Trichococcus palustris (DSM 9172, CIP 105359, Z-7189)

Name: Trichococcus palustris (DSM 9172, CIP 105359, Z-7189)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2282

Type strain

Strain Designation Z-7189

Culture col. no. DSM 9172 CIP 105359 Z-7189

NCBI tax ID(s) 140314

Special Collections DSMZ CIP

History <- T.N. Zhilina, Z-7189 CIP <- 1997, DSM <- T.N. Zhilina: strain Z-7189

Links

Trichococcus palustris Z-7189 is a microaerophile, Gram-positive, oval-shaped bacterium that was isolated from swamp.

Gram-positive oval-shaped microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 48588

CIP 105359,DSM 9172

@ref 20215

Last LPSN update 2026-02-09 11:18:15

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Carnobacteriaceae

Genus Trichococcus

Species Trichococcus palustris

Full scientific name Trichococcus palustris (Zhilina et al. 1997) Liu et al. 2002

Synonyms (1)

Ruminococcus palustris

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
121521	positive	oval-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3503	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
39276	MEDIUM 118 - for Pasteurella, Actinobacillus and Psychrobacter frigidicola		Distilled water make up to (1000.000 ml);Yeast extract (1.000 g);Tryptocasein soy agar (40.000 g)
121521	CIP Medium 118-b	Medium recipe at CIP
121521	CIP Medium 187	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
3503	positive	growth	30
39276	positive	growth	30
121521	positive	growth	5-30
121521	negative	growth	37
121521	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
3503	microaerophile
121521	facultative anaerobe

Murein

@ref	Murein short key	Type
3503	A11.31	A4alpha L-Lys-D-Asp

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	+	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	+	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
121521	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
121521	606565 ChEBI	hippurate	+	hydrolysis
68371	15443 ChEBI	inulin	+	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	+	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
121521	17632 ChEBI	nitrate	-	reduction
121521	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	+	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121521	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
121521	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
121521	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	+	3.2.1.31	from API zym
121521	caseinase	-	3.4.21.50
121521	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121521	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121521	gamma-glutamyltransferase	-	2.3.2.2
121521	gelatinase	-
121521	lecithinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
121521	lipase	-
68382	lipase (C 14)	-		from API zym
121521	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121521	ornithine decarboxylase	-	4.1.1.17
121521	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
121521	tween esterase	-
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	ribulose monophosphate pathway	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	L-lactaldehyde degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	acetoin degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	aspartate and asparagine metabolism	100	9 of 9
66794	cyanate degradation	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	NAD metabolism	94.44	17 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	degradation of sugar alcohols	81.25	13 of 16
66794	glycogen metabolism	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	vitamin B1 metabolism	76.92	10 of 13
66794	butanoate fermentation	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	vitamin E metabolism	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	purine metabolism	70.21	66 of 94
66794	starch degradation	70	7 of 10
66794	pyrimidine metabolism	68.89	31 of 45
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	octane oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	metabolism of disaccharids	63.64	7 of 11
66794	proline metabolism	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	arginine metabolism	62.5	15 of 24
66794	alanine metabolism	62.07	18 of 29
66794	leucine metabolism	61.54	8 of 13
66794	oxidative phosphorylation	61.54	56 of 91
66794	urea cycle	61.54	8 of 13
66794	degradation of pentoses	60.71	17 of 28
66794	non-pathway related	60.53	23 of 38
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	methionine metabolism	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	allantoin degradation	55.56	5 of 9
66794	d-mannose degradation	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	histidine metabolism	51.72	15 of 29
66794	CMP-KDO biosynthesis	50	2 of 4
66794	propionate fermentation	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	suberin monomers biosynthesis	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	lysine metabolism	50	21 of 42
66794	selenocysteine biosynthesis	50	3 of 6
66794	isoprenoid biosynthesis	50	13 of 26
66794	tryptophan metabolism	47.37	18 of 38
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	glutathione metabolism	42.86	6 of 14
66794	mevalonate metabolism	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	cellulose degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	gallate degradation	40	2 of 5
66794	lipid metabolism	38.71	12 of 31
66794	carnitine metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	lipid A biosynthesis	33.33	3 of 9
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	sulfate reduction	30.77	4 of 13
66794	heme metabolism	28.57	4 of 14
66794	cholesterol biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	molybdenum cofactor biosynthesis	22.22	2 of 9

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121521	-	-	+	+	-	-	-	-	-	-	+	+	+	-	+	-	+	-	-	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
121521	not determinedn.d.	-	-	-	-	+	-	-	-	-	+	+	+	+	-	-	-	-	+	+	-	-	+	+	+	+	+	+	+	+	+	+	-	+	+	+	-	-	-	+	+/-	-	+/-	-	-	-	-	+/-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Wetland (Swamp)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3503	swamp	Russia, near Abramtsevo settlement	Russia	RUS	Europe
121521	Swamp		Russian Federation	RUS	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ296179 (>99% sequence identity) for Trichococcus from Microbeatlas

Aquatic Samples	19650
Soil Samples	4890
Animal Samples	13208
Plant Samples	929
Total Samples	38677

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3503	1	Risk group (German classification) According to TRBA 466
121521	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2619618822 annotated assembly for Trichococcus palustris DSM 9172	scaffold	GCA_900114465	140314.8	2619618822	140314	65.34

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3503	Ruminococcus palustris 16S rRNA gene, strain DSM 9172T	AJ296179	1520		140314

GC content

@ref	GC-content (mol%)	Method
3503	47.5	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Trichococcus palustris DSM 9172
NCBI: GCA_900114465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	58.00	no
125439	motility	BacteriaNetⓘ	no	57.40	no
125439	gram_stain	BacteriaNetⓘ	variable	83.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	88.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Trichococcus palustris DSM 9172
NCBI: GCA_900114465.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	74.22	no
125438	anaerobic	anaerobicⓘ	no	71.10	yes
125438	aerobic	aerobicⓘ	no	95.10	yes
125438	spore-forming	spore-formingⓘ	no	64.55	no
125438	thermophilic	thermophileⓘ	no	91.89	yes
125438	flagellated	motile2+ⓘ	no	60.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Enhanced start-up of anaerobic facultatively autotrophic biocathodes in bioelectrochemical systems.	Zaybak Z, Pisciotta JM, Tokash JC, Logan BE	J Biotechnol	10.1016/j.jbiotec.2013.10.001	2013
Phylogeny	Emended description of the genus Trichococcus, description of Trichococcus collinsii sp. nov., and reclassification of Lactosphaera pasteurii as Trichococcus pasteurii comb. nov. and of Ruminococcus palustris as Trichococcus palustris comb. nov. in the low-G+C gram-positive bacteria.	Liu JR, Tanner RS, Schumann P, Weiss N, McKenzie CA, Janssen PH, Seviour EM, Lawson PA, Allen TD, Seviour RJ	Int J Syst Evol Microbiol	10.1099/00207713-52-4-1113	2002

References

#3503	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9172
#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 )
#39276	; Curators of the CIP;
#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 )
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#121521	Collection of Institut Pasteur ; Curators of the CIP; CIP 105359
#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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Trichococcus palustris (DSM 9172, CIP 105359, Z-7189)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Metabolite utilization

Enzymes

Pathway annotation

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900114465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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