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Effects of Intravenous (IV) Omadacycline on Gut Microbiome

Effects of IV Omadacycline on Gut Microbiome

Status
Completed
Phases
Phase 4
Study type
Interventional
Source
ClinicalTrials.gov
Registry ID
NCT05515562
Enrollment
8
Registered
2022-08-25
Start date
2023-03-20
Completion date
2023-07-11
Last updated
2025-03-17

For informational purposes only — not medical advice. Sourced from public registries and may not reflect the latest updates. Terms

Conditions

Microbial Colonization

Keywords

Gut Microbiome, Clostridioides difficile

Brief summary

Given the clinical need to improve upon current antibiotic regimens for the treatment of C. difficile infection with a particular focus on the impact of therapies on gut microbiome, this study proposes to characterize the impact of Intravenous (IV) omadacycline on gut microbiome of healthy volunteers.

Detailed description

The plan to enroll eight healthy volunteers between the ages of 18 and 40 years and without history of cardiovascular, gastrointestinal, hepatic, or renal disease to receive 5 days of intravenous omadacycline followed by 5 days of oral omadacycline. Stool and saliva samples will be collected at pre-specified times and analyzed to characterize the impact of IV omadacycline on gut microbiome.

Interventions

DRUGOmadacycline Injection

All participants will receive Intravenous (IV) omadacycline

Sponsors

University of Houston
CollaboratorOTHER
High Point University
CollaboratorOTHER
Paratek Pharmaceuticals Inc
CollaboratorINDUSTRY
Wake Forest University Health Sciences
Lead SponsorOTHER

Study design

Allocation
NA
Intervention model
SINGLE_GROUP
Primary purpose
TREATMENT
Masking
NONE

Eligibility

Sex/Gender
ALL
Age
18 Years to 40 Years
Healthy volunteers
Yes

Inclusion criteria

* 18-40 years of age * Willing and able to comply with all study procedures * Considered healthy without history of cardiovascular, gastrointestinal, hepatic, or renal disease * males or females - females of child bearing potential must agree to use a highly effective contraception during the study and for at least 7 days after the last dose of omadacycline

Exclusion criteria

* Consumed probiotics within 30 days before enrollment * Consumed antibiotics within 90 days prior to enrollment * Known hypersensitivity to omadacycline or tetracycline-class antibiotics * pregnant or breastfeeding * in the opinion of the investigator is experiencing signs or symptoms of acute illness that increase the risk of adverse effects from participating in the study * previously participated in the study

Design outcomes

Primary

MeasureTime frameDescription
Phylum Level Mean Proportional Relative AbundanceDay 30In general, the healthy volunteer analyses will assess changes in total and species-specific microbiota over time as well as changes in microbial diversity.
Bacterial DNA Per Gram of StoolBaselinenanograms (ng) per gram of stool for bacterial DNA
Order Level Mean Proportional Relative AbundanceBaselineOrder Level Mean Proportional Relative Abundance - Relative abundance % for order

Countries

United States

Participant flow

Participants by arm

ArmCount
Intravenous (IV) Omadacycline
All participants will receive 5 days of IV omadacycline followed by 5 days of oral omadacycline Omadacycline Injection: All participants will receive Intravenous (IV) omadacycline
8
Total8

Baseline characteristics

CharacteristicIntravenous (IV) Omadacycline
Age, Continuous29.875 years
STANDARD_DEVIATION 4.2
Ethnicity (NIH/OMB)
Hispanic or Latino
2 Participants
Ethnicity (NIH/OMB)
Not Hispanic or Latino
6 Participants
Ethnicity (NIH/OMB)
Unknown or Not Reported
0 Participants
Race (NIH/OMB)
American Indian or Alaska Native
0 Participants
Race (NIH/OMB)
Asian
0 Participants
Race (NIH/OMB)
Black or African American
0 Participants
Race (NIH/OMB)
More than one race
0 Participants
Race (NIH/OMB)
Native Hawaiian or Other Pacific Islander
0 Participants
Race (NIH/OMB)
Unknown or Not Reported
0 Participants
Race (NIH/OMB)
White
8 Participants
Sex: Female, Male
Female
4 Participants
Sex: Female, Male
Male
4 Participants

Adverse events

Event typeEG000
affected / at risk
deaths
Total, all-cause mortality
0 / 8
other
Total, other adverse events
7 / 8
serious
Total, serious adverse events
0 / 8

Outcome results

Primary

Bacterial DNA Per Gram of Stool

nanograms (ng) per gram of stool for bacterial DNA

Time frame: Baseline

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolBacteroides thetaiotaomicron2.74 10^7 ng/gStandard Deviation 6.11
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolBlautia coccoides608 10^7 ng/gStandard Deviation 2.39
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolClostridium leptum3.84 10^7 ng/gStandard Deviation 1.73
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolPrevotella14.9 10^7 ng/gStandard Deviation 46.6
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolEubacteria2220 10^7 ng/gStandard Deviation 953
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolEnterobacteriaceae1.42 10^7 ng/gStandard Deviation 5.57
Primary

Bacterial DNA Per Gram of Stool

nanograms (ng) per gram of stool for bacterial DNA

Time frame: End of Therapy up to Day 10

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolBacteroides thetaiotaomicron0.849 10^7 ng/gStandard Deviation 1.43
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolBlautia coccoides9.97 10^7 ng/gStandard Deviation 14.7
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolClostridium leptum.0148 10^7 ng/gStandard Deviation 0.013
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolPrevotella4.25 10^7 ng/gStandard Deviation 7.3
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolEubacteria103 10^7 ng/gStandard Deviation 113
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolEnterobacteriaceae21.9 10^7 ng/gStandard Deviation 37.4
Primary

Bacterial DNA Per Gram of Stool

nanograms (ng) per gram of stool for bacterial DNA

Time frame: During Therapy up to Day 6

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolEubacteria197 10^7 ng/gStandard Deviation 157
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolEnterobacteriaceae9.77 10^7 ng/gStandard Deviation 31.5
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolBacteroides thetaiotaomicron.954 10^7 ng/gStandard Deviation 3.05
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolBlautia coccoides30.0 10^7 ng/gStandard Deviation 22.9
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolClostridium leptum.0488 10^7 ng/gStandard Deviation 0.0553
Intravenous (IV) OmadacyclineBacterial DNA Per Gram of StoolPrevotella2.41 10^7 ng/gStandard Deviation 22.8
Primary

Order Level Mean Proportional Relative Abundance

Order Level Mean Proportional Relative Abundance - Relative abundance % for order

Time frame: Day 10

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Actinobacteriota o_Bifidobacteriales0.164 Relative abundance % for orderStandard Deviation 0.0979
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Actinobacteriota o_Coriobacteriales0.0324 Relative abundance % for orderStandard Deviation 0.0368
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacteroidota o_Bacteroidales0.0459 Relative abundance % for orderStandard Deviation 0.0848
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Euryarchaeota o_Methanobacteriales0.152 Relative abundance % for orderStandard Deviation 0.262
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Erysipelotrichales0.229 Relative abundance % for orderStandard Deviation 0.0546
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Lachnospirales0.0616 Relative abundance % for orderStandard Deviation 0.0473
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Lactobacillales0.0128 Relative abundance % for orderStandard Deviation 0.0104
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Oscillospirales0.0363 Relative abundance % for orderStandard Deviation 0.0725
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Peptostreptococcales- Tissierellales0.0156 Relative abundance % for orderStandard Deviation 0.0238
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Veillonellales- Selenomonadales0.0915 Relative abundance % for orderStandard Deviation 0.142
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Verrucomicrobiota o_Verrucomicrobiales0.210 Relative abundance % for orderStandard Deviation 0.203
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Proteobacteria o_Enterobacterales0.147 Relative abundance % for orderStandard Deviation 0.112
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative AbundanceOther Orders <2%0.00783 Relative abundance % for orderStandard Deviation 0.00772
Primary

Order Level Mean Proportional Relative Abundance

Order Level Mean Proportional Relative Abundance - Relative abundance % for order

Time frame: Baseline

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Actinobacteriota o_Bifidobacteriales0.0349 Relative abundance % for orderStandard Deviation 0.0265
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Actinobacteriota o_Coriobacteriales0.0925 Relative abundance % for orderStandard Deviation 0.0389
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacteroidota o_Bacteroidales0.0135 Relative abundance % for orderStandard Deviation 0.0152
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Euryarchaeota o_Methanobacteriales0.0388 Relative abundance % for orderStandard Deviation 0.0933
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Erysipelotrichales0.0693 Relative abundance % for orderStandard Deviation 622
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Lachnospirales0.417 Relative abundance % for orderStandard Deviation 0.157
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Lactobacillales0.0429 Relative abundance % for orderStandard Deviation 0.0273
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Oscillospirales0.188 Relative abundance % for orderStandard Deviation 0.0883
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Peptostreptococcales- Tissierellales0.0213 Relative abundance % for orderStandard Deviation 0.0109
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Veillonellales- Selenomonadales0.0107 Relative abundance % for orderStandard Deviation 0.00754
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Verrucomicrobiota o_Verrucomicrobiales0.0173 Relative abundance % for orderStandard Deviation 0.0227
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Proteobacteria o_Enterobacterales0.0204 Relative abundance % for orderStandard Deviation 0.0342
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative AbundanceOther Orders <2%0.0336 Relative abundance % for orderStandard Deviation 0.032
Primary

Order Level Mean Proportional Relative Abundance

Order Level Mean Proportional Relative Abundance - Relative abundance % for order

Time frame: Day 5

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Actinobacteriota o_Bifidobacteriales0.105 Relative abundance % for orderStandard Deviation 0.0358
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Actinobacteriota o_Coriobacteriales0.120 Relative abundance % for orderStandard Deviation 0.0314
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacteroidota o_Bacteroidales0.0507 Relative abundance % for orderStandard Deviation 0.0812
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Euryarchaeota o_Methanobacteriales0.000447 Relative abundance % for orderStandard Deviation 0.0001
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Erysipelotrichales0.0148 Relative abundance % for orderStandard Deviation 0.0143
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Lachnospirales0.204 Relative abundance % for orderStandard Deviation 0.0845
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Lactobacillales0.0505 Relative abundance % for orderStandard Deviation 0.0632
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Oscillospirales0.0653 Relative abundance % for orderStandard Deviation 0.0507
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Peptostreptococcales- Tissierellales0.0163 Relative abundance % for orderStandard Deviation 0.0161
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Veillonellales- Selenomonadales0.0685 Relative abundance % for orderStandard Deviation 0.0881
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Verrucomicrobiota o_Verrucomicrobiales0.131 Relative abundance % for orderStandard Deviation 0.106
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Proteobacteria o_Enterobacterales0.158 Relative abundance % for orderStandard Deviation 0.141
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative AbundanceOther Orders <2%0.0175 Relative abundance % for orderStandard Deviation 0.0168
Primary

Order Level Mean Proportional Relative Abundance

Order Level Mean Proportional Relative Abundance - Relative abundance % for order

Time frame: Day 30

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Actinobacteriota o_Bifidobacteriales0.0880 Relative abundance % for orderStandard Deviation 0.0515
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Actinobacteriota o_Coriobacteriales0.0779 Relative abundance % for orderStandard Deviation 0.053
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacteroidota o_Bacteroidales0.0270 Relative abundance % for orderStandard Deviation 0.0313
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Euryarchaeota o_Methanobacteriales0.0391 Relative abundance % for orderStandard Deviation 0.103
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Erysipelotrichales0.0356 Relative abundance % for orderStandard Deviation 0.0365
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Lachnospirales0.416 Relative abundance % for orderStandard Deviation 0.169
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Lactobacillales0.0306 Relative abundance % for orderStandard Deviation 0.0265
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Oscillospirales0.0971 Relative abundance % for orderStandard Deviation 0.0941
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Peptostreptococcales- Tissierellales0.0271 Relative abundance % for orderStandard Deviation 0.0197
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Bacillota o_Veillonellales- Selenomonadales0.0657 Relative abundance % for orderStandard Deviation 0.119
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Verrucomicrobiota o_Verrucomicrobiales0.0371 Relative abundance % for orderStandard Deviation 0.075
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative Abundancep_Proteobacteria o_Enterobacterales0.0400 Relative abundance % for orderStandard Deviation 0.0611
Intravenous (IV) OmadacyclineOrder Level Mean Proportional Relative AbundanceOther Orders <2%0.0186 Relative abundance % for orderStandard Deviation 0.0198
Primary

Phylum Level Mean Proportional Relative Abundance

In general, the healthy volunteer analyses will assess changes in total and species-specific microbiota over time as well as changes in microbial diversity.

Time frame: Day 30

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceActinobacteriota0.167 % gram positive (+) for phylumStandard Deviation 0.0622
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceBacteroidota0.0271 % gram positive (+) for phylumStandard Deviation 0.0314
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceBacillota0.686 % gram positive (+) for phylumStandard Deviation 0.114
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceEuryarchaeota0.0391 % gram positive (+) for phylumStandard Deviation 0.103
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceVerrucomicrobiota0.0371 % gram positive (+) for phylumStandard Deviation 0.075
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceProteobacteria0.0399 % gram positive (+) for phylumStandard Deviation 0.061
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceOther Phyla <2%0.00324 % gram positive (+) for phylumStandard Deviation 0.00809
Primary

Phylum Level Mean Proportional Relative Abundance

In general, the healthy volunteer analyses will assess changes in total and species-specific microbiota over time as well as changes in microbial diversity.

Time frame: Day 10

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceActinobacteriota0.198 % gram positive (+) for phylumStandard Deviation 0.101
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceBacteroidota0.0459 % gram positive (+) for phylumStandard Deviation 0.0848
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceBacillota0.246 % gram positive (+) for phylumStandard Deviation 0.191
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceEuryarchaeota0.152 % gram positive (+) for phylumStandard Deviation 0.262
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceVerrucomicrobiota0.210 % gram positive (+) for phylumStandard Deviation 0.203
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceProteobacteria0.147 % gram positive (+) for phylumStandard Deviation 0.112
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceOther Phyla <2%0.00105 % gram positive (+) for phylumStandard Deviation 0.00144
Primary

Phylum Level Mean Proportional Relative Abundance

In general, the healthy volunteer analyses will assess changes in total and species-specific microbiota over time as well as changes in microbial diversity.

Time frame: Day 5

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceActinobacteriota0.225 % gram positive (+) for phylumStandard Deviation 0.0469
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceBacteroidota0.0507 % gram positive (+) for phylumStandard Deviation 0.0812
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceBacillota0.432 % gram positive (+) for phylumStandard Deviation 0.0814
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceEuryarchaeota0 % gram positive (+) for phylumStandard Deviation 0.0001
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceVerrucomicrobiota0.131 % gram positive (+) for phylumStandard Deviation 0.106
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceProteobacteria0.158 % gram positive (+) for phylumStandard Deviation 0.141
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceOther Phyla <2%0.00310 % gram positive (+) for phylumStandard Deviation 0.00407
Primary

Phylum Level Mean Proportional Relative Abundance

In general, the healthy volunteer analyses will assess changes in total and species-specific microbiota over time as well as changes in microbial diversity.

Time frame: Baseline

ArmMeasureGroupValue (MEAN)Dispersion
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceActinobacteriota0.130 % gram positive (+) for phylumStandard Deviation 0.039
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceBacteroidota0.0135 % gram positive (+) for phylumStandard Deviation 0.0152
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceBacillota0.779 % gram positive (+) for phylumStandard Deviation 0.0879
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceEuryarchaeota0.0388 % gram positive (+) for phylumStandard Deviation 0.0933
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceVerrucomicrobiota0.0173 % gram positive (+) for phylumStandard Deviation 0.0227
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceProteobacteria0.0205 % gram positive (+) for phylumStandard Deviation 0.0342
Intravenous (IV) OmadacyclinePhylum Level Mean Proportional Relative AbundanceOther Phyla <2%0.00110 % gram positive (+) for phylumStandard Deviation 0.0019

Source: ClinicalTrials.gov · Data processed: Feb 4, 2026