Sharpea azabuensis KH1P5

2026-09-02T15:51:42Z

Gussam: /* Methylating E. coli Strains */

[[File:Sabu tube.png|thumb|''S. azabuensis'' KH1P5 in liquid culture exhibiting its dense layer of EPS. Source: Dr. Roy Rodriguez Carrero|346x346px]]

== Introduction ==
''[[Sharpea azabuensis]]'' KH1P5 is a high-interest microbe to the Global Methane Hub. It produces a thick, mucoidal layer of [[wikipedia:Extracellular_polymeric_substance|extracellular polymeric substance (EPS)]] that requires removal before work with the culture.

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|New Zealand, Kelly Lab
|-
|Sequenced by:
|Sam Mahoney Kurpe
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|Methyltransferases cloned by:
|Roy Rodriguez Carrero
|-
|MIC and Culturing Conditions by:
|Roy Rodriguez Carrero
|-
|Transformation by:
|Roy Rodriguez Carrero
|}

== Genome ==
[[File:S azabuensis circos.png|Circos plot of ''S. azabuensis'' KH1P5. Source: Dr. William G. Alexander|center|thumb]]

== DefenseFinder Results ==

== Methylome ==
While ''S. azabuensis'' KH1P5 possesses two putative Type II restriction endonucleases, no methylation is detectable in the isolate. Also, these two genes do not methylate in ''E. coli'' strains, suggesting that they're vestigial defense systems.

== Methylating E. coli Strains ==
Use a strain of ''E. coli'' that lacks dam, dcm, and hsdRMS, such as ...

== Culturing Conditions ==
''S. azabuensis'' KH1P5 grows well in stock [[RCM]] at 37 °C.

== Antibiotic MIC Tests ==
[[File:Sabu MIC.png|left|thumb|MIC tests of ''S. azabuensis''. Source: Dr. Roy Rodriguez Carrero]]
{| class="wikitable"
!antibiotic
!concentration (ug/mL)
|-
|chloramphenicol
|0.38
|-
|erythromycin
|1
|-
|kanamycin
|resistant
|-
|spectinomycin
|96
|-
|tetracycline
|0.23
|}

== Protocols ==

* [[Removal of extracellular material via chelation washing]]

== Transformation Results ==

== External Links ==

Prevotella ruminicola

2026-07-17T14:10:27Z

Gussam: /* Methylome */

{{Short description|Species of anaerobic rumen bacterium}}
{{Speciesbox
| genus = Prevotella
| species = ruminicola
| authority = (Bryant et al. 1958) Shah and Collins 1990
| type_strain = ATCC 19189; Bryant 23; DSM 19721; JCM 8958
| synonyms =
* ''Bacteroides ruminicola'' Bryant et al. 1958
* ''Xylanibacter ruminicola'' (Bryant et al. 1958) Hitch et al. 2023
| synonyms_ref = <ref name="LPSN">{{cite web |title=Species: Prevotella ruminicola |website=List of Prokaryotic names with Standing in Nomenclature |publisher=Leibniz Institute DSMZ |url=https://lpsn.dsmz.de/species/prevotella-ruminicola |access-date=6 July 2026}}</ref>
}}

'''''Prevotella ruminicola''''' is a species of [[obligate anaerobe|obligately anaerobic]] bacterium in the family ''[[Prevotellaceae]]''. It is associated with the [[rumen]] of [[cattle]] and other [[ruminants]], where it contributes to the [[fermentation]] of plant-derived substrates. The species was originally described from the bovine rumen as ''Bacteroides ruminicola'' in 1958 and was later transferred to the genus ''[[Prevotella]]''.<ref name="Bryant1958">{{cite journal |last1=Bryant |first1=M. P. |last2=Small |first2=Nola |last3=Bouma |first3=Cecelia |last4=Chu |first4=Hilda |title=Bacteroides ruminicola n. sp. and Succinimonas amylolytica; the new genus and species; species of succinic acid-producing anaerobic bacteria of the bovine rumen |journal=Journal of Bacteriology |year=1958 |volume=76 |issue=1 |pages=15–23 |doi=10.1128/jb.76.1.15-23.1958 |pmid=13563384 |pmc=290147}}</ref><ref name="Shah1990">{{cite journal |last1=Shah |first1=H. N. |last2=Collins |first2=D. M. |title=Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides |journal=International Journal of Systematic Bacteriology |year=1990 |volume=40 |issue=2 |pages=205–208 |doi=10.1099/00207713-40-2-205 |pmid=2223612}}</ref>

== Taxonomy ==
The species was first described in 1958 as ''Bacteroides ruminicola'', one of several [[succinic acid]]-producing anaerobic bacteria isolated from bovine rumen material.<ref name="Bryant1958" /> In 1990, the genus ''Prevotella'' was proposed for several species formerly classified in ''Bacteroides'', including the transfer of ''B. ruminicola'' to ''Prevotella ruminicola''.<ref name="Shah1990" />

In 1997, ruminal isolates previously assigned to ''P. ruminicola'' were re-examined. This work led to the proposal of ''Prevotella brevis'', ''Prevotella bryantii'', and ''Prevotella albensis'', and to a narrower definition of ''P. ruminicola''.<ref name="Avgustin1997">{{cite journal |last1=Avgustin |first1=Gorazd |last2=Wallace |first2=R. John |last3=Flint |first3=Harry J. |title=Phenotypic diversity among ruminal isolates of Prevotella ruminicola: proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and redefinition of Prevotella ruminicola |journal=International Journal of Systematic Bacteriology |year=1997 |volume=47 |issue=2 |pages=284–288 |doi=10.1099/00207713-47-2-284 |pmid=9103611}}</ref>

A later genome-based taxonomic study proposed the combination ''Xylanibacter ruminicola''.<ref name="Hitch2022">{{cite journal |last1=Hitch |first1=Thomas C. A. |last2=Bisdorf |first2=Kevin |last3=Afrizal |first3=Afrizal |last4=Riedel |first4=Thomas |last5=Overmann |first5=Jörg |last6=Strowig |first6=Till |last7=Clavel |first7=Thomas |title=A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter |journal=Systematic and Applied Microbiology |year=2022 |volume=45 |issue=6 |doi=10.1016/j.syapm.2022.126354 |pmid=36067550|doi-access=free }}</ref> The List of Prokaryotic names with Standing in Nomenclature currently lists ''Prevotella ruminicola'' as the correct name and treats ''Xylanibacter ruminicola'' as a synonym.<ref name="LPSN" />

== Characteristics ==
''P. ruminicola'' is an obligately anaerobic, Gram-negative, rod-shaped bacterium. The species name ''ruminicola'' means "inhabitant of the rumen".<ref name="LPSN" />

The species is [[saccharolytic]] and has been studied for its ability to use non-cellulosic plant polysaccharides. ''P. ruminicola'' has been reported to contribute to [[hemicellulose]] utilization in the bovine rumen, including the degradation of [[xylan]].<ref name="Dodd2009">{{cite journal |last1=Dodd |first1=Dylan |last2=Kocherginskaya |first2=Svetlana A. |last3=Spies |first3=M. Ashley |last4=Beery |first4=Kyle E. |last5=Abbas |first5=Charles A. |last6=Mackie |first6=Roderick I. |last7=Cann |first7=Isaac K. O. |title=Biochemical analysis of a β-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23 |journal=Journal of Bacteriology |year=2009 |volume=191 |issue=10 |pages=3328–3338 |doi=10.1128/JB.01628-08 |pmid=19304844 |pmc=2687155}}</ref>

== Culturing ==
What kind of media do I like? Are there any issues to worry about? Links should go to media recipes and protocols for culturing.

== Genome ==
{| class="wikitable"
|+
![[Replicon]]
!Length
!%GC content
|-
|chr1
|3.5 Mbp
|56.7%
|}

== Methylome ==
{| class="wikitable"
|+
!motif
!motifs methylated
!motifs total
!% methylated
|-
|G(6mA)TC
|24558
|25441
|96.5%
|-
|CGW(5mC)G
|11111
|12222
|whatever%
|-
|C(4mC)GG
|20222
|25555
|yep%
|}
Add % of data explained

== References ==
{{Reflist}}

{{Taxonbar|from=Q61764147}}

[[Category:Bacteroidia]]

Global Methane Hub Wikipedia - User contributions [en]

Sharpea azabuensis KH1P5

Prevotella ruminicola