Data · dataset · 2026
Investigating the metabolic function of the rumen microbiome
Listed in ZivaHub and Deakin Research Online and DMU Figshare and UCL Research Data Repository — shown once because both records carry DOI 10.17034/32633523.v1
The enormity of bacterial diversity is such that taxonomy is necessary for classification.
Description
Taxonomy has historically used an array of different classification techniques, from GC content, to morphology, biochemical capability, and more recently,16S rDNA and whole genome analyses. Currently, there is no standard approach to placing a bacterium taxonomically, leading to a large degree of subjectivity.<br><br>Average nucleotide identity (ANI) analyses of 71 culture-based genomes and 64<br>metagenome-assembled genomes revealed vast genetic diversity, with the genomes clustering into 59 genera and 75 species.
Where these species formed groups of four or more genomes, pangenomic analyses were carried out on both these groups, and the original taxa they had been assigned to (<i>Butyrivibrio fibrisolvens</i>, <i>Butyrivibrio proteoclasticus</i>, <i>Butyrivibrio hungatei</i>, <i>Pseudobutyrivibrio ruminis</i>, <i>Pseudobutyrivibrio xylanivorans</i>, and an additional unnamed <i>Butyrivibrio sp</i> group). Core genes only formed 0.66-8.50% of the genomes of the original taxa, revealing a wealth of accessory genes.
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In contrast, the core genes for the groups formed by ANIm analysis composed 38.48-76.67% of the genomes. Many of the accessory genes were identified as carbohydrate active enzymes, belonging to glycosyl hydrolase families 2, 3, 5, 13, and 43. Cloning and expression of a selection of these genes was attempted, but success was limited due to time constraints.<br><br>The culture-based genomes were bioprospected for linoleate isomerases, and putative enzymes identified.
Two of these were selected for expression and purification. The resulting proteins were incubated with linoleic acid and the incubations analysed via gas chromatography. Whilst peaks could be seen at appropriate retention times, it is inconclusive as to whether this is as a result of these proteins catalysing the breakdown of linoleic acid.
This thesis provides the largest pangenomic study on<i> Butyrivibrio</i> and <i>Pseudobutyrivibrio</i> to date. As such, it provides novel insight into the functional and genomic capacity of these dominant rumen bacteria.<br>
Links
Where it is published
- DOI doi.org/10.17034/32633523.v1 ↗
DOI / persistent id · from zivahub uct ac za
Catalogue records · 1
- OAI-PMH record api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Af… ↗
metadata API · from zivahub uct ac za
Topics
- From keywords
- Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Economics & Finance · Economics & Finance · Economics & Finance · Economics & Finance · Life Sciences · Life Sciences · Life Sciences · Life Sciences
- Inferred from text
- Microbial taxonomy 83%
Provenance · 4 source records, 17 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ZivaHub | oai:figshare.com:article/32633523 | 13 d ago | JSON v1 |
| Deakin Research Online | oai:figshare.com:article/32633523 | 13 d ago | JSON v1 |
| DMU Figshare | oai:figshare.com:article/32633523 | 13 d ago | JSON v1 |
| UCL Research Data Repository | oai:figshare.com:article/32633523 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:field:310409 | enrichment · zivahub uct ac za | taxonomy-embedding@1.1.0 | title+keywords+description (83%) |
| concepts[field].local:field:earth-environmental | mapping · figshare dmu ac uk | connector:figshare_dmu_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · dro deakin edu au | connector:dro_deakin_edu_au@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · figshare dmu ac uk | connector:figshare_dmu_ac_uk@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[field].local:field:economics-finance | mapping · dro deakin edu au | connector:dro_deakin_edu_au@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · dro deakin edu au | connector:dro_deakin_edu_au@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · figshare dmu ac uk | connector:figshare_dmu_ac_uk@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · rdr ucl ac uk | connector:rdr_ucl_ac_uk@1.0.0 | |
| description | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | /metadata/dc/description |
| license_text | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| publication_date | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| title | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | /metadata/dc/title |