Barnesiella viscericola (CCUG 55593, DSM 18177, JCM 13660)

Name: Barnesiella viscericola (CCUG 55593, DSM 18177, JCM 13660)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12518

Type strain

Strain Designation C46

Culture col. no. CCUG 55593 DSM 18177 JCM 13660 C46

NCBI tax ID(s) 880074 397865

Special Collections DSMZ CCUG JCM Literature strains

History <- M. Sakamoto; C46 <- P. T. N. Lan M. Sakamoto <-- P. T. N. Lan C46.

Links

Barnesiella viscericola C46 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from chicken caecum.

Gram-negative rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 294005

JCM 13660,DSM 18177,CCUG 55593

@ref 20215

Last LPSN update 2026-02-09 11:20:51

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Barnesiellaceae

Genus Barnesiella

Species Barnesiella viscericola

Full scientific name Barnesiella viscericola Sakamoto et al. 2007

BacDive ID	Other strains from **Barnesiella viscericola** (1)	Type strain
161392	B. viscericola JCM 13661

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31956	negative	6.35 µm	1.2 µm	rod-shaped
125438	negative				97.041
125439	negative				98.9

Colony morphology

@ref	Incubation period
7411	2-3 days
60660	2 days

Pigmentation

31956

Productionno

Multimedia

@ref:	66793
multimedia content:	EM_DSM_18177_1.jpg
multimedia.multimedia content:	EM_DSM_18177_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
7411	COLUMBIA BLOOD AGAR (DSMZ Medium 429)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
7411	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
7411	positive	growth	37
60660	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7411	anaerobe
31956	anaerobe
60660	anaerobe
125439	anaerobe	98

Spore formation

@ref	Spore formation	Confidence
31956
125438		92.978
125439		99.7

Observation

67770

Observationquinones: MK-11, MK-12

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31956	30089 ChEBI	acetate	+	carbon source
31956	17057 ChEBI	cellobiose	+	carbon source
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
31956	4853 ChEBI	esculin	+	hydrolysis
31956	17234 ChEBI	glucose	+	carbon source
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
31956	17306 ChEBI	maltose	+	carbon source
31956	37684 ChEBI	mannose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
31956	16634 ChEBI	raffinose	+	carbon source
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
31956	30031 ChEBI	succinate	+	carbon source
31956	17992 ChEBI	sucrose	+	carbon source
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
31956	alkaline phosphatase	+	3.1.3.1
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	+	3.2.1.51	from API rID32A
31956	alpha-galactosidase	+	3.2.1.22
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
31956	gelatinase	+
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glycin 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	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	glycogen metabolism	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	biotin biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	starch degradation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	vitamin B1 metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	photosynthesis	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	threonine metabolism	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	pyrimidine metabolism	68.89	31 of 45
66794	purine metabolism	68.09	64 of 94
66794	octane oxidation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of hexoses	61.11	11 of 18
66794	lipoate biosynthesis	60	3 of 5
66794	proline metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	alanine metabolism	51.72	15 of 29
66794	ethanol fermentation	50	1 of 2
66794	methionine metabolism	50	13 of 26
66794	arginine metabolism	50	12 of 24
66794	kanosamine biosynthesis II	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	histidine metabolism	48.28	14 of 29
66794	lysine metabolism	47.62	20 of 42
66794	lipid metabolism	45.16	14 of 31
66794	cysteine metabolism	44.44	8 of 18
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	tryptophan metabolism	42.11	16 of 38
66794	non-pathway related	42.11	16 of 38
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	polyamine pathway	39.13	9 of 23
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	oxidative phosphorylation	37.36	34 of 91
66794	metabolism of disaccharids	36.36	4 of 11
66794	d-xylose degradation	36.36	4 of 11
66794	glutathione metabolism	35.71	5 of 14
66794	sphingosine metabolism	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	pantothenate biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	urea cycle	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	glycine metabolism	30	3 of 10
66794	Entner Doudoroff pathway	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	carnitine metabolism	25	2 of 8
66794	degradation of sugar acids	24	6 of 25
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	heme metabolism	21.43	3 of 14

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
7411	-	+/-	+	+	-	+	+/-	-	-	+	-	-	+	+	-	-	+	-	-	+	-	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
7411	chicken caecum	Japan	JPN	Asia
67770	Chicken cecum

Taxonmaps

69479

Global distribution of 16S sequence AB267809 (>99% sequence identity) for Barnesiella viscericola subclade from Microbeatlas

Aquatic Samples	558
Soil Samples	419
Animal Samples	12135
Plant Samples	119
Total Samples	13231

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7411	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	ASM51291v1 assembly for Barnesiella viscericola DSM 18177 C46, DSM 18177	complete	GCA_000512915	880074.29	2509276067	880074	98.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7411	Barnesiella viscericola gene for 16S ribosomal RNA, partial sequence	AB267809	1461		880074

GC content

@ref	GC-content (mol%)	Method
7411	52.0
31956	52
67770	52	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: Barnesiella viscericola DSM 18177 strain C46, DSM 18177
PATRIC: 880074.29

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.70	no
125439	motility	BacteriaNetⓘ	no	56.40	no
125439	gram_stain	BacteriaNetⓘ	negative	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Barnesiella viscericola DSM 18177 C46, DSM 18177
NCBI: GCA_000512915.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.04	yes
125438	anaerobic	anaerobicⓘ	yes	83.65	yes
125438	aerobic	aerobicⓘ	no	89.85	yes
125438	spore-forming	spore-formingⓘ	no	92.98	yes
125438	thermophilic	thermophileⓘ	no	93.26	yes
125438	flagellated	motile2+ⓘ	no	88.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Monochromatic Light Impacts the Growth Performance, Intestinal Morphology, Barrier Function, Antioxidant Status, and Microflora of Yangzhou Geese.	Luo G, Cheng Y, Xu Y, Liu J, Yang W, Liu J, Guo B, Zhu H.	Animals (Basel)	10.3390/ani15121815	2025
	The Effect of Exogenous Bile Acids on Antioxidant Status and Gut Microbiota in Heat-Stressed Broiler Chickens.	Yin C, Xia B, Tang S, Cao A, Liu L, Zhong R, Chen L, Zhang H.	Front Nutr	10.3389/fnut.2021.747136	2021
	Differential gliding motility responses of Chryseobacterium sp. strain PMSZPI isolated from uranium ore deposit on hard and soft substrates.	Yermunja L, Acharya C.	Curr Res Microb Sci	10.1016/j.crmicr.2024.100309	2024
Pathogenicity	Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice.	Smith BJ, Miller RA, Schmidt TM.	mSphere	10.1128/msphere.00851-21	2021
	Lactobacillus acidophilus potentiates oncolytic virotherapy through modulating gut microbiota homeostasis in hepatocellular carcinoma.	Zhang J, Yang J, Luo J, Wu W, Luo H, Wei W, Lyu H, Wang Y, Yi H, Zhang Y, Fan Z, Lyu H, Kanakaveti VP, Qin B, Yuan P, Yang R, Zhang H, Zuo T, Felsher DW, Lee MH, Li K.	Nat Commun	10.1038/s41467-025-58407-z	2025
	To Fiber or Not to Fiber: The Swinging Pendulum of Fiber Supplementation in Patients with Inflammatory Bowel Disease.	Haskey N, Gold SL, Faith JJ, Raman M.	Nutrients	10.3390/nu15051080	2023
	The Gut Microbiome Advances Precision Medicine and Diagnostics for Inflammatory Bowel Diseases.	Mousa WK, Al Ali A.	Int J Mol Sci	10.3390/ijms252011259	2024
	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
	Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis.	Schwartz MH, Wang H, Pan JN, Clark WC, Cui S, Eckwahl MJ, Pan DW, Parisien M, Owens SM, Cheng BL, Martinez K, Xu J, Chang EB, Pan T, Eren AM.	Nat Commun	10.1038/s41467-018-07675-z	2018
Genetics	Loss of sex and age driven differences in the gut microbiome characterize arthritis-susceptible 0401 mice but not arthritis-resistant 0402 mice.	Gomez A, Luckey D, Yeoman CJ, Marietta EV, Berg Miller ME, Murray JA, White BA, Taneja V.	PLoS One	10.1371/journal.pone.0036095	2012
Metabolism	Using Tn-seq To Identify Pigmentation-Related Genes of Porphyromonas gingivalis: Characterization of the Role of a Putative Glycosyltransferase.	Klein BA, Cornacchione LP, Collins M, Malamy MH, Duncan MJ, Hu LT.	J Bacteriol	10.1128/jb.00832-16	2017
Transcriptome	Microbiota Alters and Its Correlation with Molecular Regulation Underlying Depression in PCOS Patients.	Yu L, Chen X, Bai X, Fang J, Sui M.	Mol Neurobiol	10.1007/s12035-023-03744-7	2024
Genetics	Host genetic regulation of specific functional groups in the rumen microbiome of dairy cows: Implications for lactation trait.	Bai H, Lai Z, Zhang J, Zheng X, Zhang J, Jin W, Lin L, Mao S.	J Adv Res	10.1016/j.jare.2024.11.012	2025
Pathogenicity	3-O-Acetyl-11-Keto-beta-Boswellic Acid Suppresses Colitis-Associated Colorectal Cancer by Inhibiting the NF-Kb Signaling Pathway and Remodeling Gut Microbiota.	Xu F, Li W, Zheng XJ, Hao Y, Yang YH, Yang H, Zhang S, Cao WX, Li XX, Zhang X, Du GH, Ji TF, Wang JH.	Oncol Res	10.32604/or.2025.062386	2025
	Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle.	Ye X, Sahana G, Lund MS, Li B, Cai Z.	Anim Microbiome	10.1186/s42523-025-00386-z	2025
	Machine learning prediction of obesity-associated gut microbiota: identifying Bifidobacterium pseudocatenulatum as a potential therapeutic target.	Wu H, Li Y, Jiang Y, Li X, Wang S, Zhao C, Yang X, Chang B, Yang J, Qiao J.	Front Microbiol	10.3389/fmicb.2024.1488656	2024
	Impact of a defined bacterial community including and excluding Megamonas hypermegale on broiler cecal microbiota and resistance to Salmonella infection.	Schultz Marcolla C, Ju T, Ten K, Sivakumar Sharma U, Moeun L, Willing BP.	Appl Environ Microbiol	10.1128/aem.00948-25	2025
	Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity.	Kaspersen HP, Estensmo EL, Slettemeas JS, Haverkamp THA, Sjurseth SK, Granstad S, Sekse C, Frederiksen RF, Urdahl AM.	Microb Genom	10.1099/mgen.0.001466	2025
	Low-Protein-Fed Chickens Benefit from Probiotic L. salivarius and L. johnsonii on Performance and Microbiota.	Dong X, Dou X, Tang H, Huang Y, Wu G, Dong W, Wang H, Jiao H, Mei Y, Ren M.	Animals (Basel)	10.3390/ani15223346	2025
Pathogenicity	Administration of a Recombinant Fusion Protein of IFN-gamma and CD154 Inhibited the Infection of Chicks with Salmonella enterica.	Zhang J, Ren G, Li W, Xie H, Yang Z, Wang J, Zhou Y, Wang X.	Vet Sci	10.3390/vetsci12020112	2025
	Beneficial effects of Lactobacillus plantarum on growth performance, immune status, antioxidant function and intestinal microbiota in broilers.	Xiao X, Cui T, Qin S, Wang T, Liu J, Sa L, Wu Y, Zhong Y, Yang C.	Poult Sci	10.1016/j.psj.2024.104280	2024
	Gut infection and dysbiosis are hallmarks of severe SARS-CoV-2 variants.	Nagaraj SK, Joy CM, Shiraz R, Narayan R, Kaur S, Khatun O, Dubey S, Ng J, Mishra N, Tripathi S.	Npj Viruses	10.1038/s44298-025-00158-1	2025
	Succession, Replacement, and Modification of Chicken Litter Microbiota.	Kubasova T, Faldynova M, Crhanova M, Karasova D, Zeman M, Babak V, Rychlik I.	Appl Environ Microbiol	10.1128/aem.01809-22	2022
Genetics	Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing.	Cao J, Wang S, Ding R, Liu Y, Yuan B.	PeerJ	10.7717/peerj.19260	2025
	Comparative Analysis of the Gut Microbiota of Thai Indigenous Chicken Fed House Crickets.	T-Thienprasert NP, Jaithon T, Klomkliew P, Chanchaem P, Suwanasopee T, Koonawootrittriron S, Kovitvadhi A, Chundang P, Pongprayoon P, Kityakarn S, Luksirikul P, Payungporn S.	Animals (Basel)	10.3390/ani15071070	2025
	Modulation of the Gut Microbiota by the Plantaricin-Producing Lactiplantibacillus plantarum D13, Analysed in the DSS-Induced Colitis Mouse Model.	Butorac K, Novak J, Banic M, Lebos Pavunc A, Culjak N, Orsolic N, Odeh D, Perica J, Suskovic J, Kos B.	Int J Mol Sci	10.3390/ijms242015322	2023
	Mucosal Hub Bacteria as Potential Targets for Improving High-Fat Diet-Related Intestinal Barrier Injury.	Shao L, Zhang B, Song Y, Lyu Z, Zhang W, Yang W, Fu J, Li J, Shi J.	Can J Infect Dis Med Microbiol	10.1155/cjid/3652740	2024
	Flavonoids, Isoquinoline Alkaloids, and Their Combinations Affect Growth Performance, Inflammatory Status, and Gut Microbiome of Broilers Under High Stocking Density and Heat Stress.	Insawake K, Songserm T, Songserm O, Theapparat Y, Adeyemi KD, Rassmidatta K, Ruangpanit Y.	Animals (Basel)	10.3390/ani15010071	2024
	Potential application of pig (Sus scrofa domestica) skin peptide-iron chelates in the treatment of iron deficiency anemia and regulation of intestinal flora metabolism.	Huang S, Deng H, Liang K, Zhao X, Zhang J.	Front Nutr	10.3389/fnut.2025.1553668	2025
	Characterization and Evaluation of Lactobacillus plantarum LC5.2 Isolated from Thai Native Pigs for its Probiotic Potential in Gut Microbiota Modulation and Immune Enhancement.	Khongkool K, Taweechotipatr M, Payungporn S, Sawaswong V, Lertworapreecha M.	J Microbiol Biotechnol	10.4014/jmb.2503.03028	2025
	Early fecal microbiota transplantation from high abdominal fat chickens affects recipient cecal microbiome and metabolism.	Song J, Luo C, Liu Z, Liu J, Xie L, Zhang X, Xie Z, Li X, Ma Z, Ding J, Li H, Xiang H.	Front Microbiol	10.3389/fmicb.2023.1332230	2023
	Seasonal Influence on Rumen Microbiota, Rumen Fermentation, and Enteric Methane Emissions of Holstein and Jersey Steers under the Same Total Mixed Ration.	Islam M, Kim SH, Son AR, Ramos SC, Jeong CD, Yu Z, Kang SH, Cho YI, Lee SS, Cho KK, Lee SS.	Animals (Basel)	10.3390/ani11041184	2021
	Effects of indoor and outdoor rearing system on geese biochemical parameters and cecal microbial composition.	Lin YY, Chang PE, Shen SY, Wang SD.	Poult Sci	10.1016/j.psj.2023.102731	2023
	Comparative analysis of gut microbiota between common (Macaca fascicularis fascicularis) and Burmese (M. f. aurea) long-tailed macaques in different habitats.	Muhammad R, Klomkliew P, Chanchaem P, Sawaswong V, Kaikaew T, Payungporn S, Malaivijitnond S.	Sci Rep	10.1038/s41598-023-42220-z	2023
Pathogenicity	Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua.	Mills M, Lee S, Piperata BA, Garabed R, Choi B, Lee J.	Microbiome	10.1186/s40168-023-01636-5	2023
Pathogenicity	Phenotyping of Fecal Microbiota of Winnie, a Rodent Model of Spontaneous Chronic Colitis, Reveals Specific Metabolic, Genotoxic, and Pro-inflammatory Properties.	Tala A, Guerra F, Resta SC, Calcagnile M, Barca A, Tredici SM, De Donno MD, Vacca M, Liso M, Chieppa M, De Angelis M, Verri T, Bozzetti MG, Bucci C, Alifano P.	Inflammation	10.1007/s10753-022-01706-0	2022
Phylogeny	Full-length 16S rDNA sequencing based on Oxford Nanopore Technologies revealed the association between gut-pharyngeal microbiota and tuberculosis in cynomolgus macaques.	Sawaswong V, Chanchaem P, Klomkliew P, Rotcheewaphan S, Meesawat S, Kemthong T, Kaewparuehaschai M, Noradechanon K, Ekatat M, Kanitpun R, Srilohasin P, Warit S, Chaiprasert A, Malaivijitnond S, Payungporn S.	Sci Rep	10.1038/s41598-024-53880-w	2024
Genetics	Impact of commercial gut health interventions on caecal metagenome and broiler performance.	Pangga GM, Star-Shirko B, Psifidi A, Xia D, Corcionivoschi N, Kelly C, Hughes C, Lavery U, Richmond A, Ijaz UZ, Gundogdu O.	Microbiome	10.1186/s40168-024-02012-7	2025
Genetics	Antigenic operon fragmentation and diversification mechanism in Bacteroidota impacts gut metagenomics and pathobionts in Crohn's disease microlesions.	Bank NC, Singh V, McCourt B, Burberry A, Roberts KD, Grubb B, Rodriguez-Palacios A.	Gut Microbes	10.1080/19490976.2024.2350150	2024
	An Outdoor Access Period Improves Chicken Cecal Microbiota and Potentially Increases Micronutrient Biosynthesis.	Varriale L, Coretti L, Dipineto L, Green BD, Pace A, Lembo F, Menna LF, Fioretti A, Borrelli L.	Front Vet Sci	10.3389/fvets.2022.904522	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
Genetics	Comparative Genomics of Bacteroides fragilis Group Isolates Reveals Species-Dependent Resistance Mechanisms and Validates Clinical Tools for Resistance Prediction.	Wallace MJ, Jean S, Wallace MA, Burnham CD, Dantas G.	mBio	10.1128/mbio.03603-21	2022
Genetics	Longitudinal fecal microbiome and metabolite data demonstrate rapid shifts and subsequent stabilization after an abrupt dietary change in healthy adult dogs.	Lin CY, Jha AR, Oba PM, Yotis SM, Shmalberg J, Honaker RW, Swanson KS.	Anim Microbiome	10.1186/s42523-022-00194-9	2022
	Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers.	Li J, Guo Y, Liu J, Guo F, Du L, Yang Y, Li X, Ma Y.	J Immunother Cancer	10.1136/jitc-2023-007420	2023
	Gut Anaerobes Capable of Chicken Caecum Colonisation.	Kubasova T, Kollarcikova M, Crhanova M, Karasova D, Cejkova D, Sebkova A, Matiasovicova J, Faldynova M, Sisak F, Babak V, Pokorna A, Cizek A, Rychlik I.	Microorganisms	10.3390/microorganisms7120597	2019
	The Effect of Antibiotics Treatment on the Maternal Immune Response and Gut Microbiome in Pregnant and Non-Pregnant Mice.	Faas MM, Liu Y, Wekema L, Weiss GA, van Loo-Bouwman CA, Silva Lagos L.	Nutrients	10.3390/nu15122723	2023
Phylogeny	Impact of a Model Used to Simulate Chronic Socio-Environmental Stressors Encountered during Spaceflight on Murine Intestinal Microbiota.	Alauzet C, Cunat L, Wack M, Lanfumey L, Legrand-Frossi C, Lozniewski A, Agrinier N, Cailliez-Grimal C, Frippiat JP.	Int J Mol Sci	10.3390/ijms21217863	2020
	Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice.	Le Bastard Q, Ward T, Sidiropoulos D, Hillmann BM, Chun CL, Sadowsky MJ, Knights D, Montassier E.	Sci Rep	10.1038/s41598-018-24342-x	2018
	Tetragenococcus halophilus Alleviates Intestinal Inflammation in Mice by Altering Gut Microbiota and Regulating Dendritic Cell Activation via CD83.	Islam SMS, Ryu HM, Sohn S.	Cells	10.3390/cells11121903	2022
	S-(-)-Oleocanthal Ex Vivo Modulatory Effects on Gut Microbiota.	Qusa MH, Abdelwahed KS, Hill RA, El Sayed KA.	Nutrients	10.3390/nu15030618	2023
Genetics	When old metagenomic data meet newly sequenced genomes, a case study.	Li X, Naser SA, Khaled A, Hu H, Li X.	PLoS One	10.1371/journal.pone.0198773	2018
	Microbiota Induced Changes in the Immune Response in Pregnant Mice.	Faas MM, Liu Y, Borghuis T, van Loo-Bouwman CA, Harmsen H, de Vos P.	Front Immunol	10.3389/fimmu.2019.02976	2019
	Characterizing the gut (Gallus gallus) microbiota following the consumption of an iron biofortified Rwandan cream seeded carioca (Phaseolus Vulgaris L.) bean-based diet.	Reed S, Neuman H, Glahn RP, Koren O, Tako E.	PLoS One	10.1371/journal.pone.0182431	2017
	Potential for Prebiotics as Feed Additives to Limit Foodborne Campylobacter Establishment in the Poultry Gastrointestinal Tract.	Kim SA, Jang MJ, Kim SY, Yang Y, Pavlidis HO, Ricke SC.	Front Microbiol	10.3389/fmicb.2019.00091	2019
Genetics	Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling.	Fidler G, Tolnai E, Stagel A, Remenyik J, Stundl L, Gal F, Biro S, Paholcsek M.	Sci Rep	10.1038/s41598-020-60304-y	2020
Phylogeny	Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family.	Lagkouvardos I, Lesker TR, Hitch TCA, Galvez EJC, Smit N, Neuhaus K, Wang J, Baines JF, Abt B, Stecher B, Overmann J, Strowig T, Clavel T.	Microbiome	10.1186/s40168-019-0637-2	2019
Metabolism	Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy.	Iebba V, Guerrieri F, Di Gregorio V, Levrero M, Gagliardi A, Santangelo F, Sobolev AP, Circi S, Giannelli V, Mannina L, Schippa S, Merli M.	Sci Rep	10.1038/s41598-018-26509-y	2018
	Effect of antimicrobial growth promoter administration on the intestinal microbiota of beef cattle.	Reti KL, Thomas MC, Yanke LJ, Selinger LB, Inglis GD.	Gut Pathog	10.1186/1757-4749-5-8	2013
	Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages.	Li Z, Gurung M, Rodrigues RR, Padiadpu J, Newman NK, Manes NP, Pederson JW, Greer RL, Vasquez-Perez S, You H, Hioki KA, Moulton Z, Fel A, De Nardo D, Dzutsev AK, Nita-Lazar A, Trinchieri G, Shulzhenko N, Morgun A.	J Exp Med	10.1084/jem.20220017	2022
Metabolism	Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis.	Meisel M, Mayassi T, Fehlner-Peach H, Koval JC, O'Brien SL, Hinterleitner R, Lesko K, Kim S, Bouziat R, Chen L, Weber CR, Mazmanian SK, Jabri B, Antonopoulos DA.	ISME J	10.1038/ismej.2016.114	2017
Phylogeny	A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity.	Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N, Wortmann E, Liu T, Devendran S, Lesker TR, Hernandez SB, Heine V, Buhl EM, M D'Agostino P, Cumbo F, Fischoder T, Wyschkon M, Looft T, Parreira VR, Abt B, Doden HL, Ly L, Alves JMP, Reichlin M, Flisikowski K, Suarez LN, Neumann AP, Suen G, de Wouters T, Rohn S, Lagkouvardos I, Allen-Vercoe E, Sproer C, Bunk B, Taverne-Thiele AJ, Giesbers M, Wells JM, Neuhaus K, Schnieke A, Cava F, Segata N, Elling L, Strowig T, Ridlon JM, Gulder TAM, Overmann J, Clavel T.	Nat Commun	10.1038/s41467-020-19929-w	2020
Pathogenicity	Arabinoxylan and Pectin Metabolism in Crohn's Disease Microbiota: An In Silico Study.	Sabater C, Calvete-Torre I, Ruiz L, Margolles A	Int J Mol Sci	10.3390/ijms23137093	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	Coprobacter fastidiosus gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from infant faeces.	Shkoporov AN, Khokhlova EV, Chaplin AV, Kafarskaia LI, Nikolin AA, Polyakov VY, Shcherbakova VA, Chernaia ZA, Efimov BA.	Int J Syst Evol Microbiol	10.1099/ijs.0.052126-0	2013
Phylogeny	Dialister succinatiphilus sp. nov. and Barnesiella intestinihominis sp. nov., isolated from human faeces.	Morotomi M, Nagai F, Sakon H, Tanaka R.	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/000810-0	2008
Phylogeny	Barnesiella viscericola gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from chicken caecum.	Sakamoto M, Lan PTN, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64709-0	2007

References

#7411	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18177
#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 )
#28212	IJSEM 342 2007 ( DOI 10.1099/ijs.0.64709-0 , PubMed 17267976 )
#31956	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28212
#60660	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55593
#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 )
#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 )
#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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Barnesiella viscericola (CCUG 55593, DSM 18177, JCM 13660)

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