtop sequencers now allows small labs to perform their 16S rRNA sequencing in-house in a matter of days. Here, an approach for 16S rRNA gene amplicon sequencing using a benchtop next-generation sequencer is detailed. The environmental DNA is first amplified by PCR using primers that contain sequencing adapters and barcodes. They are then coupled to spherical particles via emulsion PCR. The particles are loaded on a disposable chip and the chip is inserted in the sequencing machine after which the sequencing is performed. The sequences are retrieved in fastq format, filtered and the barcodes are used to establish the sample membership of the reads. The filtered and binned reads are then further analyzed using publically available tools. An example analysis where the reads were classified with a taxonomy-finding algorithm within the software package Mothur is given. The method outlined here is simple, inexpensive and straightforward and should help smaller labs to take advantage from the ongoing genomic revolution.

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Characterization of the dynamics of initial bacterial colonization of nonconserved forage in the bovine rumen

Cited by 85 publications

References 55 publications

High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

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