Phyllobacterium myrsinacearum (DSM 5893, ATCC 43591, LMG 1t1)

Name: Phyllobacterium myrsinacearum (DSM 5893, ATCC 43591, LMG 1t1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11875

Type strain

Culture col. no. DSM 5893 ATCC 43591 LMG 1t1 NCIMB 12128 NBRC 100017 7 more

NCBI tax ID(s) 28101

Special Collections DSMZ CCUG JCM CIP

History <- ATCC <- NCIMB <- J. De Ley, LMG <- D. Knösel IAM 13587 <-- LMG 1(t1) <-- D. Knösel. CIP <- 2004, CCUG <- 1995, LMG, Phyllobacterium rubiacearum <- 1973, D. Knösel

Links

Phyllobacterium myrsinacearum DSM 5893 is an obligate aerobe, mesophilic, Gram-negative prokaryote of the family Phyllobacteriaceae.

Gram-negative motile rod-shaped obligate aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 127101

LMG 1t1,LMG 1,CCUG 34964,NCIB 12128,ATCC43591,DSM 5893,IAM13587,NCIMB 12128,CECT 4452,NBRC 100017,ATCC BAA-446,CIP 108235,HAMBI 1991,HAMBI 2264,KACC 10501,CFBP 5555,NCIB 121284,JCM 20934,NCPPB 4123

@ref 20215

Last LPSN update 2026-02-09 11:20:41

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Phyllobacteriaceae

Genus Phyllobacterium

Species Phyllobacterium myrsinacearum

Full scientific name Phyllobacterium myrsinacearum (ex Knösel 1962) Knösel 1984

Synonyms (1)

Phyllobacterium rubiacearum

BacDive ID	Other strains from **Phyllobacterium myrsinacearum** (7)	Type strain
11874	P. myrsinacearum DSM 5892, ATCC 43590, IAM 13584, JCM 20932, ... (type strain)
148168	P. myrsinacearum CCUG 34963, LMG 3, JCM 20933, IAM 13586
148169	P. myrsinacearum CCUG 34964, LMG 1, CIP 108235
153955	P. myrsinacearum CCUG 51764
156835	P. myrsinacearum CCUG 65979
156868	P. myrsinacearum CCUG 66194
163014	P. myrsinacearum JCM 20931, CCUG 34961, IAM 13583, LMG 2.1

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
121213	negative	rod-shaped
125438	negative		98
125439	negative		98.7

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2351	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
36708	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121213	CIP Medium 72	Medium recipe at CIP
121213	CIP Medium 328	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2351	positive	growth	26	mesophilic
36708	positive	growth	25	mesophilic
67770	positive	growth	30	mesophilic
121213	positive	growth	25-30	mesophilic
121213	negative	growth	10
121213	negative	growth	37
121213	negative	growth	41
121213	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
121213	obligate aerobe
125439	aerobe	98.3

Spore formation

@ref	Spore formation	Confidence
125439		96.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121213	NaCl	positive	growth	0-2 %
121213	NaCl		growth	4 %
121213	NaCl		growth	6 %
121213	NaCl		growth	8 %
121213	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121213	16947 ChEBI	citrate	+	carbon source
121213	4853 ChEBI	esculin	+	hydrolysis
121213	606565 ChEBI	hippurate	+	hydrolysis
121213	17632 ChEBI	nitrate	-	reduction
121213	17632 ChEBI	nitrate	-	respiration
121213	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121213	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121213	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
121213	15688 ChEBI	acetoin	-
121213	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121213	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
121213	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
121213	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
121213	caseinase	-	3.4.21.50
121213	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121213	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121213	gamma-glutamyltransferase	+	2.3.2.2
121213	gelatinase	-
121213	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121213	lipase	-
68382	lipase (C 14)	-		from API zym
121213	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
121213	ornithine decarboxylase	-	4.1.1.17
121213	oxidase	+
121213	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
121213	tryptophan deaminase	-
121213	tween esterase	-
121213	urease	+	3.5.1.5
68382	valine arylamidase	-		from API zym

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
121213	-	+	+	+	-	+	-	-	+	+	+	+	-	-	-	+	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121213	not determinedn.d.	+	+	+	+	+	-	-	+	-	+	+	-	-	-	-	+	+	-	+	+	+	+	+	+	+	-	+	-	+	+	+	+	+	+	+	-	+	+	-	+	-	+	-	-	-	-	-	-	+	+	+	+	-	+	+	+	+	-	-	+	+	-	+	+	+	-	-	-	-	-	+	+	-	+	-	-	-	-	-	+	+	+	+	-	+	-	+	-	+	+	+	+	-	+	+	-	-	+	+

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
36708		Stuttgart-Hohenheim	Germany	DEU	Europe
67770	Leaf nodule
121213	Plant, Leaf nodule, Pavetta zimmermanniana	Stuttgart Hohenheim	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2351	1	Risk group (German classification) According to TRBA 466
121213	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
67770	ASM421665v1 assembly for Phyllobacterium myrsinacearum DSM 5893	scaffold	GCA_004216655	28101.7	2799112214	28101	72.97

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Phyllobacterium myrsinacearum gene for 16S rRNA, strain: IAM 13587	D12790	1430		28101
124043	Phyllobacterium myrsinacearum gene for 16S rRNA, partial sequence, strain: NBRC 100017.	AB681130	1410		28101

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Phyllobacterium myrsinacearum DSM 5893
NCBI: GCA_004216655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.90	no
125439	motility	BacteriaNetⓘ	yes	63.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	98.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phyllobacterium myrsinacearum strain DSM 5893
PATRIC: 28101.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	96.30	yes
125438	spore-forming	spore-formingⓘ	no	87.90	no
125438	aerobic	aerobicⓘ	yes	84.34	yes
125438	thermophilic	thermophileⓘ	no	97.75	no
125438	flagellated	motile2+ⓘ	no	51.53	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition.	Travin DY, Watson ZL, Metelev M, Ward FR, Osterman IA, Khven IM, Khabibullina NF, Serebryakova M, Mergaert P, Polikanov YS, Cate JHD, Severinov K.	Nat Commun	10.1038/s41467-019-12589-5	2019
	Molecular self-assembly mediates the flocculation activity of benzimidazole derivatives against E. coli.	Drewek I, Pietka A, Tran TQ, Blazhynska M, Jenistova A, Chipot C, Barth A, Surin M, Leclere P, Wattiez R, Muller RN, Stanicki D, Laurent S.	Sci Rep	10.1038/s41598-025-13837-z	2025
Pathogenicity	Expression of tfx and sensitivity to the rhizobial peptide antibiotic trifolitoxin in a taxonomically distinct group of alpha-proteobacteria including the animal pathogen Brucella abortus.	Triplett EW, Breil BT, Splitter GA.	Appl Environ Microbiol	10.1128/aem.60.11.4163-4166.1994	1994
Genetics	Impact of scented candle use on indoor air quality and airborne microbiome.	Yun H, Seo JH, Kim YG, Yang J.	Sci Rep	10.1038/s41598-025-95010-0	2025
	A new selective culture medium for isolation of Burkholderia cepacia complex in pharmaceutical industry.	Yu M, Wang S, Zhong Y, Yuan L, An L, Feng D, Liu Z, Ma S.	Front Microbiol	10.3389/fmicb.2025.1631983	2025
	Racial Disparities in Plasma Cytokine and Microbiome Profiles.	Fan KD, Ogunrinde E, Wan Z, Li C, Jiang W.	Microorganisms	10.3390/microorganisms12071453	2024
	Crown Gall Induced by a Natural Isolate of Brucella (Ochrobactrum) pseudogrignonense Containing a Tumor-Inducing Plasmid.	Hooykaas MJG, Hooykaas PJJ.	Microorganisms	10.3390/microorganisms13010102	2025
	Clinical and epidemiological aspects of spondylodiscitis in a tertiary care hospital in South India.	Thimmappa L, Hebbar S, Bhat SN.	Infez Med	10.53854/liim-3204-7	2024
Phylogeny	Bacterial classification based on metagenomic analysis in peritoneal dialysis effluent of patients with chronic kidney disease.	Visedthorn S, Klomkliew P, Sawaswong V, Sivapornnukul P, Chanchaem P, Saejew T, Pavatung P, Kanjanabuch T, Payungporn S.	Biomed Rep	10.3892/br.2024.1790	2024
	Influence of the initial microbiota on eggplant shibazuke pickle and eggplant juice fermentation.	Sawada K, Yamada T.	Microbiol Spectr	10.1128/spectrum.00464-24	2024
	Pneumocystis jirovecii is a potential pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly.	Magne F, Ruiz-Ruiz S, Perez-Brocal V, Ponce CA, Bustamante R, Martin VS, Gutierrez M, Gatti G, Vargas SL, Moya A.	Commun Biol	10.1038/s42003-025-07810-9	2025
	Effects of Different Production Methods on the Quality and Microbial Diversity of Sauerkraut in Northeast China.	Liu W, Wang Y, Zhao T, Zheng Y, Mu G, Qian F.	Foods	10.3390/foods13233947	2024
	Aerobiology and Environmental Zonation in Gypsum Caves: A Comparative Study of Culturing and NGS Approaches.	Martin-Pozas T, Fernandez-Cortes A, Calaforra JM, Sanchez-Moral S, Saiz-Jimenez C, Jurado V.	Microb Ecol	10.1007/s00248-025-02591-4	2025
	The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children.	Wu Z, Jiang M, Jia M, Sang J, Wang Q, Xu Y, Qi L, Yang W, Feng L.	Commun Biol	10.1038/s42003-025-07559-1	2025
Enzymology	Sustaining the growth of Pinaceae trees under nutrient-limited edaphic conditions via plant-beneficial bacteria.	Puri A, Padda KP, Chanway CP.	PLoS One	10.1371/journal.pone.0238055	2020
Pathogenicity	Autotoxins in continuous tobacco cropping soils and their management.	Chen Y, Yang L, Zhang L, Li J, Zheng Y, Yang W, Deng L, Gao Q, Mi Q, Li X, Zeng W, Ding X, Xiang H.	Front Plant Sci	10.3389/fpls.2023.1106033	2023
	Novel Agrobacterium fabrum str. 1D1416 for Citrus Transformation.	Alabed D, Tibebu R, Ariyaratne M, Shao M, Milner MJ, Thomson JG.	Microorganisms	10.3390/microorganisms12101999	2024
	Variation in blood microbial lipopolysaccharide (LPS) contributes to immune reconstitution in response to suppressive antiretroviral therapy in HIV.	Luo Z, Health SL, Li M, Yang H, Wu Y, Collins M, Deeks SG, Martin JN, Scott A, Jiang W.	EBioMedicine	10.1016/j.ebiom.2022.104037	2022
Phylogeny	Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion.	Maquia IS, Fareleira P, Videira E Castro I, Brito DRA, Soares R, Chauque A, Ferreira-Pinto MM, Lumini E, Berruti A, Ribeiro NS, Marques I, Ribeiro-Barros AI.	Microorganisms	10.3390/microorganisms8091291	2020
Metabolism	Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica.	Mesa V, Navazas A, Gonzalez-Gil R, Gonzalez A, Weyens N, Lauga B, Gallego JLR, Sanchez J, Pelaez AI.	Appl Environ Microbiol	10.1128/aem.03411-16	2017
	Macroalga-Derived Alginate Oligosaccharide Alters Intestinal Bacteria of Atlantic Salmon.	Gupta S, Lokesh J, Abdelhafiz Y, Siriyappagouder P, Pierre R, Sorensen M, Fernandes JMO, Kiron V.	Front Microbiol	10.3389/fmicb.2019.02037	2019
	Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection.	Stressmann FA, Bernal-Bayard J, Perez-Pascual D, Audrain B, Rendueles O, Briolat V, Bruchmann S, Volant S, Ghozlane A, Haussler S, Duchaud E, Levraud JP, Ghigo JM.	ISME J	10.1038/s41396-020-00807-8	2021
	Long-term continuously monocropped peanut significantly changed the abundance and composition of soil bacterial communities.	Chen M, Liu H, Yu S, Wang M, Pan L, Chen N, Wang T, Chi X, Du B.	PeerJ	10.7717/peerj.9024	2020
	Bacterial communities in urban aerosols collected with wetted-wall cyclonic samplers and seasonal fluctuations of live and culturable airborne bacteria.	Ravva SV, Hernlem BJ, Sarreal CZ, Mandrell RE.	J Environ Monit	10.1039/c1em10753d	2012
	Multi-Dimensional Elimination of beta-Lactams in the Rural Wetland: Molecule Design and Screening for More Antibacterial and Degradable Substitutes.	Sun S, Li Z, Ren Z, Li Y.	Molecules	10.3390/molecules27238434	2022
	Legumes of the Sardinia Island: Knowledge on Symbiotic and Endophytic Bacteria and Interactive Software Tool for Plant Species Determination.	Muresu R, Porceddu A, Concheri G, Stevanato P, Squartini A.	Plants (Basel)	10.3390/plants11111521	2022
	Metagenomic and Transcriptomic Analyses Reveal the Differences and Associations Between the Gut Microbiome and Muscular Genes in Angus and Chinese Simmental Cattle.	Zheng Y, Chen J, Wang X, Han L, Yang Y, Wang Q, Yu Q.	Front Microbiol	10.3389/fmicb.2022.815915	2022
Phylogeny	Weight shapes the intestinal microbiome in preterm infants: results of a prospective observational study.	Heida FH, Kooi EMW, Wagner J, Nguyen TY, Hulscher JBF, van Zoonen AGJF, Bos AF, Harmsen HJM, de Goffau MC.	BMC Microbiol	10.1186/s12866-021-02279-y	2021
	Ultrastructure of interaction in alginate beads between the microalga Chlorella vulgaris with its natural associative bacterium Phyllobacterium myrsinacearum and with the plant growth-promoting bacterium Azospirillum brasilense.	Lebsky VK, Gonzalez-Bashan LE, Bashan Y.	Can J Microbiol	10.1139/cjm-47-1-1	2001
Metabolism	Changes in the metabolism of the microalga Chlorella vulgaris when coimmobilized in alginate with the nitrogen-fixing Phyllobacterium myrsinacearum.	Gonzalez-Bashan LE, Lebsky VK, Hernandez JP, Bustillos JJ, Bashan Y.	Can J Microbiol	10.1139/cjm-46-7-653	2000
Metabolism	Clinical implications of calcifying nanoparticles in dental diseases: a critical review.	Alenazy MS, Mosadomi HA.	Int J Nanomedicine	10.2147/ijn.s51538	2014
	Phytoremediation technologies and their mechanism for removal of heavy metal from contaminated soil: An approach for a sustainable environment.	Sharma JK, Kumar N, Singh NP, Santal AR.	Front Plant Sci	10.3389/fpls.2023.1076876	2023
	Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment.	Sun X, Li M, Xia L, Fang Z, Yu S, Gao J, Feng Q, Yang P.	Sci Rep	10.1038/s41598-020-72035-1	2020
	Development of an efficient marker-free soybean transformation method using the novel bacterium Ochrobactrum haywardense H1.	Cho HJ, Moy Y, Rudnick NA, Klein TM, Yin J, Bolar J, Hendrick C, Beatty M, Castaneda L, Kinney AJ, Jones TJ, Chilcoat ND.	Plant Biotechnol J	10.1111/pbi.13777	2022
Phylogeny	Culturable bacterial endophytes isolated from Mangrove tree (Rhizophora apiculata Blume) enhance seedling growth in Rice.	Deivanai S, Bindusara AS, Prabhakaran G, Bhore SJ.	J Nat Sci Biol Med	10.4103/0976-9668.136233	2014
	Bibliometric Analysis of Algal-Bacterial Symbiosis in Wastewater Treatment.	Qi Y, Chen X, Hu Z, Song C, Cui Y.	Int J Environ Res Public Health	10.3390/ijerph16061077	2019
	Bacterial Community and PHB-Accumulating Bacteria Associated with the Wall and Specialized Niches of the Hindgut of the Forest Cockchafer (Melolontha hippocastani).	Alonso-Pernas P, Arias-Cordero E, Novoselov A, Ebert C, Rybak J, Kaltenpoth M, Westermann M, Neugebauer U, Boland W.	Front Microbiol	10.3389/fmicb.2017.00291	2017
Phylogeny	Complete genomic sequence and phylogenomics analysis of Agrobacterium strain AB2/73: a new Rhizobium species with a unique mega-Ti plasmid.	Hooykaas MJG, Hooykaas PJJ.	BMC Microbiol	10.1186/s12866-021-02358-0	2021
	Community Analysis of Root- and Tuber-Associated Bacteria in Field-Grown Potato Plants Harboring Different Resistance Levels against Common Scab.	Kobayashi A, Kobayashi YO, Someya N, Ikeda S.	Microbes Environ	10.1264/jsme2.me15109	2015
Genetics	Plant biomacromolecule delivery methods in the 21st century.	Rustgi S, Naveed S, Windham J, Zhang H, Demirer GS.	Front Genome Ed	10.3389/fgeed.2022.1011934	2022
	Streptomyces Dominate the Soil Under Betula Trees That Have Naturally Colonized a Red Gypsum Landfill.	Zappelini C, Alvarez-Lopez V, Capelli N, Guyeux C, Chalot M.	Front Microbiol	10.3389/fmicb.2018.01772	2018
	Shifts Between and Among Populations of Wheat Rhizosphere Pseudomonas, Streptomyces and Phyllobacterium Suggest Consistent Phosphate Mobilization at Different Wheat Growth Stages Under Abiotic Stress.	Breitkreuz C, Buscot F, Tarkka M, Reitz T.	Front Microbiol	10.3389/fmicb.2019.03109	2019
Enzymology	Absence of zoonotic Bartonella species in questing ticks: first detection of Bartonella clarridgeiae and Rickettsia felis in cat fleas in the Netherlands.	Tijsse-Klasen E, Fonville M, Gassner F, Nijhof AM, Hovius EK, Jongejan F, Takken W, Reimerink JR, Overgaauw PA, Sprong H.	Parasit Vectors	10.1186/1756-3305-4-61	2011
	The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis.	Hotterbeekx A, Xavier BB, Bielen K, Lammens C, Moons P, Schepens T, Ieven M, Jorens PG, Goossens H, Kumar-Singh S, Malhotra-Kumar S.	Sci Rep	10.1038/srep36507	2016
Metabolism	Transfer of DNA from Bacteria to Eukaryotes.	Lacroix B, Citovsky V.	mBio	10.1128/mbio.00863-16	2016
	Studies on lipid A isolated from Phyllobacterium trifolii PETP02^T lipopolysaccharide.	Zamlynska K, Komaniecka I, Zebracki K, Mazur A, Sroka-Bartnicka A, Choma A.	Antonie Van Leeuwenhoek	10.1007/s10482-017-0872-0	2017
Phylogeny	Novel clade of alphaproteobacterial endosymbionts associated with stinkbugs and other arthropods.	Matsuura Y, Kikuchi Y, Meng XY, Koga R, Fukatsu T.	Appl Environ Microbiol	10.1128/aem.00673-12	2012
Enzymology	Attempted isolation of Nanobacterium sp. microorganisms from upper urinary tract stones.	Drancourt M, Jacomo V, Lepidi H, Lechevallier E, Grisoni V, Coulange C, Ragni E, Alasia C, Dussol B, Berland Y, Raoult D.	J Clin Microbiol	10.1128/jcm.41.1.368-372.2003	2003
	The effects of high-tannin leaf litter from transgenic poplars on microbial communities in microcosm soils.	Winder RS, Lamarche J, Constabel CP, Hamelin RC.	Front Microbiol	10.3389/fmicb.2013.00290	2013
Phylogeny	Aerobic methanotrophic communities at the Red Sea brine-seawater interface.	Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy MA, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H, Siam R.	Front Microbiol	10.3389/fmicb.2014.00487	2014
	Effects of Escherichia coli on mixotrophic growth of Chlorella minutissima and production of biofuel precursors.	Higgins BT, VanderGheynst JS.	PLoS One	10.1371/journal.pone.0096807	2014
	Identification and Plant Interaction of a Phyllobacterium sp., a Predominant Rhizobacterium of Young Sugar Beet Plants.	Lambert B, Joos H, Dierickx S, Vantomme R, Swings J, Kersters K, Van Montagu M.	Appl Environ Microbiol	10.1128/aem.56.4.1093-1102.1990	1990
Genetics	Genome sequence of Ensifer adhaerens OV14 provides insights into its ability as a novel vector for the genetic transformation of plant genomes.	Rudder S, Doohan F, Creevey CJ, Wendt T, Mullins E.	BMC Genomics	10.1186/1471-2164-15-268	2014
	An alternative interpretation of nanobacteria-induced biomineralization.	Cisar JO, Xu DQ, Thompson J, Swaim W, Hu L, Kopecko DJ.	Proc Natl Acad Sci U S A	10.1073/pnas.97.21.11511	2000
	Unconventional genomic organization in the alpha subgroup of the Proteobacteria.	Jumas-Bilak E, Michaux-Charachon S, Bourg G, Ramuz M, Allardet-Servent A.	J Bacteriol	10.1128/jb.180.10.2749-2755.1998	1998
Phylogeny	Discordant phylogenies within the rrn loci of Rhizobia.	van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindstrom K, Eardly BD.	J Bacteriol	10.1128/jb.185.10.2988-2998.2003	2003
Metabolism	Characterization of an atrazine-degrading Pseudaminobacter sp. isolated from Canadian and French agricultural soils.	Topp E, Zhu H, Nour SM, Houot S, Lewis M, Cuppels D.	Appl Environ Microbiol	10.1128/aem.66.7.2773-2782.2000	2000
	Molecular diversity of rhizobia occurring on native shrubby legumes in southeastern australia	Lafay B, Burdon JJ.	Appl Environ Microbiol	10.1128/aem.64.10.3989-3997.1998	1998
	Third Generation Genome Sequencing Reveals That Endobacteria in Nematophagous Fungi Esteya vermicola Contain Multiple Genes Encoding for Nematicidal Proteins.	Wang R, Dong L, Chen Y, Wang S, Qu L	Front Microbiol	10.3389/fmicb.2022.842684	2022
Phylogeny	Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend.	Mergaert J, Cnockaert MC, Swings J	Int J Syst Evol Microbiol	10.1099/00207713-52-5-1821	2002
Phylogeny	Characterization of Phyllobacterium spp. isolated from root nodules of Melilotus albus (white sweet clover) grown in Canada and description of Phyllobacterium meliloti sp. nov.	Bromfield ESP, Cloutier S, Hynes MF.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006876	2025
Enzymology	Phyllobacterium pellucidum sp. nov., isolated from soil.	Park Y, Ten LN, Maeng S, Chang Y, Jung HY, Kim MK.	Arch Microbiol	10.1007/s00203-021-02205-w	2021
Phylogeny	Oricola cellulosilytica gen. nov., sp. nov., a cellulose-degrading bacterium of the family Phyllobacteriaceae isolated from surface seashore water, and emended descriptions of Mesorhizobium loti and Phyllobacterium myrsinacearum.	Hameed A, Shahina M, Lai WA, Lin SY, Young LS, Liu YC, Hsu YH, Young CC.	Antonie Van Leeuwenhoek	10.1007/s10482-014-0370-6	2015
	Lutibaculum baratangense gen. nov., sp. nov., a novel proteobacterium isolated from a mud volcano, Andamans, India.	Kumar AP, Srinivas TNR, Madhu S, Shivaji S.	Int J Syst Evol Microbiol	10.1099/ijs.0.027094-0	2010
Phylogeny	Emended description of the genus Phyllobacterium and description of four novel species associated with plant roots: Phyllobacterium bourgognense sp. nov., Phyllobacterium ifriqiyense sp. nov., Phyllobacterium leguminum sp. nov. and Phyllobacterium brassicacearum sp. nov.	Mantelin S, Saux MF, Zakhia F, Bena G, Bonneau S, Jeder H, de Lajudie P, Cleyet-Marel JC.	Int J Syst Evol Microbiol	10.1099/ijs.0.63911-0	2006
Phylogeny	Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils.	Valverde A, Velazquez E, Fernandez-Santos F, Vizcaino N, Rivas R, Mateos PF, Martinez-Molina E, Igual JM, Willems A.	Int J Syst Evol Microbiol	10.1099/ijs.0.63551-0	2005

References

#2351	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5893
#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 )
#36708	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#121213	Collection of Institut Pasteur ; Curators of the CIP; CIP 108235
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Phyllobacterium myrsinacearum (DSM 5893, ATCC 43591, LMG 1t1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

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Antibiotic resistance

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API zym

API biotype100

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Genome browser: GCA_004216655

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