Kits for detecting bacterial nucleic acid

1. A kit for the detection of Lactobacillus sp. and G. vaginalis , the kit comprising:

a plurality of labeled detection probes, wherein the plurality of labeled detection probes comprises

(a) a first Lactobacillus -specific labeled detection probe that specifically hybridizes to a Lactobacillus sp. target nucleic acid, wherein the first Lactobacillus -specific labeled detection probe comprises a target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:9, and

(b) a first G. vaginalis -specific labeled detection probe that specifically hybridizes to a G. vaginalis target nucleic acid, wherein the first G. vaginalis -specific labeled detection probe comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 1-19 of SEQ ID NO:14, wherein at least one of the plurality of labeled detection probes comprises a chemiluminescent or fluorescent label.

2. The kit of claim 1 , wherein the kit (i) does not comprise a labeled detection probe that specifically hybridizes to a target nucleic acid from any fungal species and (ii) does not comprise a labeled detection probe that specifically hybridizes to a target nucleic acid from any bacterial species other than Lactobacillus sp. or G. vaginalis.

3. The kit of claim 1 , wherein the first Lactobacillus -specific labeled detection probe specifically hybridizes to at least one of a L. gasseri target nucleic acid, a L. crispatus target nucleic acid, and a L. jensenii target nucleic acid.

4. The kit of claim 1 , wherein

(a) the nucleotide sequence of the first Lactobacillus -specific labeled detection probe consists of the nucleotide sequence of SEQ ID NO:9; and/or

(b) the nucleotide sequence of the first G. vaginalis -specific labeled detection probe consists of the nucleotide sequence of SEQ ID NO:14.

5. The kit of claim 1 , wherein the plurality of labeled detection probes further comprises

(a) a first Eggerthella -specific labeled detection probe that specifically hybridizes to an Eggerthella sp. target nucleic acid; and/or

(b) a second Lactobacillus -specific labeled detection probe that specifically hybridizes to the Lactobacillus sp. target nucleic acid.

6. The kit of claim 5 , wherein

(a) the first Eggerthella -specific labeled detection probe comprises a target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:18, or wherein the nucleotide sequence of the first Eggerthella -specific labeled detection probe consists of the nucleotide sequence of SEQ ID NO:18; and/or

(b) the second Lactobacillus -specific labeled detection probe comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 6-21 of SEQ ID NO:10, or wherein the nucleotide sequence of the second Lactobacillus -specific labeled detection probe consists of the nucleotide sequence of SEQ ID NO:10.

7. The kit of claim 1 , further comprising at least two Lactobacillus -specific amplification oligomers for amplifying a target region of the Lactobacillus sp. target nucleic acid, and/or at least two G. vaginalis -specific amplification oligomers for amplifying a target region of the G. vaginalis target nucleic acid.

8. The kit of claim 7 , wherein (A) the at least two Lactobacillus -specific amplification oligomers comprises

(a) a first Lactobacillus -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 28-45 of SEQ ID NO:7, or residues 28-45 of SEQ ID NO:8, or

wherein the nucleotide sequence of the first Lactobacillus -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8; and

(b) a second Lactobacillus -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:6, or wherein the nucleotide sequence of the second Lactobacillus -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:6; and/or wherein

(B) the at least two G. vaginalis -specific amplification oligomers comprises

(a) a first G. vaginalis -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 28-45 of SEQ ID NO:13, or wherein the nucleotide sequence of the first G. vaginalis -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:13; and

(b) a second G. vaginalis -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:12, or wherein the nucleotide sequence of the second G. vaginalis -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:12.

9. The kit of claim 8 , wherein the kit comprises the first and second Lactobacillus -specific amplification oligomers of (A)(a) and (A)(b) and further comprises a third Lactobacillus -specific amplification oligomer for amplifying the Lactobacillus sp. target region,

wherein the first Lactobacillus -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 28-45 of SEQ ID NO:7, or wherein the nucleotide sequence of the first Lactobacillus -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:7; and wherein

(c) the third Lactobacillus -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 28-45 of SEQ ID NO:8, or wherein the nucleotide sequence of the third Lactobacillus -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:8.

10. The kit of claim 5 , further comprising at least two Eggerthella -specific amplification oligomers for amplifying a target region of the Eggerthella sp. target nucleic acid comprising

(a) a first Eggerthella -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 28-51 of SEQ ID NO:17, or wherein the nucleotide sequence of the first Eggerthella -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:17; and/or

(b) a second Eggerthella -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:16, or wherein the nucleotide sequence of the second Eggerthella -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:16.

11. The kit of claim 7 , further comprising one or more reagents suitable for performing in vitro nucleic acid amplification selected from the group consisting of buffers, salt, nucleotide triphosphates, and enzymes.

12. The kit of claim 1 , further comprising at least one capture probe oligomer, wherein the at least one capture probe oligomer comprises a Lactobacillus -specific capture probe oligomer and/or a G. vaginalis -specific capture probe oligomer.

13. The kit of claim 12 , wherein

(a) the Lactobacillus -specific capture probe oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 1-12 of SEQ ID NO:5, or wherein the nucleotide sequence of the Lactobacillus -specific capture probe oligomer consists of the nucleotide sequence of SEQ ID NO:5; and/or

(b) the G. vaginalis -specific capture probe oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 1-17 of SEQ ID NO:11, or wherein the nucleotide sequence of the G. vaginalis -specific capture probe oligomer consists of the nucleotide sequence of SEQ ID NO:11.

14. The kit of claim 5 , further comprising an Eggerthella -specific capture probe oligomer.

15. The kit of claim 14 , wherein the Eggerthella -specific capture probe oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 1-21 of SEQ ID NO:15, or wherein the nucleotide sequence of the Eggerthella -specific capture probe oligomer consists of the nucleotide sequence of SEQ ID NO:15.

16. The kit of claim 10 , further comprising

(A) at least two Lactobacillus -specific amplification oligomers for amplifying a target region of the Lactobacillus sp. nucleic acid comprising

(a) a first Lactobacillus -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 28-45 of SEQ ID NO:7, or residues 28-45 of SEQ ID NO:8, or wherein the nucleotide sequence of the first Lactobacillus -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8; and

(b) a second Lactobacillus -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:6, or wherein the nucleotide sequence of the second Lactobacillus -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:6; and/or

(B) at least two G. vaginalis -specific amplification oligomers for amplifying a target region of the G. vaginalis target nucleic acid, comprising (a) a first G. vaginalis -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 28-45 of SEQ ID NO:13, or wherein the nucleotide sequence of the first G. vaginalis -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:13; and

(b) a second G. vaginalis -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:12, or wherein the nucleotide sequence of the second G. vaginalis -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:12.

17. The kit of claim 16 , wherein the kit comprises the first and second Lactobacillus -specific amplification oligomers of (A)(a) and (A)(b) and further comprises a third Lactobacillus -specific amplification oligomer for amplifying the Lactobacillus sp. target region, wherein

(a) the first Lactobacillus -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 28-45 of SEQ ID NO:7, or wherein the nucleotide sequence of the first Lactobacillus -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:7; and wherein

(c) the third Lactobacillus -specific amplification oligomer comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 28-45 of SEQ ID NO:8, or wherein the nucleotide sequence of the first Lactobacillus -specific amplification oligomer consists of the nucleotide sequence of SEQ ID NO:8.

18. A kit for the detection of Lactobacillus sp., G. vaginalis , and Eggerthella sp., the kit comprising: a plurality of labeled detection probes, wherein the plurality of labeled detection probes comprises

(a) a first Lactobacillus -specific labeled detection probe that specifically hybridizes to a Lactobacillus sp. target nucleic acid, wherein the first Lactobacillus -specific labeled detection probe comprises a target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:9, or wherein the nucleotide sequence of the first Lactobacillus -specific labeled detection probe consists of the nucleotide sequence of SEQ ID NO:9;

(b) a first G. vaginalis -specific labeled detection probe that specifically hybridizes to a G. vaginalis target nucleic acid, wherein the first G. vaginalis -specific labeled detection probe comprises a target-hybridizing sequence consisting of the nucleotide sequence of residues 1-19 of SEQ ID NO:14, or wherein the nucleotide sequence of the first G. vaginalis -specific labeled detection probe consists of the nucleotide sequence of SEQ ID NO:14; and

(c) a first Eggerthella -specific labeled detection probe that specifically hybridizes to an Eggerthella sp. target nucleic acid, wherein the Eggerthella -specific labeled detection probe comprises a target-hybridizing sequence consisting of the nucleotide sequence of SEQ ID NO:18, or wherein the nucleotide sequence of the first Eggerthella -specific labeled detection probe consists of the nucleotide sequence of SEQ ID NO:18,

wherein at least one of the plurality of labeled detection probes comprises a chemiluminescent or fluorescent label.

19. The kit of claim 1 , wherein at least one of the plurality of labeled detection probes comprises a fluorescent label and a quencher.

20. The kit of claim 19 , wherein the labeled detection probe(s) comprising the fluorescent label and the quencher is/are selected from the group consisting of a molecular torch and a molecular beacon.