HOMD ::Subspecies:clade-029

Subspecies: clade-029 (HMT-0029) Primary Body Site: Oral

Full Lineage: Bacteria; Spirochaetota; Spirochaetia; Spirochaetales; Treponemataceae; Treponema; Treponema vincentii; clade-029

LINKS: Ecology Home | HMT-0029: [Body Sites Data] [Taxon Description] | Life Page: clade-029

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Oral:

SUBP-- Subgingival Plaque

SUPP -- Supragingival Plaque

PERIO -- Periodontal

AKE -- Attached Keratinized Gingiva

BMU -- Buccal Mucosa

HPA -- Hard Palate

SAL -- Saliva

THR -- Throat

PTO -- Palatine Tonsils

TDO -- Tongue Dorsum

Nasal:

ANA -- Anterior Nares

Skin:

LRC -- L_Retroauricular Crease

RRC -- R_Retroauricular Crease

LAF -- L_Antecubital Fossa

RAF -- R_Antecubital Fossa

Vaginal:

VIN -- Vaginal Introitus

MVA -- Mid Vagina

PFO -- Posterior Fornix

Gut:

STO -- Stool

Prev - Prevalence
10^thp - 10^th percentile
90^thp - 90^th percentile
ND - less than 0.001%

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Available Datasets:
HMP Mapping Eren V1-V3 Eren V3-V5 HMP V1-V3 HMP V3-V5 ND:Metaphlan Dewhirst 35x9

No Available Datasets for Subspecies: clade-029

Human Microbiome Project Mapping (Data from healthy subjects. - not published)

No Notes

	SUBP	SUPP	PERIO	AKE	BMU	HPA	SAL	THR	PTO	TDO	ANA	LRC	RRC	RAF	VIN	MVA	PFO	STO
Avg (%)	0.16	0.03	0.27	0	0	0	0.01	0	0.02	0.01	0	0	0	0	0	0	0	0
n	24	395	24	15	323	1	8	7	22	423	65	23	30	1	4	8	94	375
10^thp	0	0	0.01	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
90^thp	0.34	0.06	0.87	0	0.01	0	0.03	0.01	0.06	0.02	0	0	0	0	0	0	0	0
Stdev	0.37	0.11	0.35	0	0.01	0	0.01	0	0.02	0.02	0	0	0	0	0	0	0	0
Prev(%)	29.17	11.65	37.50	0	0	0	0	0	0	1.89	0	0	0	0	0	0	0	0

Eren V1-V3 www.pnas.org (Data from healthy subjects.)

Notes:
reads equally close to T. medium and T. vincentii were assigned half to each taxon

	SUBP	SUPP	AKE	BMU	HPA	SAL	THR	PTO	TDO	STO
Avg (%)	0.02	0.01	0	0	0.01	0.01	0.02	0.02	0.02	0
n	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
10^thp	0	0	0	0	0	0	0	0	0	0
90^thp	0.07	0.01	0	0	0.02	0.04	0.06	0.06	0.04	0
Stdev	0.05	0.04	0	0.01	0.02	0.03	0.04	0.04	0.05	0
Prev(%)	20.78	10.39	2.60	10.39	22.08	28.57	27.27	25.97	28.57	1.30

Eren V3-V5 www.pnas.org (Data from healthy subjects.)

Notes:
Reads equally close to T. vincentii and T. sp. HMT 231 were assigned half to each taxon.

	SUBP	SUPP	AKE	BMU	HPA	SAL	THR	PTO	TDO	STO
Avg (%)	0.21	0.06	0	0.01	0.01	0.03	0.03	0.07	0.01	0
n	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
10^thp	0	0	0	0	0	0	0	0	0	0
90^thp	0.57	0.20	0	0.03	0.02	0.08	0.05	0.15	0.03	0
Stdev	0.44	0.17	0.01	0.06	0.02	0.04	0.15	0.23	0.03	0
Prev(%)	52.70	39.87	6.08	25.68	22.30	48.65	37.16	46.62	27.70	0

Human Microbiome Project 16S RefSeq (V1-V3) (Data from healthy subjects. - not published)

No Notes

	SUBP	SUPP	AKE	BMU	HPA	SAL	THR	PTO	TDO	ANA	LRC	RRC	LAF	RAF	VIN	MVA	PFO	STO
Avg (%)	0.01	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
n	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
10^thp	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
90^thp	0.02	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Stdev	0.08	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
Prev(%)	14.57	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

Human Microbiome Project 16S RefSeq (V3-V5) (Data from healthy subjects. - not published)

Notes:
Because HMT-231 is not present individually, all equidistant reads were assigned to HMT-029 at these sites (PTO,SUBP,THR).

Neither HMT-029 nor HMT-231 were present singularly so these reads were split evenly at these sites (SAL,SUPP).

	SUBP	SUPP	AKE	BMU	HPA	SAL	THR	PTO	TDO	ANA	LRC	RRC	LAF	RAF	VIN	MVA	PFO	STO
Avg (%)	0.42	0.07	0	0	0	0.06	0.17	0.27	0.05	0	0	0	0	0	0	0	0	0
n	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
10^thp	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
90^thp	1.33	0.22	0	0	0	0.16	0.43	0.66	0.14	0	0	0	0	0	0	0	0	0
Stdev	0.69	0.22	0	0	0	0.14	0.49	0.74	0.16	0	0	0	0	0	0	0	0	0
Prev(%)	57.53	41.22	0	0	0	58.33	46.11	64.48	36.50	0	0	0	0	0	0	0	0	0

Dewhirst 35x9 (35 Taxa by 9 Oral Sites. - not published)

No Notes

	SUBP	SUPP	AKE	BMU	HPA	SAL	THR	PTO	TDO	ANA
Avg (%)	0.04	0	0.01	0	0.01	0.01	0.02	0.02	0.01	0
n	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
10^thp	0	0	0	0	0	0	0	0	0	0
90^thp	0.02	0	0.03	0	0	0.02	0.03	0.04	0.02	0
Stdev	0.26	0	0.04	0	0.04	0.01	0.05	0.04	0.02	0
Prev(%)	25.68	20.59	30.23	17.14	14.29	26.00	42.42	54.84	27.50	0

Human Microbiome Project Metaphlan (Data from healthy subjects. - not published)

No Notes

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