2026-10-28T23:48:24Z

Yuqili: /* Methylome */

== Introduction ==

== Global Methane Hub Metadata ==
{| class="wikitable"
|+
|Origin:
|Illinois, Mackie Lab
|-
|Sequenced by:
|Yuqi Li
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|MIC and Culturing Conditions by:
|Yuqi Li
|}

== Genome ==
[[File:139BGenome.png|none|thumb|Circos plot of ''Acetitomaculum ruminis'' 139B. Source: Yuqi Li]]

== DefenseFinder Results ==

== Methylome ==
{| class="wikitable"
!Motif
!Percent methylated
|-
|CTGC(6mA)G
| align="right" |95.68%
|-
|TA(6mA)GNNNNNNTCC
| align="right" |95.61%
|-
|GG(6mA)NNNNNNCTTA
| align="right" |96.1%
|-
|G(6mA)TGNNNNNNTCC
| align="right" |84.95%
|-
|GG(6mA)NNNNNNCATT
| align="right" |92.38%
|-
|G(6mA)TCG
| align="right" |89.82%
|-
|A(6mA)TGNNNNNNTCC
| align="right" |96.19%
|-
|GG(6mA)NNNNNNCATT
| align="right" |90.36%
|-
|GAT(5mC)
| align="right" |32.66%
|}

== Methylating E. coli Strains ==

== Culturing Conditions ==

== Antibiotic MIC Tests ==

== Protocols ==

== Transformation Results ==

== External Links ==

Acetitomaculum ruminis 139BT

2026-10-28T23:45:05Z

Yuqili: /* Global Methane Hub Metadata */

File:139BGenome.png

2026-10-28T23:44:17Z

Yuqili:

139BGenome

Ruminococcus productus B43

2026-10-28T23:40:26Z

Yuqili: Created page with " == Introduction == == Global Methane Hub Metadata == {| class="wikitable" |+ |Origin: | |- |Sequenced by: | |- |Assembled by: | |- |Methylome called by: | |- |Methyltransferases cloned by: | |- |MIC and Culturing Conditions by: | |- |Transformation by: | |} == Genome == == DefenseFinder Results == == Methylome == == Methylating E. coli Strains == == Culturing Conditions == == Antibiotic MIC Tests == == Protocols == == Transformation Results == == External Link..."

2026-10-28T22:58:34Z

Yuqili:

MB2003

Prevotella bryantii B14

2026-10-28T22:51:29Z

Yuqili: /* Antimicrobial MIC Tests */

[[File:B14SEM.jpg|thumb|Scanning electron microscopy (SEM) image of ''Prevotella bryantii'' B14, showing its characteristic rod-shaped morphology. Source: Yuqi Li]]

== Introduction ==
'''''Segatella bryantii'' B14'''

''Segatella bryantii'' B14 (DSM 11371), formerly ''Prevotella bryantii'', was isolated from rumen contents of a Holstein cow fed alfalfa hay in the USA [1]. It was originally named as ''Bacteroides ruminicola'' subsp. ''brevis'' and subsequently changed to ''Prevotella bryantii'' [2]. The strain was originally designated B14 but B14 is commonly used. B14 has been the focus of many studies and is able to ferment a wide range of carbohydrates [3, 4]. The genes involved in xylan degradation have been characterized [5].

Taxonomic analysis of the genus ''Prevotella'' lists B14 as the ''Segatella bryantii'' type strain [6]. However, NCBI now records B14 and C21a as belonging to the species ''Segatella baroniae'', although the reason for this is unclear.

Draft genome sequences are available for B14 (3.6 Mb) [7]. Resequencing indicates that ''Segatella bryantii'' strains (B14 and C21a) each have two replicons of ~2.5 and ~1.0 Mb. Two other sequenced ''P. bryantii'' cultures (TC1-1, TS1-5) have a similar genomic architecture suggesting this is a feature of this species.

The B14 genome encodes a large conjugative transposon [8] although this has not been characterized in detail or shown to be transferable. Based on the presence of a the traG gene (TIGR03783) large conjugative transposons may be encoded by other rumen ''Prevotella'' strains.

LPSN: ''Segatella bryantii'' (Avguštin et al. 1997) Hitch et al. 2023.

NCBI: ''Segatella baroniae''.

GTBD: ''Prevotella bryantii''.

Risk group: 2.

== Global Methane Hub Metadata ==
{| class="wikitable"
|Origin:
|Illinois, Mackie Lab
|-
|Sequenced by:
|Yuqi Li
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|MIC and Culturing Conditions by:
|Yuqi Li
|}

== Genome ==
[[File:P. bryantii B14.png|center|thumb|Circos plot of ''P. bryantii'' B14. Source: Yuqi Li]]

== DefenseFinder Results ==
add here

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|GTC(6mA)NNNNNRTC/G(6mA)YNNNNNTGAC
|75.00%/80.51%
|-
|GTHN(6mA)NCC
|76.99%
|-
|GTC(6mA)G
|71.12%
|-
|A(6mA)CNNNNNGGG/C(4mC)CNNNNNGTT
|82.78%/
|-
|GG(5mC)GT
|82.25%
|-
|A(5mC)GCC
|81.20%
|}

== Methylating ''E. coli'' ==
add here

== Culturing Conditions ==
''Prevotella bryantii'' B14 grows well in M2GSC or M2G medium at 37 °C under strictly anaerobic conditions. Cells can be grown overnight in either medium. B14 can also be grown on M10G agar plates, with colonies typically appearing after 36–72 h of incubation. Cultures and agar plates are maintained in an anaerobic chamber containing 95% CO2 and 5% H2.

== Antimicrobial MIC Tests ==
[[File:Data 2.jpg|thumb|MIC tests of ''P. bryantii'' B14. Source: Yuqi Li|left]]
{| class="wikitable"
!Antibiotic
!Concentration ('''μ'''g/mL)
|-
|Ampicillin
|0.52
|-
|Kanamycin
|Resistant (>200 μg/mL)
|-
|Chloramphenicol
|Resistant (>200 μg/mL)
|-
|Tetracycline
|0.20
|-
|Gentamicin
|Resistant (>200 μg/mL)
|-
|Streptomycin
|Resistant (>200 μg/mL)
|-
|Erythromycin
|4.3
|}

== Protocols ==
add here

== Transformation Results ==
add here

== External Links ==
[1] Bryant MP, Small N, Bouma C, Chu H. 1958. ''Bacteroides ruminicola'' n. sp. and ''Succinimonas amylolytica''; the new genus and species. Species of succinic acid-producing anaerobic bacteria of the bovine rumen. J Bacteriol 76: 15-23. doi: 10.1128/jb.76.1.15-23.1958.

[2] Avgustin G, Wallace RJ, Flint HJ. 1997. 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''. Int J Syst Bacteriol 47: 284-8. doi: 10.1099/00207713-47-2-284.

[3] Accetto T, Avguštin G. 2019. The diverse and extensive plant polysaccharide degradative apparatuses of the rumen and hindgut ''Prevotella'' species: A factor in their ubiquity? Syst Appl Microbiol 42: 107-116. doi: 10.1016/j.syapm.2018.10.001.

[4] <nowiki>https://bacdive.dsmz.de/strain/12536</nowiki>.

[5] Dodd D, Mackie RI, Cann IK. 2011. Xylan degradation, a metabolic property shared by rumen and human colonic Bacteroidetes. Mol Microbiol 79: 292-304. doi: 10.1111/j.1365-2958.2010.07473.x.

[6] Hitch TCA, Bisdorf K, Afrizal A, Riedel T, Overmann J, Strowig T, Clavel T. 2022. A taxonomic note on the genus ''Prevotella'': Description of four novel genera and emended description of the genera ''Hallella'' and ''Xylanibacter''. Syst Appl Microbiol 45: 126354. doi: 10.1016/j.syapm.2022.126354.

[7] Purushe J, Fouts DE, Morrison M, White BA, Mackie RI; North American Consortium for Rumen Bacteria; Coutinho PM, Henrissat B, Nelson KE. 2010. Comparative genome analysis of ''Prevotella ruminicola'' and ''Prevotella bryantii'': insights into their environmental niche. Microb Ecol 60: 721-9. doi: 10.1007/s00248-010-9692-8.

[8] Gorenc K, Accetto T, Avguštin G. 2012. Bioinformatic evidence and characterization of novel putative large conjugative transposons residing in genomes of genera ''Bacteroides'' and ''Prevotella''. Folia Microbiol (Praha) 57: 285-90. doi: 10.1007/s12223-012-0126-5.

Prevotella ruminicola 23T

2026-10-28T22:48:26Z

Yuqili:

[[File:SEMP23.jpg|thumb|Scanning electron microscopy image of ''Prevotella ruminicola'' 23. Source: Yuqi Li]]

== Introduction ==
'''''Prevotella ruminicola'' 23T''' (ATCC 19189, DSM 19721), also known as ''Xylanibacter ruminicola'' 23, is an obligately anaerobic, Gram-negative bacterium originally isolated from the bovine rumen [1]. It is the type strain of ''P. ruminicola'' and was originally described as ''Bacteroides ruminicola'' by Bryant et al. in 1958 [1]. The species was subsequently transferred to the genus ''Prevotella'' in 1990 [2].

''P. ruminicola'' 23 contributes to the degradation of plant polysaccharides in the rumen, particularly xylan and other hemicelluloses. Its genome encodes numerous carbohydrate-active enzymes involved in the degradation of non-cellulosic polysaccharides [3]. Several xylan-degrading enzymes have been characterized, including a bifunctional xylanase/endoglucanase and a GH10 xylanase–ferulic acid esterase [4, 5].

The genome sequence of ''P. ruminicola'' 23 is available under GenBank accession CP002006 [3]. The species was reclassified as ''Xylanibacter ruminicola'' following a taxonomic revision of the genus ''Prevotella'' [6]. However, LPSN currently retains ''Prevotella ruminicola'' as the correct name.

LPSN: ''Prevotella ruminicola'' (Bryant et al. 1958) Shah and Collins 1990.

NCBI: ''Xylanibacter ruminicola'' (Bryant et al. 1958) Hitch et al. 2023.

Type strain: ATCC 19189 = DSM 19721 = JCM 8958 = Bryant 23.

Genome: CP002006.

Risk group: 2.

== Global Methane Hub Metadata ==
{| class="wikitable"
|Origin:
|Illinois, Mackie Lab
|-
|Sequenced by:
|Yuqi Li
|-
|Assembled by:
|William G. Alexander
|-
|Methylome called by:
|William G. Alexander
|-
|MIC and Culturing Conditions by:
|Yuqi Li
|}

== Genome ==
[[File:Circos plot of P. ruminicola 23.png|thumb|Circos plot of ''P. ruminicola'' 23T. Source: Yuqi Li|center]]

== Methylome ==
{| class="wikitable"
|+
!Motif
!Percent methylated
|-
|G(6mA)TC
|95.98
|-
|CYC(6mA)NNNNNNNTCG/CG(6mA)NNNNNNNTGRG
|86.34/95.59
|-
|GR(5mC)GYC
|95.15
|-
|GG(5mC)C
|85.78
|-
|AG(5mC)TC
|84.75
|-
|GAG(5mC)T
|77.28
|}

== Culturing Conditions ==
''Prevotella ruminicola'' 23 grows well in M2GSC or M2G medium at 37 °C under strictly anaerobic conditions. ''P. ruminicola'' 23 can also be cultivated on M10G agar plates. Cultures and agar plates are maintained in an anaerobic chamber containing 95% CO2 and 5% H2.

== Antimicrobial MIC Tests ==
[[File:P23MIC.jpg|left|thumb|MIC tests of ''P. ruminicola'' 23. Source: Yuqi Li]]
{| class="wikitable"
!Antibiotic
!Concentration ('''μ'''g/mL)
|-
|Ampicillin
|Resistant (>200 μg/mL)
|-
|Kanamycin
|Resistant (>200 μg/mL)
|-
|Chloramphenicol
|1.03
|-
|Tetracycline
|0.31
|-
|Gentamicin
|Resistant (>200 μg/mL)
|-
|Streptomycin
| < 0.0625
|-
|Erythromycin
|1.29
|}

== External Links ==
[1] Bryant MP, Small N, Bouma C, Chu H. 1958. ''Bacteroides ruminicola'' n. sp. and ''Succinimonas amylolytica''; the new genus and species; species of succinic acid-producing anaerobic bacteria of the bovine rumen. J Bacteriol 76:15–23. doi:10.1128/JB.76.1.15-23.1958.

[2] Shah HN, Collins DM. 1990. ''Prevotella'', a new genus to include ''Bacteroides melaninogenicus'' and related species formerly classified in the genus ''Bacteroides''. Int J Syst Bacteriol 40:205–208. doi:10.1099/00207713-40-2-205.

[3] Purushe J, Fouts DE, Morrison M, White BA, Mackie RI, et al. 2010. Comparative genome analysis of ''Prevotella ruminicola'' and ''Prevotella bryantii'': insights into their environmental niche. Microb Ecol 60:721–729. doi:10.1007/s00248-010-9692-8.

[4] Whitehead TR. 1993. Analyses of the gene and amino acid sequence of the ''Prevotella (Bacteroides) ruminicola'' 23 xylanase reveals unexpected homology with endoglucanases from other genera of bacteria. Curr Microbiol 27:27–33. doi:10.1007/BF01576830.

[5] Dodd D, Kocherginskaya SA, Spies MA, Beery KE, Abbas CA, Mackie RI, Cann IKO. 2009. Biochemical analysis of a β-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in ''Prevotella ruminicola'' 23. J Bacteriol 191:3328–3338. doi:10.1128/JB.01628-08.

[6] Hitch TCA, Bisdorf K, Afrizal A, Riedel T, Overmann J, Strowig T, Clavel T. 2022. A taxonomic note on the genus ''Prevotella'': Description of four novel genera and emended description of the genera ''Hallella'' and ''Xylanibacter''. Syst Appl Microbiol 45:126354. doi:10.1016/j.syapm.2022.126354.