Implantation failure limits the success rate of natural and in vitro fertilization (IVF)-assisted conceptions. Evidence suggests dysbiosis in the female reproductive tract impacts implantation failure. However, whether gut dysbiosis influences implantation failure and whether it accompanies reproductive tract dysbiosis remains unexplored. Method: We recruited 11fertile women as the controls, and a cohort of 20 women diagnosed with implantation-failure associated infertility, which included 10

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... men diagnosed with recurrent implantation failure (RIF), and 10 women diagnosed with unexplained infertility (UE). Using next-generation amplicon sequencing, we compared the diversity, structure, and composition of faecal and vaginal bacteria of the controls with that of the infertile cohort. While we sequenced faecal samples of all the participants (n=31), we could only sequence 8 vaginal samples in each group (n=24). Results: Compared with the controls, α-diversity of the gut bacteria, analysed by Chao 1 and Shannon indices, among the infertile groups declined (p < 0.05). β-diversity between the controls and infertile cohort, measured by both Bray-Curtis and Jaccard distances, differed significantly (p < 0.05). Taxa analysis of the gut bacteria revealed enrichment of Gram-positive bacteria, mainly of the phylum Firmicutes, in the RIF group. In contrast, Gram-negative bacteria were relatively more abundant in the UE group. Additionally, mucus-producing bacteria genera such as Prevotella and Sutterella declined in the infertile cohort (p < 0.05). Intriguingly, significant enrichment (p < 0.05) of the genus Hungatella, associated with trimethylamine N-oxide (TMAO) production, occurred in the infertile cohort. Vaginal microbiota was dominated by L. iners across the groups, with the UE group showing the highest levels. Of the three groups, the RIF group had the least diverse vaginal microbiota. Taxa analysis showed higher levels of anaerobic bacteria such as Leptotrichia, Snethia, and Prevotella in the controls. Conclusion: We posit that in the setting of the compromised gut mucosal barrier, the phyla Firmicutes generates TNF-α-driven systemic inflammation, leading to RIF, whereas an overload of Gram-negative bacteria induces IL-6-driven systemic inflammation, leading to UE. Additionally, Hungatella-induced elevation of TMAO levels causes platelet hypercoagulability, synergistically contributing to implantation failure. Finally, vaginal dysbiosis does not appear to co-occur with gut dysbiosis.