Urban Microbiomes in Narita, Chiba, Japan: Shotgun Metagenome Sequences of a Train Station

ABSTRACT

Here, we performed shotgun metagenome sequencing of swab samples collected on floors at a train station in Narita City, Chiba, Japan. The taxonomic analysis revealed that Actinobacteria and Proteobacteria were the dominant phyla. The data will contribute to insight into the microbiome community on the surfaces of urban built environments.

ANNOUNCEMENT

Increasing urbanization creates a high-density urban environment and leads to a continual interaction between humans and urban microorganisms (1, 2) that influence human health and biosafety (2, 3). Urban transit systems, such as trains and buses, host large numbers of passengers (4) and may facilitate constant contact of human commensals with environmental microbes (1). This system offers an ideal model to examine transfers of the urban and interindividual community microbiome (1, 4), and floors have the highest diversity of characterized microbiomes compared with other surfaces (5). In this study, we used shotgun metagenomic sequencing to profile microbial communities on floors in a train station.

Two floor samples were collected at the public area in a train station in Narita City, Chiba Prefecture, Japan, in 2021 using Isohelix swabs (Cell Projects Ltd., Maidstone, UK) prefilled with 400 mL of DNA/RNA Shield medium in barcoded tubes (Zymo Research Co., CA). Sampling supplies were provided by the MetaSUB International Consortium (http://metasub.org). Metagenomic DNA was extracted using the ZymoBiomics DNA miniprep kit (Zymo Research Co.) according to the manufacturer’s instructions. DNA quantitation was done using Qubit double-stranded DNA (dsDNA) high-sensitivity (HS) assay kits (ThermoFisher Scientific Inc., MA) according to the kit procedure. DNA was then subjected to shotgun metagenomic sequencing using the 2 × 150-bp paired-end read DNBSEQ-G400RS high-throughput sequencing set (MGITech Co., Tokyo, Japan) (6) performed at Genome Lead Co. Ltd. (Kagawa, Japan). The metagenomic library was prepared using the MGIEasy FS DNA library prep set (MGITech Co.) with 10 cycles of real-time PCR amplification.

Initially, 1,515,930 sequence reads were generated with a mean length of 150 bp. Quality trimming of sequence reads was then performed by applying the program Fastp 0.23.2 (7) and yielded 1,455,502 paired-end reads with an average read length of 148 bp. The reads were mapped to a database of clade-specific marker genes using Bowtie 2 with the “--very-sensitive” option (8), and the relative abundance of microbial taxa in the metagenome was estimated using the coverage of clade-specific marker genes using MetaPhlAn 3 (9) and was visualized using the Pavian package (10) running on the R program (https://www.r-project.org/).

Taxonomic analysis was shown in Fig. 1; all reads were assigned to Bacteria which consisted of phyla Actinobacteria (60.4%) and Proteobacteria (39.6%), of which both are commonly identified in the built environment (2, 11). Within Actinobacteria, Corynebacteriales (46.7%) and Mycobacteriaceae (16.4%) represented the most abundant order and family, respectively. The most prominent genus was Mycolicibacterium which was dominated by Mycolicibacterium obuense. The following other species were also identified: Tsukamurella tyrosinosolvens (14.3%), Cutibacterium acnes (9.9%), Williamsia marianensis (8.9%), Corynebacterium striatum (7.3%), and Micrococcus aloeverae (3.4%). C. acnes, a commensal human skin flora, has been reported as the most relatively abundant microbial species in metagenomic samples collected in 60 cities (2). The phylum Proteobacteria comprises the class Alphaproteobacteria (35.6%) and Gammaproteobacteria (4%). Within the Alphaproteobacteria, the most abundant genus was Paracoccus (25%) belonging to the family Rhodobacteraceae and the order Rhodobacterales. This genus comprised the species Paracoccus versutus (13.9%) and Paracoccus pantotrophus (11.1%). Pseudomonas fluvialis (4%) was identified within the class Gammaproteobacteria. This information contributes to catalogizing the unique and complex microbial communities in urban public transit systems.

FIG 1.

Taxonomic classification of microbial communities recovered from metagenomic shotgun sequence using MetaPhlAn 3.0 and visualized with Pavian package. Taxonomic ranks are abbreviated as follows: K, kingdom; P, phylum; C, class; O, order; F, family; G, genus; and S, species.

Data availability.

The raw sequencing reads have been deposited in the DDBJ Sequence Read Archive (DRA) under the accession number DRR403243. The sample information is available under the DDBJ BioSample accession number SAMD00520086. The project information is available under the DDBJ BioProject accession number PRJDB14136, under the umbrella BioProject accession number PRJDB13760. The code and scripts to run the bioinformatics tools are available online at https://github.com/haruosuz/bioproject. Default parameters were used for all software unless otherwise noted.