Rumen bacterium
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA529805 | ENA |
REPOSITORIES: ENA
Dataset's files
primary
| Action | DRS | |||
|---|---|---|---|---|
| SRR8811970.fastq.gz | Fastqsanger.gz | |||
| SRR8811980.fastq.gz | Fastqsanger.gz | |||
| SRR8811971.fastq.gz | Fastqsanger.gz | |||
| SRR8811981.fastq.gz | Fastqsanger.gz | |||
| SRR8811972.fastq.gz | Fastqsanger.gz |
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Project description:With the help of the bacteria in the rumen, ruminants can effectively convert human inedible plant fiber to edible food (meat and milk). However, the understanding of rumen bacteriome in dairy cows is still limited, especially in a large population under the same diet, breed, and milking period. Here we described the sequencing data of 16S rRNA gene of rumen bacteriome from 334 mid-lactation Holstein dairy cows generated using the Illumina HiSeq 2500 (PE250) platform. A total of 24,030,828 raw reads with an average of 71,946?±?13,450 sequences per sample were obtained. The top ten genera with highest relative abundance accounted for 60.65% of total bacterial sequences. We observed 4,460 overall operational taxonomic units (1,827?±?94 per sample) based on a 97% nucleotide sequence identity between reads. Totally 6,082 amplicon sequence variants (672?±?131 per sample) were identified in 334 samples. The shareable datasets can be re-used by researchers to assess other rumen bacterial-related biological functions in dairy cows towards the improvement of animal production and health.
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Project description:Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides. The genomes of the rumen microbiota encode thousands of enzymes adapted to digestion of the plant matter that dominates the ruminant diet. We assembled 4,941 rumen microbial metagenome-assembled genomes (MAGs) using approximately 6.5 terabases of short- and long-read sequence data from 283 ruminant cattle. We present a genome-resolved metagenomics workflow that enabled assembly of bacterial and archaeal genomes that were at least 80% complete. Of note, we obtained three single-contig, whole-chromosome assemblies of rumen bacteria, two of which represent previously unknown rumen species, assembled from long-read data. Using our rumen genome collection we predicted and annotated a large set of rumen proteins. Our set of rumen MAGs increases the rate of mapping of rumen metagenomic sequencing reads from 15% to 50-70%. These genomic and protein resources will enable a better understanding of the structure and functions of the rumen microbiota.
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Project description:Genomic analysis of Clostridium sp. NCR, an anaerobic Gram positive bacterium which was isolated from rumen fluid of Mehsani breed of buffalo revealed presence of various environmental gene tags (EGTs) involved in pathways for utilizing a wide range of substrates. Here we report the sequence of this rumen isolate, its whole genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession number JQHY00000000. The genome comprises of a 3.62-Mb draft genome with a G + C content of 28.10%, which encodes a total of 3126 proteins. Functional analysis provides information about the microbe's role in maintaining host homeostasis and its fiber degradation potential.
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Project description:<h4>Background</h4>Variation of microorganism communities in the rumen of cattle (Bos taurus) is of great interest because of possible links to economically or environmentally important traits, such as feed conversion efficiency or methane emission levels. The resolution of studies investigating this variation may be improved by utilizing untargeted massively parallel sequencing (MPS), that is, sequencing without targeted amplification of genes. The objective of this study was to develop a method which used MPS to generate "rumen metagenome profiles", and to investigate if these profiles were repeatable among samples taken from the same cow. Given faecal samples are much easier to obtain than rumen fluid samples; we also investigated whether rumen metagenome profiles were predictive of faecal metagenome profiles.<h4>Results</h4>Rather than focusing on individual organisms within the rumen, our method used MPS data to generate quantitative rumen micro-biome profiles, regardless of taxonomic classifications. The method requires a previously assembled reference metagenome. A number of such reference metagenomes were considered, including two rumen derived metagenomes, a human faecal microflora metagenome and a reference metagenome made up of publically available prokaryote sequences. Sequence reads from each test sample were aligned to these references. The "rumen metagenome profile" was generated from the number of the reads that aligned to each contig in the database. We used this method to test the hypothesis that rumen fluid microbial community profiles vary more between cows than within multiple samples from the same cow. Rumen fluid samples were taken from three cows, at three locations within the rumen. DNA from the samples was sequenced on the Illumina GAIIx. When the reads were aligned to a rumen metagenome reference, the rumen metagenome profiles were repeatable (P?<?0.00001) by cow regardless of location of sampling rumen fluid. The repeatability was estimated at 9%, albeit with a high standard error, reflecting the small number of animals in the study. Finally, we compared rumen microbial profiles to faecal microbial profiles. Our hypothesis, that there would be a stronger correlation between faeces and rumen fluid from the same cow than between faeces and rumen fluid from different cows, was not supported by our data (with much greater significance of rumen versus faeces effect than animal effect in mixed linear model).<h4>Conclusions</h4>We have presented a simple and high throughput method of metagenome profiling to assess the similarity of whole metagenomes, and illustrated its use on two novel datasets. This method utilises widely used freeware. The method should be useful in the exploration and comparison of metagenomes.
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Project description:The capacity of the rumen microbiota to produce volatile fatty acids (VFAs) has important implications in animal well-being and production. We investigated temporal changes of the rumen microbiota in response to butyrate infusion using pyrosequencing of the 16S rRNA gene. Twenty one phyla were identified in the rumen microbiota of dairy cows. The rumen microbiota harbored 54.5±6.1 genera (mean ± SD) and 127.3±4.4 operational taxonomic units (OTUs), respectively. However, the core microbiome comprised of 26 genera and 82 OTUs. Butyrate infusion altered molar percentages of 3 major VFAs. Butyrate perturbation had a profound impact on the rumen microbial composition. A 72 h-infusion led to a significant change in the numbers of sequence reads derived from 4 phyla, including 2 most abundant phyla, Bacteroidetes and Firmicutes. As many as 19 genera and 43 OTUs were significantly impacted by butyrate infusion. Elevated butyrate levels in the rumen seemingly had a stimulating effect on butyrate-producing bacteria populations. The resilience of the rumen microbial ecosystem was evident as the abundance of the microorganisms returned to their pre-disturbed status after infusion withdrawal. Our findings provide insight into perturbation dynamics of the rumen microbial ecosystem and should guide efforts in formulating optimal uses of probiotic bacteria treating human diseases.
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Project description:Mannheimia succiniciproducens, a rumen bacterium belonging to the family Pasteurellaceae, has two putative ?-galactosidase genes, bgaA and bgaB, encoding polypeptides whose deduced amino acid sequences share 56% identity with each other and show approximately 30% identity to the Escherichia coli gene for LacZ. The M. succiniciproducens bgaA (MsbgaA) gene-deletion mutant was not able to grow on lactose as the sole carbon source, suggesting its essential role in lactose metabolism, whereas the MsbgaB gene-deletion mutant did not show any growth defect on a lactose medium. Furthermore, the expression of the MsbgaA gene was induced by the addition of lactose in the growth medium, whereas the MsbgaB gene was constitutively expressed independently of a carbon source. Biochemical characterization of the recombinant proteins revealed that MsBgaA is more efficient than MsBgaB in hydrolyzing o-nitrophenyl-?-d-galactopyranoside and p-nitrophenyl-?-d-galactopyranoside. MsBgaA was highly specific for the hydrolysis of lactose, with a catalytic efficiency of 46.9 s(-1) mM(-1). However, MsBgaB was more efficient for the hydrolysis of lactulose than lactose, and the catalytic efficiency was 10.0 s(-1) mM(-1). Taken together, our results suggest that the ?-galactosidase paralogues of M. succiniciproducens BgaA and BgaB play a critical role in lactose metabolism and in an unknown but likely specific function for rumen bacteria, respectively.
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Project description:A Gram-negative, strictly anaerobic mucin-degrading bacterium, which we designated strain E39T, was isolated from the rumen epithelium of Korean cattle. The cells were non-motile and had a coccus morphology. Growth of strain E39T was observed at 30-45°C (optimum, 39°C), pH 6.5-8.5 (optimum, pH 7.5), and in the presence of 0.0-1.0% (w/v) NaCl (optimum, 0.0-0.5%). Strain E39T contained C16:0, C18:0, C18:1 ω9c, iso-C15:0, and anteiso-C15:0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine, unidentified aminophospholipid, and unidentified lipids. The major respiratory isoprenoid quinones were MK-8 and MK-9. The major fermented end-products of mucin were acetate and succinate. The G+C content of the genomic DNA was 46.4 mol%. Strain E39T was most closely related to Alloprevotella rava 81/4-12T with an 87.3% 16S rRNA gene sequence similarity. On the basis of phenotypic, chemotaxonomic, and molecular properties, strain E39T represents a novel genus of the family Prevotellaceae; as such, the name Pseudoprevotella muciniphila gen. nov., sp. nov. is proposed. A functional annotation of the whole genome sequences of P. muciniphila E39T revealed that this bacterium has a putative mucin-degrading pathway and biosynthetic pathways of extracellular polymeric substances and virulence factors which enable bacteria to adhere to the epithelial cells and avoid the host's immune responses.
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Project description:Determining the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals. Butyrivibrio proteoclasticus B316(T) is a gram-positive, butyrate-forming rumen bacterium with a key role in plant polysaccharide degradation. The 4.4 Mb genome consists of 4 replicons; a chromosome, a chromid and two megaplasmids. The chromid is the smallest reported for all bacteria, and the first identified from the phylum Firmicutes. B316 devotes a large proportion of its genome to the breakdown and reassembly of complex polysaccharides and has a highly developed glycobiome when compared to other sequenced bacteria. The secretion of a range of polysaccharide-degrading enzymes which initiate the breakdown of pectin, starch and xylan, a subtilisin family protease active against plant proteins, and diverse intracellular enzymes to break down oligosaccharides constitute the degradative capability of this organism. A prominent feature of the genome is the presence of multiple gene clusters predicted to be involved in polysaccharide biosynthesis. Metabolic reconstruction reveals the absence of an identifiable gene for enolase, a conserved enzyme of the glycolytic pathway. To our knowledge this is the first report of an organism lacking an enolase. Our analysis of the B316 genome shows how one organism can contribute to the multi-organism complex that rapidly breaks down plant material in the rumen. It can be concluded that B316, and similar organisms with broad polysaccharide-degrading capability, are well suited to being early colonizers and degraders of plant polysaccharides in the rumen environment.
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