Opportunistic pathogens enriched in showerhead biofilms

Feazel, Leah M.; Baumgartner, Laura K.; Peterson, Kristen L.; Frank, Daniel N.; Harris, J. Kirk; Pace, Norman R.

doi:10.1073/pnas.0908446106

Cited by 485 publications

(405 citation statements)

References 54 publications

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“…Across all gated events, 232 total 16S sequences were within the domain Bacteria. Some of the most highly detected genera such as Acinetobacter and Sphingomonas are consistent with those found in microbial communities associated with drinking water distribution systems (17,38,39). From the 32 wells with 100 low-fluorescent events in each, 6 wells produced a 16S sequence.…”

Section: Resultssupporting

confidence: 65%

“…S7), which suggests that this phylum has a cosmopolitan distribution, although typically found at low relative abundance. Its ecological distribution (derived from published and unpublished studies that have deposited related sequences in GenBank) includes domestic water sources (17,39,45), acidic cave biofilms, acid mine drainage biofilms (46), wastewater biofilms (47), soil, contaminated groundwater and subsurface sites (48,49), aquatic moss, hypersaline mats, peat bogs, and peat swamps (30,50). These and additional environments where TM6 was detected in 16S rRNA gene clone libraries, including a number of biofilm-related samples, are highlighted in SI Appendix, Table S1.…”

Section: Phylogenetic and Phylogenomic Analyses Of Candidate Phylum Tm6mentioning

confidence: 99%

“…Several studies indicate that TM6 16S sequences are commonly detected in biofilms from domestic water systems (SI Appendix, Table S1). Five such sequences were discovered along with potential opportunistic pathogens in showerhead biofilms (17). A recent study of a more than 20-y-old drinking water network that compared bacterial core communities in bulk water and associated biofilms revealed that the biofilm samples contained a unique community with no overlapping phylotypes with the bulk water samples (45).…”

Section: Phylogenetic and Phylogenomic Analyses Of Candidate Phylum Tm6mentioning

confidence: 99%

“…Several pathogens including Escherichia coli, Legionella pneumophila (10-13), Vibrio cholerae (14), and Helicobacter pylori (15,16) have been detected in biofilms within water distribution systems. A recent 16S rRNA gene (abbreviated henceforth as 16S unless otherwise stated) molecular survey also revealed significant loads of Mycobacterium avium in showerhead biofilms (17). Based on these findings, indoor environments can clearly serve as significant reservoirs of pathogenic bacteria, and therefore there is great interest in investigating the rare and abundant bacterial species within biofilms in these environments.…”

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confidence: 99%

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Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

McLean

Lombardo

Badger

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

166

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The "dark matter of life" describes microbes and even entire divisions of bacterial phyla that have evaded cultivation and have yet to be sequenced. We present a genome from the globally distributed but elusive candidate phylum TM6 and uncover its metabolic potential. TM6 was detected in a biofilm from a sink drain within a hospital restroom by analyzing cells using a highly automated single-cell genomics platform. We developed an approach for increasing throughput and effectively improving the likelihood of sampling rare events based on forming small random pools of single-flow-sorted cells, amplifying their DNA by multiple displacement amplification and sequencing all cells in the pool, creating a "mini-metagenome." A recently developed single-cell assembler, SPAdes, in combination with contig binning methods, allowed the reconstruction of genomes from these mini-metagenomes. A total of 1.07 Mb was recovered in seven contigs for this member of TM6 (JCVI TM6SC1), estimated to represent 90% of its genome. High nucleotide identity between a total of three TM6 genome drafts generated from pools that were independently captured, amplified, and assembled provided strong confirmation of a correct genomic sequence. TM6 is likely a Gram-negative organism and possibly a symbiont of an unknown host (nonfree living) in part based on its small genome, low-GC content, and lack of biosynthesis pathways for most amino acids and vitamins. Phylogenomic analysis of conserved single-copy genes confirms that TM6SC1 is a deeply branching phylum. (1), which is accomplished using multiple displacement amplification (MDA) (2-5) of genomic DNA to obtain sufficient template. We applied a high-throughput strategy to capture and sequence genomes of bacteria from a biofilm in a hospital sink including pathogens, such as the oral periodontal pathogen (Porphyromonas gingivalis) (6) and uncultivated members (this study). Despite the fact that a typical person spends ∼90% of their time indoors (7), our knowledge of the microbial diversity of the indoor environment has only recently begun to be explored using culture-independent methods (8, 9). Biofilms within water distribution systems in particular are thought to be diverse microbial communities and potential reservoirs of disease-causing organisms in the indoor environment. Several pathogens including Escherichia coli, Legionella pneumophila (10-13), Vibrio cholerae (14), and Helicobacter pylori (15, 16) have been detected in biofilms within water distribution systems. A recent 16S rRNA gene (abbreviated henceforth as 16S unless otherwise stated) molecular survey also revealed significant loads of Mycobacterium avium in showerhead biofilms (17). Based on these findings, indoor environments can clearly serve as significant reservoirs of pathogenic bacteria, and therefore there is great interest in investigating the rare and abundant bacterial species within biofilms in these environments.One approach to capture uncultivated bacteria is to isolate single bacterial cells by fluorescent activat...

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Section: Resultssupporting

confidence: 65%

Section: Phylogenetic and Phylogenomic Analyses Of Candidate Phylum Tm6mentioning

confidence: 99%

Section: Phylogenetic and Phylogenomic Analyses Of Candidate Phylum Tm6mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

McLean

Lombardo

Badger

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

166

View full text Add to dashboard Cite

show abstract

“…Neisseria have been found in sites closely associated with humans, and are, for example, a component of the microbiota of showerhead biofilms as determined by DNA analysis (Feazel et al, 2009) and mattress dust (Ege et al, 2012). Of note, there was a significant inverse correlation between the onset of hay fever with the detection of Neisseria in mattress dust, suggesting that exposure to Neisseria might confer a degree of protection to children (Ege et al, 2012).…”

Section: Free-living Neisseriamentioning

confidence: 99%