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Draft Genome Sequences of Eight Bacteria Isolated from the Indoor Environment: Staphylococcus Capitis Strain H36, S

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Draft Genome Sequences of Eight Bacteria Isolated from the Indoor Environment: Staphylococcus Capitis Strain H36, S Lymperopoulou et al. Standards in Genomic Sciences (2017) 12:17 DOI 10.1186/s40793-017-0223-9 EXTENDED GENOME REPORT Open Access Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72 Despoina S. Lymperopoulou1* , David A. Coil2, Denise Schichnes3, Steven E. Lindow1, Guillaume Jospin2, Jonathan A. Eisen2,4,5 and Rachel I. Adams1 Abstract We report here the draft genome sequences of eight bacterial strains of the genera Staphylococcus, Microbacterium, Mycobacterium, Plantibacter, and Pseudomonas. These isolates were obtained from aerosol sampling of bathrooms of five residences in the San Francisco Bay area. Taxonomic classifications as well as the genome sequence and gene annotation of the isolates are described. As part of the “Built Environment Reference Genome” project, these isolates and associated genome data provide valuable resources for studying the microbiology of the built environment. Keywords: Built environment, Shower water, Airborne bacteria, Bacterial genomes Introduction on these wet surfaces by direct contact or by inhalation Given that humans spend most of their lives in indoor from aerosolized particles. Focusing on these airborne environments [1], it is important to understand the microorganisms, Miletto & Lindow [7] collected aerosol microorganisms that can be found in these human- particles from residences for genetic analysis and identi- created structures. Previous work based on 16S rRNA fied over 300 genera which they attributed to various gene surveys has described thousands of bacterial taxa sources including tap water, human occupants, indoor from residences (e.g., [2]). Within these residences, peri- surfaces, and outdoor air. odically wet surfaces– such as shower walls, shower An important tool in studying microbial communities heads, sinks, drains – represent unique (compared to involves culturing and genome sequencing. In order to dryer areas within the home - [3–5]) and potentially expand our work on the microbiology of built environ- medically important microbial communities [6]. Humans ments [8] into a more experimental framework, we cul- could readily interface with the microbial communities tured bacteria from the air of residential bathrooms and report their genome sequences. Genome sequencing was * Correspondence: [email protected] utilized in order to provide insight into the basic biology 1Department of Plant & Microbial Biology, University of California Berkeley, of the bacteria collected in indoor environments and to Berkeley, CA, USA aid with future metagenomic and transcriptomic efforts. Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Lymperopoulou et al. Standards in Genomic Sciences (2017) 12:17 Page 2 of 15 The eight isolates within five genera were isolated Organism information during a sampling campaign of residential bathrooms Classification and features conducted in 2015. While simultaneously filtering aero- Two growth media were used for the initial isolation of sols for amplicon-based community composition ana- bacteria: lysogeny broth agar (LB, Difco Laboratories, lysis (which is in preparation and will be published Detroit, MI) and R2A agar (Difco Laboratories, Detroit, elsewhere), petri dishes were exposed to the air to isolate MI). Petri dishes were exposed to residential bathroom viable bacteria. After an initial screening of multiple iso- air for 1 h; 30 min during which shower water was run- lates by sequencing the full-length 16S rRNA gene and ning to create shower mist and 30 min after the shower carrying out preliminary taxonomic classification, eight was turned off. Petri dishes were mounted on vertical isolates were selected for further genomic sequencing surfaces (door, wall, cabinets) at a height of approxi- based on an assessment of their putative importance in mately 1.50 m. Petri dishes were brought back to the the built environment. Specifically, we favored strains laboratory, where LB plates were incubated at 28 °C for that met the following criteria: they are commonly iden- 48 h, and R2A plates were incubated at 28 °C for 5 days tified in indoor environments, they are likely inputs from and at 35 °C for 3 days. Except for Staphylococcus hominis a common source for indoor microbes (premise plumbing, strain H69, which was isolated on LB agar medium at outdoor origin [9]), and/or they (or their close relatives) 35 °C, all other strains were isolated on R2A medium can potentially impact human health. For instance, we in- (Additional file 1). Research was approved by the clude three species (four isolates) of staphylococci. CoNS University of California Committee for the Protection are typically benign inhabitants of the human skin and of Human Subjects Protocol ID 2015-02-7135, and the mucous membranes, but they are associated with infec- sampling was conducted in March, 2015. tions and can be pathogenic to humans with compromised Taxonomic classification of these isolates was undertaken immune systems [10]. Mycobacterium iranicum is a newly after genome sequencing, either using the full-length 16S described species which has been isolated from clinical rRNA gene sequences or a concatenated marker gene specimens originating in diverse countries including Iran, approach. For Microbacterium, Mycobacterium,and Greece, the Netherlands, Sweden and the USA [11], Plantibacter there were insufficient publicly available although genomic comparison indicated that this is genome sequences of close relatives for a concatenated likely an environmental bacterium [12]. Pseudomonas marker approach. In these cases, the full length 16S oryzihabitans (synonym Flavimonas oryzihabitans)has rRNA gene sequence was uploaded to the Ribosomal been isolated from water and damp environments such Database Project [16] and added to alignments containing as rice paddies and sink drains [13]. The only two de- representatives of all close relatives (as estimated from scribed species of the genus Plantibacter, P. auratus BLAST [17]). These alignments were downloaded, cleaned and P. flavus, have been detected as a tree endophyte with a custom script [18], and an approximately maxi- [14] and a component from the phyllosphere of grass mum likelihood tree was inferred using the default setting [15], respectively. Organisms within the genus Micro- in FastTree [19]. Outgroups for all trees were type strains bacterium belong to the class Actinobacteria in which of another genus or genera within the same family. The some species are known for the production of a broad sequence alignments supporting the phylogenetic trees of spectrum of secondary metabolites. The chemical this article are available in the FigShare repository [20]. ecology of microorganisms on indoor surfaces is a All strains were given a specific identifier (e.g., H83) component of our ongoing research efforts in the built based on our internal culture collection. The 16S rRNA environment. gene trees for both Microbacterium and Plantibacter Here we report a summary classification and the genera were poorly resolved (e.g., low bootstrap values), features of these eight isolates collected as part of the and these isolates were placed into polyphyletic clades Built Environment Reference Genomes initiative. Strains with respect to the names of taxa in the genera and their genomes have been deposited according to the (Additional files 2 and 3). In addition, while Microbac- following accessions: Staphylococcus capitis strain H36 terium sp. H83 falls within a clade that contains (DSM-103511; GenBank ID LWCQ00000000), S. capitis mostly M. foliorum, this name also occurs outside the strain H65 (DSM-103512; LWCP00000000), S. cohnii clade. Therefore we have not attempted to assign these strain H62 (DSM-103510; LWAC00000000), S. hominis isolates to a particular species. On the other hand, the strain H69 (DSM-103553; LVVO00000000), Microbac- rRNA gene for one isolate is found in a monophyletic terium sp. strain H83 (DSM-103506; LWCU00000000, clade with other M. iranicum isolates (Additional file 4) Pseudomonas oryzihabitans strain H72 (DSM-103505; and thus we have assigned this the name M. iranicum LWCR00000000), Mycobacterium iranicum strain H39 H39, For the Pseudomonas and Staphylococcus isolates, (DSM-103542; LWCS00000000), and finally Plantibacter the 16S rRNA gene trees were inadequate for taxonomic sp. strain H53 (DSM-103507; LWCT00000000). classification at the species level, but the genomes of Lymperopoulou et al. Standards in Genomic Sciences (2017) 12:17 Page 3 of 15 numerous sequenced representatives of close relatives Pseudomonas oryzihabitans (Fig. 2d) is a Gram- were available for further analysis. All available genome negative, non-fermenting,
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