Driving the Vaginal Microecology towards Lactobacillus Dominance by Autologous Microbiota Transplantation: Paired Metagenomic Observations in Three Subjects

Abstract Vaginal microbiota transplantation (VMT) is used to restore a Lactobacillus‑dominated vaginal microecology in women whose communities have shifted into dysbiosis. In this pilot descriptive study, three subjects (VT10, VT12 and VT13) received autologous VMT, and six paired vaginal samples collected immediately before and after the intervention were profiled by shotgun metagenomics with Kraken2 and Bracken species‑level annotation. The predefined ecological endpoint was a relative abundance of the Lactobacillus complex of at least 50%. All three subjects reached the endpoint. The Lactobacillus complex rose from 45.4% to 94.2% in VT10 (CST IV with L. iners dominance converted to CST I with L. crispatus), from 69.1% to 98.8% in VT12 (CST I maintained, L. crispatus expanded), and from 19.3% to 82.2% in VT13 (CST IV dominated by Gardnerella vaginalis converted to an L. acidophilus‑dominated community). Alpha diversity decreased sharply in VT10 (richness 1,311 to 148; Shannon index 2.79 to 1.14) and in VT12 (richness 136 to 127; Shannon index 1.27 to 0.19), consistent with convergence to a low‑diversity Lactobacillus monoculture, and increased slightly in VT13 (richness 173 to 206). Paired Bray‑Curtis dissimilarity was 0.516, 0.299 and 0.695 respectively. Fifteen taxa decreased in all three subjects with |log2FC| >= 1, predominantly Prevotella species, G. vaginalis, Hoylesella buccalis and Fenollaria massiliensis. Two engraftment modes were observed: species replacement in VT10, and expansion of the pre‑existing dominant Lactobacillus in VT12 and VT13. These hypothesis‑generating observations indicate that VMT can move the vaginal community into a Lactobacillus‑dominated state; adequately powered studies with formal ethical approval are required before any clinical claim is made. Important Limitation and Ethics Statement This work is an exploratory working paper. The empirical part includes only three subjects receiving autologous vaginal microbiota transplantation, with a single post‑intervention sampling point per subject. This work was conducted without prior formal institutional ethics‑committee approval and without documented written informed consent for research use of the samples. All subject‑identifying information has been fully de‑identified, and samples are referred to by laboratory serial numbers only. The observations are purely descriptive preliminary findings and cannot serve as clinical evidence, nor should they be cited as evidence of efficacy or safety. Further adequately powered studies with formal ethical review are required to validate these results.