Aminobacterium colombiense (DSM 12261, ALA-1)

Multimedia

• @ref:	66793
  multimedia content:	EM_DSM_12261_1.jpg
  multimedia.multimedia content:	EM_DSM_12261_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
4661	AMINOMONAS MEDIUM (DSMZ Medium 846)		Medium recipe at MediaDive	Name: AMINOMONAS MEDIUM (DSMZ Medium 846) Composition: Yeast extract 1.99402 g/l Na2CO3 1.49551 g/l L-Serine 1.04686 g/l NaCl 0.997009 g/l Na2S x 9 H2O 0.498504 g/l KCl 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l MgCl2 x 6 H2O 0.398804 g/l KH2PO4 0.299103 g/l NH4Cl 0.299103 g/l K2HPO4 0.199402 g/l CaCl2 x 2 H2O 0.149551 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l NaOH 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Folic acid 1.99402e-05 g/l Biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l Distilled water

Culture temp

Oxygen tolerance

Spore formation

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	threonine metabolism	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CMP-KDO biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	lipid A biosynthesis	88.89	8 of 9
66794	peptidoglycan biosynthesis	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	citric acid cycle	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	NAD metabolism	72.22	13 of 18
66794	photosynthesis	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	phenylalanine metabolism	69.23	9 of 13
66794	purine metabolism	67.02	63 of 94
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	alanine metabolism	65.52	19 of 29
66794	histidine metabolism	65.52	19 of 29
66794	glycolysis	64.71	11 of 17
66794	proline metabolism	63.64	7 of 11
66794	isoleucine metabolism	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	leucine metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	starch degradation	60	6 of 10
66794	Entner Doudoroff pathway	60	6 of 10
66794	methylglyoxal degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	methionine metabolism	57.69	15 of 26
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	propanol degradation	57.14	4 of 7
66794	oxidative phosphorylation	57.14	52 of 91
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	lysine metabolism	52.38	22 of 42
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	tetrahydrofolate metabolism	50	7 of 14
66794	non-pathway related	50	19 of 38
66794	ethanol fermentation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	lactate fermentation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	glycine metabolism	50	5 of 10
66794	glutathione metabolism	50	7 of 14
66794	biotin biosynthesis	50	2 of 4
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	valine metabolism	44.44	4 of 9
66794	degradation of hexoses	44.44	8 of 18
66794	allantoin degradation	44.44	4 of 9
66794	chorismate metabolism	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	tryptophan metabolism	42.11	16 of 38
66794	arginine metabolism	41.67	10 of 24
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	degradation of sugar alcohols	37.5	6 of 16
66794	ketogluconate metabolism	37.5	3 of 8
66794	tyrosine metabolism	35.71	5 of 14
66794	lipid metabolism	35.48	11 of 31
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	nitrate assimilation	33.33	3 of 9
66794	sulfate reduction	30.77	4 of 13
66794	polyamine pathway	26.09	6 of 23
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	degradation of pentoses	25	7 of 28
66794	ascorbate metabolism	22.73	5 of 22

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence AF069287 (>99% sequence identity) for Aminobacterium colombiense subclade from Microbeatlas

Aquatic Samples	111
Soil Samples	6
Animal Samples	1
Plant Samples	1
Total Samples	119

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2588v1 assembly for Aminobacterium colombiense DSM 12261	complete	GCA_000025885	572547.3	646564503	572547	98.54

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4661	Aminobacterium colombiense 16S ribosomal RNA gene, partial sequence	AF069287	1519		572547

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Whole-genome draft assemblies of Paracoccus pantotrophus DSM 11073 and Paracoccus sp. AS002: Phylogenetics entails classification as Paracoccus versutus AS002.	Pal U, Bachmann D, Fenske L, Blank LM, Tiso T.	J Biosci Bioeng	10.1016/j.jbiosc.2025.09.003	2025
	Culture-based and culture-independent approach for the study of the methanogens and obligate anaerobes from different landfill sites.	Prakash O, Dewala SR, Nimonkar Y, Patil SK, Chauhan A, Yadav A, Dhotre DP, Ranade DR.	Front Microbiol	10.3389/fmicb.2023.1273037	2023
	Two-stage enrichment of hydrogen-oxidizing bacteria as biofertilizers.	Zhang W, Li YX, Niu Y, Zhang F, Li YB, Zeng RJ.	Chemosphere	10.1016/j.chemosphere.2020.128932	2021
	Enrichment of hydrogen-oxidizing bacteria with nitrate recovery as biofertilizers in the mixed culture.	Zhang W, Niu Y, Li YX, Zhang F, Jianxiong Zeng R.	Bioresour Technol	10.1016/j.biortech.2020.123645	2020
Enzymology	To the Understanding of Catalysis by D-Amino Acid Transaminases: A Case Study of the Enzyme from Aminobacterium colombiense.	Shilova SA, Khrenova MG, Matyuta IO, Nikolaeva AY, Rakitina TV, Klyachko NL, Minyaev ME, Boyko KM, Popov VO, Bezsudnova EY.	Molecules	10.3390/molecules28052109	2023
	Draft Genome Sequence of Clostridium ultunense Strain BS (DSMZ 10521), Recovered from a Mixed Culture.	Wei Y, Zhou H, Zhang L, Zhang J, Wang Y, Wang S, Zhou Z, Yan X.	Genome Announc	10.1128/genomea.01269-13	2014
	Characterizing the DNA Methyltransferases of Haloferax volcanii via Bioinformatics, Gene Deletion, and SMRT Sequencing.	Ouellette M, Gogarten JP, Lajoie J, Makkay AM, Papke RT.	Genes (Basel)	10.3390/genes9030129	2018
	Identification of a Putative CodY Regulon in the Gram-Negative Phylum Synergistetes.	Geng J, Luo S, Shieh HR, Wang HY, Hu S, Chen YM.	Int J Mol Sci	10.3390/ijms23147911	2022
	Developing a mesophilic co-culture for direct conversion of cellulose to butanol in consolidated bioprocess.	Wang Z, Cao G, Zheng J, Fu D, Song J, Zhang J, Zhao L, Yang Q.	Biotechnol Biofuels	10.1186/s13068-015-0266-3	2015
	Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction.	Tang L, Zhu S, Mastriani E, Fang X, Zhou YJ, Li YG, Johnston RN, Guo Z, Liu GR, Liu SL.	Sci Rep	10.1038/srep43565	2017
	Characterization of the replicator region of megaplasmid pTAV3 of Paracoccus versutus and search for plasmid-encoded traits.	Bartosik D, Baj J, Bartosik AA, Wlodarczyk M.	Microbiology (Reading)	10.1099/00221287-148-3-871	2002
Genetics	Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle.	Detman A, Mielecki D, Plesniak L, Bucha M, Janiga M, Matyasik I, Chojnacka A, Jedrysek MO, Blaszczyk MK, Sikora A.	Biotechnol Biofuels	10.1186/s13068-018-1106-z	2018
Metabolism	Pure-culture growth of fermentative bacteria, facilitated by H2 removal: bioenergetics and H2 production.	Adams CJ, Redmond MC, Valentine DL.	Appl Environ Microbiol	10.1128/aem.72.2.1079-1085.2006	2006
	A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor.	Li A, Chu Y, Wang X, Ren L, Yu J, Liu X, Yan J, Zhang L, Wu S, Li S.	Biotechnol Biofuels	10.1186/1754-6834-6-3	2013
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Phylogeny	A freshwater cyanophage whose genome indicates close relationships to photosynthetic marine cyanomyophages.	Dreher TW, Brown N, Bozarth CS, Schwartz AD, Riscoe E, Thrash C, Bennett SE, Tzeng SC, Maier CS.	Environ Microbiol	10.1111/j.1462-2920.2011.02502.x	2011
Genetics	Complete genome sequence of Aminobacterium colombiense type strain (ALA-1).	Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.902116	2010
Phylogeny	Methanobacterium kanagiense sp. nov., a hydrogenotrophic methanogen, isolated from rice-field soil.	Kitamura K, Fujita T, Akada S, Tonouchi A.	Int J Syst Evol Microbiol	10.1099/ijs.0.026013-0	2011
Phylogeny	Aminobacterium colombiensegen. nov. sp. nov., an amino acid-degrading anaerobe isolated from anaerobic sludge.	Baena S, Fardeau ML, Labat M, Ollivier B, Thomas P, Garcia JL, Patel BK	Anaerobe	10.1006/anae.1998.0170	1998