Background  In recent years, with the development of shipping economy, the physical and mental health in long-term voyagers have attracted much attention.

  Objective  To investigate the distribution and variation characteristics over time of pharyngeal flora in long-term voyage, and provide references for follow-up studies on its prevention and in-depth investigation.

  Methods  The study recruited 30 volunteers (18 males, 12 females, with age of 20-53 years) with long-term voyage from September 2017 to January 2018, including 8 medical support personnels, 8 sailors, 8 crew members and 6 logistics support personnels. A total of 120 throat swabs were collected at 4 time points, before sailing and 1, 3, 4 months after sailing. High-throughput sequencing was carried out according to the time of collection. The species composition and richness information of the samples were obtained by amplicon sequence variants (ASVs) analysis.

  Results  Of the 120 samples, sequencing failed in 4 samples. The major phyla obtained by sequencing from 116 samples were Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, Proteobacteria, Verrucomicrobia, Cyanobacteria and Saccharibacteria. The major genera were Prevotella, Bacteroides, Ruminococcus, Neisseria, Haemophilus, Lactobacillus and Anaerococcus. There were obvious differences in the bacterial abundance. Compared with before sailing, waterborne microorganisms were detected from throat swabs after 1 month of sailing, such as Fibrophaga, Sphingomonas, and Desulfovibrio. Actinomycetes and Corynebacterium were the genus with the highest microbial abundance after 3 months of sailing. Firmicutes and Bifidobacteria increased to the highest abundance, Bacteroidetes decreased to the lowest, and Verrucomicrophyla gradually disappeared after 4 months of sailing.

  Conclusion  The pharyngeal flora of long-term voyagers is basically the same as normal people, but cyanobacteria are only detected in long-term voyagers. During the voyage, the constitution and diversity of pharyngeal flora change over time, and the waterborne microorganisms also increase over time.