Acetivibrio saccincola (DSM 101079, CECT 9155, GGR1)

Name: Acetivibrio saccincola (DSM 101079, CECT 9155, GGR1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132679

Type strain

Strain Designation GGR1

Culture col. no. DSM 101079 CECT 9155 GGR1

NCBI tax ID(s) 1677857

Special Collections DSMZ Literature strains

Links

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

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

Name and taxonomic classification

SI-ID 396620

CECT 9155,DSM 101079

@ref 20215

Last LPSN update 2025-12-16 10:01:34

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Oscillospiraceae

Genus Acetivibrio

Species Acetivibrio saccincola

Full scientific name Acetivibrio saccincola (Koeck et al. 2016) Tindall 2019

Synonyms (2)

Herbivorax saccincola
Hungateiclostridium saccincola

BacDive ID	Other strains from **Acetivibrio saccincola** (1)	Type strain
164132	A. saccincola JCM 31827, DSM 104321

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
25017	positive	5.0-10.0 µm	0.2 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Medium used
25017	1.0-2.0 mm	dark yellow	circular	GS2 agar plates

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
25017	GS2 agar plates			6g yeast extract, 2.9g K2HPO4, 2.1g urea, 1.5g KH2PO4, 2.9g trisodium citrate dihydrate, 1.0g cysteine hydrochloride monohydrate, 10 g MOPS, 0.1g MgCl2.6H2O, 0.015g CaCl2.2H2O, 0.125mg FeSO4 .7H2O and 0.01 % resazurin
24468	CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255)		Medium recipe at MediaDive	Name: CLOSTRIDIUM (GS) MEDIUM (DSMZ Medium 255; with strain-specific modifications) Composition: Cellulose 9.98004 g/l Morpholinopropane sulfonic acid 9.98004 g/l Yeast extract 5.98802 g/l Cellobiose 4.99002 g/l Urea 1.99601 g/l L-Cysteine HCl x H2O 0.998004 g/l K2HPO4 x 3 H2O 0.998004 g/l KH2PO4 0.499002 g/l MgCl2 x 6 H2O 0.499002 g/l CaCl2 x 2 H2O 0.0499002 g/l FeSO4 x 7 H2O 0.0012475 g/l Sodium resazurin 0.000499002 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24468	positive	growth	55	thermophilic
25017	positive	growth	45-65	thermophilic
25017	positive	optimum	60	thermophilic

Culture pH

@ref	Ability	Type	PH	PH range
25017	positive	optimum	7
25017	positive	growth	6.5-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
25017	anaerobe
125438	anaerobe	94.843
125439	anaerobe	99.6

Spore formation

@ref	Type of spore	Spore formation
25017	endospore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25017	NaCl	positive	growth	0-2.0 %(w/v)
25017	NaCl		optimum	0.2 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25017	22599 ChEBI	arabinose	-	growth
25017		casein	-	hydrolysis
25017	17057 ChEBI	cellobiose	+	carbon source
25017	62968 ChEBI	cellulose	+	carbon source
25017	16947 ChEBI	citrate	-	degradation
25017	28757 ChEBI	fructose	-	growth
25017	16813 ChEBI	galactitol	-	fermentation
25017	28260 ChEBI	galactose	+	carbon source
25017	17234 ChEBI	glucose	+	carbon source
25017	17295 ChEBI	L-phenylalanine	-	other
25017	17716 ChEBI	lactose	-	growth
25017	25094 ChEBI	lysine	-	other
25017	37684 ChEBI	mannose	-	growth
25017	18257 ChEBI	ornithine	-	other
25017	30911 ChEBI	sorbitol	+	carbon source
25017	28017 ChEBI	starch	-	growth
25017	17992 ChEBI	sucrose	-	growth
25017	16189 ChEBI	sulfate	-	reduction
25017	27897 ChEBI	tryptophan	-	energy source
25017	16199 ChEBI	urea	-	hydrolysis
25017	37166 ChEBI	xylan	+	carbon source
25017	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25017	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
25017	35581 ChEBI	indole	-

Enzymes

@ref	Value	Activity	Ec
25017	catalase	-	1.11.1.6
25017	tryptophan deaminase	-	4.1.99.1

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Bioreactor	-
#Engineered	#Industrial	#Plant (Factory)
#Engineered	#Laboratory	-
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24468	thermophilic (55 °C) lab scale biogas plant	Freising near Munich	Germany	DEU	Europe	48.3996	11.7297 48.3996/11.7297

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24468	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM284439v1 assembly for Acetivibrio saccincola GGR1	complete	GCA_002844395	1677857.3	2775506833	1677857	97.33

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24468	Clostridium sp. GGR1 partial 16S rRNA gene, isolate GGR1	LN868252	1421		1677857

GC content

@ref	GC-content (mol%)	Method
25017	34.9	genome sequence analysis
24468	34.9	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acetivibrio saccincola GGR1
NCBI: GCA_002844395

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	85.40	no
125439	motility	BacteriaNetⓘ	yes	82.70	no
125439	gram_stain	BacteriaNetⓘ	variable	77.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acetivibrio saccincola GGR1
NCBI: GCA_002844395.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	64.77	yes
125438	anaerobic	anaerobicⓘ	yes	94.84	no
125438	aerobic	aerobicⓘ	no	97.87	yes
125438	spore-forming	spore-formingⓘ	yes	75.47	yes
125438	thermophilic	thermophileⓘ	yes	56.13	yes
125438	flagellated	motile2+ⓘ	yes	80.28	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Discovery and Biosynthesis of Celluxanthenes, Antibacterial Arylpolyene Alkaloids From Diverse Cellulose-Degrading Anaerobic Bacteria.	Ishida K, Krabbe J, Meisinger PR, Shabuer G, Schieferdecker S, Cyrulies M, Tank C, Barnes E, Paetz C, Hertweck C.	Angew Chem Int Ed Engl	10.1002/anie.202503697	2025
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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Acetivibrio saccincola (DSM 101079, CECT 9155, GGR1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002844395

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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