Restoration of Antibiotics Related Infant Microbiota Perturbations by Autologous Fecal Transplant (aFMT-babies)

May 7, 2026 updated by: Maria Gloria Dominguez-Bello, Ph.D, Rutgers, The State University of New Jersey

Fecal Microbiota Transplantation (Autologous) in Infants Treated With Antibiotics

Antibiotics are lifesaving therapeutic drugs which have been used by adults, children, and infants alike for decades. There is an increase in global use of antibiotics over the course of lifetime and earlier in lifetime, with some countries recording as high as 12 courses a year in children younger than two. While antibiotics are successful in eradicating many pathogenic bacteria, research has demonstrated significant effect on beneficial gut microbiota, including long-lasting shift in the dynamics, composition, richness, and maturity of the intestinal flora. Microbiota alterations during early life, including through antibiotics use as well as birth via C-section, constitute a developmental perturbation, which increases the risk of modern diseases of immune and metabolic dysfunction. Strong epidemiological evidence suggests associations between early stressors of the microbiota and a number of common diseases, such as obesity, asthma, allergies, celiac disease, and Type 1 Diabetes. Furthermore, excess antibiotic exposure is associated with the development of neurological and psychiatric disorders. Currently, no strategies exist to restore the microbiome other than reliance on spontaneous repair mechanism, which often takes months in a healthy individual barring further antibiotic exposure. Contrary to popular belief, ingestion of probiotics, particularly after antibiotics, has been demonstrated to slow down the repair as it introduces an exogenous and massive amounts of only a few types of bacterial strains into a finely-tuned ecosystem of hundreds of different strains.

It is hypothesized that by preserving the child's microbiome prior to antibiotic therapy and reintroducing it afterwards through an autologous fecal matter transplant (FMT) will assist in a quick, effective, and host-specific microbiome recolonization to the levels and patterns to those prior to antibiotics. This would in turn reduce the overall loss of microbiome diversity over the child's lifespan, essentially providing a 'reset' option to the child's most unadulterated version of microbiome. This approach utilizes delivering the sample by mixing it in maternal milk or formula and feeding it to the child through a bottle, which can be performed anywhere without any discomfort for the child.

Study Overview

Status

Recruiting

Conditions

Intervention / Treatment

Detailed Description

Antibiotics are lifesaving therapeutic drugs which have been used by adults, children, and infants alike for decades. There is an increase in global use of antibiotics over the course of lifetime and earlier in lifetime, with some countries recording as high as 12 courses a year in children younger than two. While antibiotics are successful in eradicating many pathogenic bacteria, research has demonstrated significant effect on beneficial gut microbiota, including long-lasting shift in the dynamics, composition, richness, and maturity of the intestinal flora.

Microbiota alterations during early life, including through antibiotics use as well as birth via C-section, constitute a developmental perturbation, which increases the risk of modern diseases of immune and metabolic dysfunction. Strong epidemiological evidence suggests associations between early stressors of the microbiota and a number of common diseases, such as obesity, asthma, allergies, celiac disease, and Type 1 Diabetes. There is evidence from mouse experiments of early perturbations in microbiota transmission at birth (such as C-section birthing) causing changes in the microbiome, increasing weight gain, and inhibiting intestinal expression of immune genes in neonates. Furthermore, excess antibiotic exposure is associated with the development of neurological and psychiatric disorders. Given the tendency of early perturbations to increase disease risks, it is important to evaluate effects of significant perturbations to microbiome at early ages, such as through antibiotic use.

Currently, no strategies exist to restore the microbiome other than reliance on spontaneous repair mechanism, which often takes months in a healthy individual barring further antibiotic exposure. Modern lifestyle and urban environments, however, work against this spontaneous repair, significantly reducing the microbiome diversity not only generationally but within an individual's lifespan. Contrary to popular belief, ingestion of probiotics, particularly after antibiotics, has been demonstrated to slow down the repair as it introduces an exogenous and massive amounts of only a few types of bacterial strains into a finely-tuned ecosystem of hundreds of different strains.

It is hypothesized that by preserving the child's microbiome prior to antibiotic therapy and reintroducing it afterwards through an autologous fecal matter transplant (FMT) will assist in a quick, effective, and host-specific microbiome recolonization to the levels and patterns to those prior to antibiotics. This would in turn reduce the overall loss of microbiome diversity over the child's lifespan, essentially providing a 'reset' option to the child's most unadulterated version of microbiome.

FMTs have been utilized, including in pediatric populations, to successfully treat recurring Clostridium difficile infections and are being investigated further as an adjunctive treatment in the management of ulcerative colitis, Crohn's Disease, and autism symptoms. Administration of heterologous FMTs (where recipient is different from donor), however, carry their own complexities - stool samples supplied by donors have to be identified and screened and are traditionally delivered in a medical setting as an out-patient procedure. The heterologous FMTs performed today layer the process with additional steps of ideal donor identification and sample screening for possible transmissible pathogens. This proposal uses an autologous sample, which means the sample comes from the healthy child and is administered to the same child after infection and the antibiotic course, conserving the absolutely unique diversity and heritage that that particular child's microbiome had before perturbation due to disease and antibiotics.

In adults, an FMT in form of a capsule for oral use has demonstrated equally successful treatment of C. difficile infection as a rectally-delivered sample. In children, since they cannot swallow capsules, FMTs are delivered as enemas and colonoscopies or through nasogastric and nasojejunal tubes, which require significant resources for the administration of the procedure including anesthesia and observation in addition to the very likely stress impact on the patient.

To evade the invasive nature of these deliveries, novel systems through oral consumption have been investigated. In C-section born infants, maternal stool sample mixed in a bottle of milk and drank by the newborns restored normal gut microbial development to resemble that of vaginally-born babies. The approach utilizes delivering the sample by mixing it in maternal milk or formula and feeding it to the child through a bottle, which can be performed anywhere without any discomfort for the child.

Early life microbiome preservation and restoration holds a tremendous therapeutic potential. Similar to the idea of umbilical stem cells harvesting where stem cells are collected from the infant's umbilical cord, stored, and used as autologous therapeutic transplants in certain cases of cancer, preserved early-life microbiome could be used after antibiotic therapy to restore the composition of the microbiome to the pre-antibiotic state. Unlike the umbilical stem cells harvesting however, fecal sample collection and administration is considerably easier, and the predicted chances for the need of restorative therapy almost certain. Clinical success of such microbiome restorative therapy would exponentially decrease the loss of microbiome diversity and dynamics over one's lifetime, and, by extension, decrease aforementioned associated risks.

The study is a correlational, case-control study comparing the effects of autologous fecal matter transplant (aFMT) after antibiotic therapy on infant microbiome. Infants and toddlers up to 4 years of age are recruited fecal samples are collected and frozen once a month throughout the duration of the study. The caregivers will be asked to notify the study team if the child has been administered antibiotics, and, after the therapy has ended, the last collected sample prior to treatment will be used for autologous transplant by mixing the frozen infant fecal pellet in milk and administering it to the child. The diversity and composition of the child's fecal microbiome trajectory prior and after the transplant will be compared, and then compare those results with the microbiome of control group of children who have received antibiotics but no intervention.

Study Type

Interventional

Enrollment (Estimated)

100

Phase

  • Phase 1

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Contact

Study Contact Backup

Study Locations

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

  • Child

Accepts Healthy Volunteers

Yes

Description

Inclusion Criteria:

  • healthy infants and toddlers 1 month to 4 years of age (regardless of birth mode, sex, or diet (breastmilk, formula, solids, etc.)

Exclusion Criteria:

  • Child's antibiotic use within 3 months before inclusion in the study
  • Documented immunological condition from the child's pediatrician

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Primary Purpose: Other
  • Allocation: Non-Randomized
  • Interventional Model: Parallel Assignment
  • Masking: Single

Arms and Interventions

Participant Group / Arm
Intervention / Treatment
Experimental: Intervention Arm
Caregivers of the participants in the intervention arm will collect monthly fecal samples while the child is healthy and right before an antibiotic treatment which has been prescribed by the pediatrician for a non-gastrointestinal condition. One day after the last dose of antibiotics, the caregiver will collect another fecal sample and then the child will orally drink 2 ounces of the autologous fecal matter transplant inoculum prepared by the research team by mixing the child's own most recent sample prior to falling ill and mixed with milk. The caregivers then continue collecting samples once a week for a month followed by once a month for five months.
Drug: autologous fecal matter transplant
Autologous fecal matter transplant will be used to re-seed the child's gut with his or her own personalized microbiome composition which was preserved prior to antibiotics use.
No Intervention: Control
Participants do not partake in the autologous fecal matter transplant that will be used to re-seed the child's gut with his or her own personalized microbiome composition which was preserved prior to antibiotics use.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
safety of the autologous FMT measured via questionnaires and medical evaluations
Time Frame: 6 months
Endpoints: Safety, defined as no/minimal serious adverse effects
6 months

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Change in gut microbiome trajectory
Time Frame: 6 months post antibiotics
Microbiome gene content will be analyzed before and after antibiotics, to compare trajectories of restored and non-restored babies.
6 months post antibiotics

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Rutgers, The State University of New Jersey

Investigators

  • Principal Investigator: Maria Gloria Dominguez-Bello, PhD, Rutgers Department of Biochemistry & Microbiology

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Actual)

August 1, 2024

Primary Completion (Estimated)

August 1, 2028

Study Completion (Estimated)

September 1, 2028

Study Registration Dates

First Submitted

August 7, 2024

First Submitted That Met QC Criteria

September 19, 2024

First Posted (Actual)

September 24, 2024

Study Record Updates

Last Update Posted (Actual)

May 13, 2026

Last Update Submitted That Met QC Criteria

May 7, 2026

Last Verified

May 1, 2026

More Information

Terms related to this study

Keywords

Other Study ID Numbers

  • Pro2022001766

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

YES

IPD Plan Description

We will not share personal identifiers.

IPD Sharing Time Frame

At the time publication of results, DNA sequences will be published as requested by the Journals, in a sequences database (such as ENA, SRA, GenBank, DDBJ).

IPD Sharing Access Criteria

Determined by the biological database of computerized ("digital") nucleic acid sequences.

IPD Sharing Supporting Information Type

  • STUDY_PROTOCOL
  • SAP
  • ANALYTIC_CODE

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

Yes

Studies a U.S. FDA-regulated device product

No

product manufactured in and exported from the U.S.

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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