Phocaeicola salanitronis (CCUG 60908, DSM 18170, JCM 13657)

Name: Phocaeicola salanitronis (CCUG 60908, DSM 18170, JCM 13657)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1615

Type strain

Strain Designation BL78

Culture col. no. CCUG 60908 DSM 18170 JCM 13657 BL78

NCBI tax ID(s) 667015 376805

Special Collections DSMZ CCUG JCM

History DSMZ <- M. Sakamoto; BL78 <- P. T. N. Lan JCM <-- M. Sakamoto <-- P. T. N. Lan BL78.

Links

Phocaeicola salanitronis BL78 is an anaerobe bacterium that was isolated from chicken caecum.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 294002

JCM 13657,DSM 18170,CCUG 54637,CCUG 60908

@ref 20215

Last LPSN update 2026-05-29 08:25:18

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Phocaeicola

Species Phocaeicola salanitronis

Full scientific name Phocaeicola salanitronis (Lan et al. 2006) García-López et al. 2020

Synonyms (1)

Bacteroides salanitronis

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	97.179
125438		91
125438	negative	91.5

Colony morphology

@ref	Type of hemolysis	Hemolysis ability	Incubation period
7344	gamma	0	2-3 days
62491			2 days

Multimedia

@ref:	66793
multimedia content:	EM_DSM_18170_1.jpg
multimedia.multimedia content:	EM_DSM_18170_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7344	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
7344	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)
7344	positive	growth	37
62491	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7344	anaerobe
62491	anaerobe
125438	anaerobe	92.008
125439	obligate anaerobe	99.174

Spore formation

@ref	Spore formation	Confidence
125439		99.842

Observation

67770

Observationquinones: MK-11, MK-12

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
7344	-	-	+	+	-	+	+	+	-	-	-	+/-	-	+/-	-	-	+	-	-	+	-	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.
7344	-	-	+	+	-	+	+	+	-	-	+	+/-	-	-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Birds	#Chicken
#Host Body-Site	#Gastrointestinal tract	#Large intestine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7344	chicken caecum	Japan	JPN	Asia
62491	Chicken caecum,healthy animal	Japan	JPN	Asia
67770	Chicken cecum

Taxonmaps

69479

Global distribution of 16S sequence AB253731 (>99% sequence identity) for Phocaeicola salanitronis subclade from Microbeatlas

Aquatic Samples	51
Soil Samples	72
Animal Samples	7152
Plant Samples	19
Total Samples	7294

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7344	1	Risk group (German 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	ASM19057v1 assembly for Phocaeicola salanitronis DSM 18170	complete	GCA_000190575	667015.3	649633013	667015	98.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7344	Bacteroides salanitronis gene for 16S ribosomal RNA, partial seuqnece, strain: JCM 13657	AB253731	1463		667015

GC content

@ref	GC-content (mol%)	Method
7344	46.9
67770	46.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM19057v1 assembly for Phocaeicola salanitronis DSM 18170
NCBI: GCA_000190575

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.17	no
125439	gram_stain	BacteriaNetⓘ	negative	97.18	no
125439	motility	BacteriaNetⓘ	no	83.50	no
125439	spore_formation	BacteriaNetⓘ	no	99.84	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phocaeicola salanitronis DSM 18170 DSM 18170
NCBI: GCA_000190575.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	91.50	no
125438	anaerobic	anaerobicⓘ	yes	92.01	yes
125438	aerobic	aerobicⓘ	no	93.36	yes
125438	spore-forming	spore-formingⓘ	no	89.43	no
125438	thermophilic	thermophileⓘ	no	93.46	yes
125438	flagellated	motile2+ⓘ	no	91.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Prevalence and genomic insights into type III-A CRISPR-Cas system acquisition in global Staphylococcus argenteus strains	Chen X, Xu L, Luo Z, Wang L, Wang Z, Li Y, Jiao X, Li Q.	Front Cell Infect Microbiol		2025
	Host-genotype-dependent cecal microbes are linked to breast muscle metabolites in Chinese chickens.	Feng Y, Liu D, Liu Y, Yang X, Zhang M, Wei F, Li D, Hu Y, Guo Y.	iScience	10.1016/j.isci.2022.104469	2022
	Investigating the cecal microbiota of broilers raised in extensive and intensive production systems.	Marcolla CS, Ju T, Lantz HL, Willing BP.	Microbiol Spectr	10.1128/spectrum.02352-23	2023
	First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China.	Zhu D, Wan J, Yang Z, Xu J, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, Chen X, Cheng A.	Front Vet Sci	10.3389/fvets.2019.00128	2019
Genetics	Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota.	Bao G, Wang M, Doak TG, Ye Y.	Front Microbiol	10.3389/fmicb.2015.00896	2015
Metabolism	Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation.	Chojnacka A, Szczesny P, Blaszczyk MK, Zielenkiewicz U, Detman A, Salamon A, Sikora A.	PLoS One	10.1371/journal.pone.0128008	2015
Phylogeny	Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca.	Kralova S, Davidova-Gerzova L, Valcek A, Bezdicek M, Rychlik I, Rezacova V, Cizek A.	Microbiol Spectr	10.1128/spectrum.01954-21	2022
Genetics	Noncontiguous finished genome sequence and description of Gabonia massiliensis gen. nov., sp. nov.	Mourembou G, Rathored J, Ndjoyi-Mbiguino A, Lekana-Douki JB, Fenollar F, Robert C, Fournier PE, Raoult D, Lagier JC.	New Microbes New Infect	10.1016/j.nmni.2015.11.002	2016
Phylogeny	Bacteroides caecicola sp. nov. and Bacteroides gallinaceum sp. nov., isolated from the caecum of an Indonesian chicken.	Irisawa T, Saputra S, Kitahara M, Sakamoto M, Sulistiani, Yulineri T, Dinoto A, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijsem.0.000899	2016
Phylogeny	Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum.	Lan PTN, Sakamoto M, Sakata S, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64517-0	2006

References

#7344	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18170
#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 )
#62491	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 60908
#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) .
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68380	Automatically annotated from API rID32A .
#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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Phocaeicola salanitronis (CCUG 60908, DSM 18170, JCM 13657)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000190575

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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