Name: Acetivibrio saccincola GGR1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132679

Type strain:

Species: Acetivibrio saccincola

Strain Designation: GGR1

Culture col. no.: DSM 101079, CECT 9155

Strain history: <- D. Köck, TU Munich, Chair of Microbiology, Freising-Weihenstephan, Germany; GGR1 <- D. Köck; {2015}

NCBI tax ID(s): 1677857 (species)

Other strains from Acetivibrio saccincola

A. saccincola JCM 31827, DSM 104321

Section

Acetivibrio saccincola GGR1 is an anaerobe, spore-forming, thermophilic bacterium that forms circular colonies and was isolated from thermophilic lab scale biogas plant.

colony-forming
Gram-positive
rod-shaped
spore-forming
anaerobe
thermophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Oscillospiraceae*
	Genus	*Acetivibrio*
	Species	**Acetivibrio saccincola**
	Full Scientific Name (PNU)	Acetivibrio saccincola (Koeck et al. 2016) Tindall 2019

	Synonym	Herbivorax saccincola
	Synonym	Hungateiclostridium saccincola

Information on morphological and physiological properties Morphology

[Ref.: #25017]	Gram stain	positive
[Ref.: #25017]	Cell length	5.0-10.0 µm
[Ref.: #25017]	Cell width	0.2 µm
[Ref.: #25017]	Cell shape	rod-shaped
[Ref.: #25017]	Motility	no

[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #25017]	Colony size	1.0-2.0 mm
[Ref.: #25017]	Colony color	dark yellow
[Ref.: #25017]	Colony shape	circular
[Ref.: #25017]	Cultivation medium used	GS2 agar plates

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25017]

Culture medium

GS2 agar plates

[Ref.: #25017]

Culture medium growth

[Ref.: #25017]

Culture medium composition

expand / minimize

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Culture medium

CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255)

[Ref.: #24468]

Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

[Ref.: #24468]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24468]	growth	55 °C
[Ref.: #25017]	growth	45-65 °C
[Ref.: #25017]	optimum	60 °C

[Ref.: #24468]	Temperature range	thermophilic
[Ref.: #25017]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %92.316

	pH	Kind of pH		pH
[Ref.: #25017]			optimum	7
[Ref.: #25017]			growth	6.5-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25017]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #25017]	Type of spore	endospore
[Ref.: #25017]	Ability of spore formation	yes
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25017]		NaCl		growth	0-2.0	%(w/v)
[Ref.: #25017]		NaCl		optimum	0.2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25017]	arabinose ChEBI	-	growth
[Ref.: #25017]	casein	-	hydrolysis
[Ref.: #25017]	cellobiose ChEBI	+	carbon source
[Ref.: #25017]	cellulose ChEBI	+	carbon source
[Ref.: #25017]	citrate ChEBI	-	degradation
[Ref.: #25017]	fructose ChEBI	-	growth
[Ref.: #25017]	galactitol ChEBI	-	fermentation
[Ref.: #25017]	galactose ChEBI	+	carbon source
[Ref.: #25017]	glucose ChEBI	+	carbon source
[Ref.: #25017]	L-phenylalanine ChEBI	-	other
[Ref.: #25017]	lactose ChEBI	-	growth
[Ref.: #25017]	lysine ChEBI	-	other
[Ref.: #25017]	mannose ChEBI	-	growth
[Ref.: #25017]	ornithine ChEBI	-	other
[Ref.: #25017]	sorbitol ChEBI	+	carbon source
[Ref.: #25017]	starch ChEBI	-	growth
[Ref.: #25017]	sucrose ChEBI	-	growth
[Ref.: #25017]	sulfate ChEBI	-	reduction
[Ref.: #25017]	tryptophan ChEBI	-	energy source
[Ref.: #25017]	urea ChEBI	-	hydrolysis
[Ref.: #25017]	xylan ChEBI	+	carbon source
[Ref.: #25017]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #25017]		indole ChEBI

	Physiological tests	Metabolite	Indole test
[Ref.: #25017]		indole ChEBI	-

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #25017]		catalase	-	1.11.1.6
[Ref.: #25017]		tryptophan deaminase	-	4.1.99.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	lipid metabolism	58.06	18 of 31
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	glutamate and glutamine metabolism	53.57	15 of 28
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	alanine metabolism	48.28	14 of 29
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	lysine metabolism	45.24	19 of 42
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	44.44	4 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #24468]	Sample type/isolated from	thermophilic (55 °C) lab scale biogas plant
[Ref.: #24468]	Geographic location (country and/or sea, region)	Freising near Munich
[Ref.: #24468]	Country	Germany
[Ref.: #24468]	Country ISO 3 Code	DEU
[Ref.: #24468]	Continent	Europe
[Ref.: #24468]	Geographic location	48.3996°/11.7297°
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Engineered	#Industrial	#Plant (Factory)
#Engineered	#Laboratory	-
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LN868252 (>99% sequence identity) for Acetivibrio saccincola subclade from Microbeatlas

Aquatic Samples	988
Soil Samples	4138
Animal Samples	1026
Plant Samples	1183
Total Samples	7335

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #24468]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #24468]	Clostridium sp. GGR1 partial 16S rRNA gene, isolate GGR1	LN868252	1421	ENA	1677857 tax ID
[Ref.: #25017]	Clostridium sp. GGR1 partial 16S rRNA gene, isolate GGR1	LN868252.1	1421	GenBank	1677857 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Acetivibrio saccincola GGR1	GCA_002844395	complete	GenBank	1677857 tax ID	*
[Ref.: #66792]	Herbivorax saccincola strain GGR1	1677857.3	complete	PATRIC	1677857 tax ID	*
[Ref.: #66792]	Acetivibrio saccincola GGR1	2775506833	complete	JGI IMG/M	1677857 tax ID	*

[Ref.: #25017]	GC-content	34.9 mol%	genome sequence analysis
[Ref.: #24468]	GC-content	34.9 mol%	sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Acetivibrio saccincola GGR1 NCBI: GCA_002844395.1
[Ref.: #69480]	gram-positive	yes	100	yes
[Ref.: #69480]	anaerobic	yes	100	yes
[Ref.: #69480]	spore-forming	yes	99.999	yes
[Ref.: #69480]	thermophile	yes	92.316	yes
[Ref.: #69480]	motile	yes	85.968	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Acetivibrio saccincola GGR1 NCBI: GCA_002844395.1
[Ref.: #69481]	spore-forming	yes	88	no

Availability in culture collections External links

[Ref.: #24468]

Culture collection no.

DSM 101079, CECT 9155

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Characterization and high-quality draft genome sequence of Herbivorax saccincola A7, an anaerobic, alkaliphilic, thermophilic, cellulolytic, and xylanolytic bacterium.	Aikawa S, Baramee S, Sermsathanaswadi J, Thianheng P, Tachaapaikoon C, Shikata A, Waeonukul R, Pason P, Ratanakhanokchai K, Kosugi A	Syst Appl Microbiol	10.1016/j.syapm.2018.01.010	2018	*
Phylogeny	Herbivorax saccincola gen. nov., sp. nov., a cellulolytic, anaerobic, thermophilic bacterium isolated via in sacco enrichments from a lab-scale biogas reactor.	Koeck DE, Mechelke M, Zverlov VV, Liebl W, Schwarz WH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001374	2016	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#24468

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101079

#25017

D. E. M. Koeck, M.,Zverlov, V. V.,Liebl, W.,Schwarz, W. H.: Herbivorax saccincola gen. nov., sp. nov., a cellulolytic, anaerobic, thermophilic bacterium isolated via in sacco enrichments from a lab-scale biogas reactor. IJSEM 66: 4458 - 4463 2016 ( DOI 10.1099/ijsem.0.001374 , PubMed 27499077 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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