Monitoring of microbial dynamics in a drinking water distribution system using the culture-free, user-friendly, MYcrobiota platform

Boers, Stefan A.; Prest, Emmanuelle I.; Taučer-Kapteijn, Maja; Knezev, Aleksandra; Schaap, Peter G.; Hays, John P.; Jansen, Ruud

doi:10.1038/s41598-018-32987-x

Cited by 14 publications

(11 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Unlike OTUs, ASVs can be resolved down to the level of single-nucleotide differences over the sequenced gene region that is expected to increase taxonomic resolution [ 104 ], although it could be argued that the fine-scale resolution obtained using ASV-based methods is actually not always desirable when processing highly complex samples. For example, the increased resolution of ASVs may increase the alpha diversity and reduce the overlap between samples, making downstream analyses more difficult compared to sequences that have been clustered into OTUs [ 105 ]. Further, OTU- and ASV-based methods will often produce comparable ecological results when the 16S rRNA gene is used as a genetic marker [ 106 ].…”

Section: Experimental Pitfalls and Biasesmentioning

confidence: 99%

Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory

Boers

Jansen

Hays

2019

Eur J Clin Microbiol Infect Dis

Self Cite

180

136

View full text Add to dashboard Cite

Recent advancements in next-generation sequencing (NGS) have provided the foundation for modern studies into the composition of microbial communities. The use of these NGS methods allows for the detection and identification of (‘difficult-to-culture’) microorganisms using a culture-independent strategy. In the field of routine clinical diagnostics however, the application of NGS is currently limited to microbial strain typing for epidemiological purposes only, even though the implementation of NGS for microbial community analysis may yield clinically important information. This lack of NGS implementation is due to many different factors, including issues relating to NGS method standardization and result reproducibility. In this review article, the authors provide a general introduction to the most widely used NGS methods currently available (i.e., targeted amplicon sequencing and shotgun metagenomics) and the strengths and weaknesses of each method is discussed. The focus of the publication then shifts toward 16S rRNA gene NGS methods, which are currently the most cost-effective and widely used NGS methods for research purposes, and are therefore more likely to be successfully implemented into routine clinical diagnostics in the short term. In this respect, the experimental pitfalls and biases created at each step of the 16S rRNA gene NGS workflow are explained, as well as their potential solutions. Finally, a novel diagnostic microbiota profiling platform (‘MYcrobiota’) is introduced, which was developed by the authors by taking into consideration the pitfalls, biases, and solutions explained in this article. The development of the MYcrobiota, and future NGS methodologies, will help pave the way toward the successful implementation of NGS methodologies into routine clinical diagnostics.

show abstract

Section: Experimental Pitfalls and Biasesmentioning

confidence: 99%

Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory

Boers

Jansen

Hays

2019

Eur J Clin Microbiol Infect Dis

Self Cite

180

136

View full text Add to dashboard Cite

show abstract

“…However, certain microbes, including opportunistic pathogens, survive disinfection and (re)grow in engineered water systems [EWSs, including DWDSs and building premise plumbing systems (PPSs)] (Hwang et al, 2012;Ashbolt, 2015a;El-Chakhtoura et al, 2018;Douterelo et al, 2019;Zhang and Liu, 2019;Zhang and Lu, 2021). Microorganisms in EWSs corrode iron and steel pipes (Ren et al, 2015;Xing et al, 2018;Zhu et al, 2019), deteriorate water taste and color (Zhou et al, 2017;Boers et al, 2018;El-Chakhtoura et al, 2018), and threaten public health [e.g., waterrelated disease outbreaks due to the (re)growth of opportunistic pathogens] (Ashbolt, 2015b;Liu et al, 2017;Wang et al, 2017;El-Chakhtoura et al, 2018;Chen et al, 2019;Zhang and Lu, 2021). Each year, more than one dozen drinking-water-related disease outbreaks occur in the United States (US), and opportunistic pathogen Legionella (mainly from EWSs) causes over 50% of these outbreaks (Beer et al, 2015;Benedict et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water

Zhang¹,

Qin

Struewing

et al. 2021

Front. Microbiol.

View full text Add to dashboard Cite

Microbial drinking water quality in premise plumbing systems (PPSs) strongly affects public health. Bacterial community structure is the essential aspect of microbial water quality. Studies have elucidated the microbial community structure in cold tap water, while the microbial community structures in hot tap and shower water are poorly understood. We sampled cold tap, hot tap, and shower water from a simulated PPS monthly for 16 consecutive months and assessed the bacterial community structures in those samples via high-throughput sequencing of bacterial 16S rRNA genes. The total relative abundance of the top five most abundant phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes) was greater than 90% among the 24 identified phyla. The most abundant families were Burkholderiaceae, Sphingomonadaceae, unclassified Alphaproteobacteria, unclassified Corynebacteriales, and Mycobacteriaceae. A multiple linear regression suggests that the bacterial community diversity increased with water temperature and the age of the simulated PPS, decreased with total chlorine residual concentration, and had a limited seasonal variation. The bacterial community in hot tap water had significantly lower Shannon and Inverse Simpson diversity indices (p < 0.05) and thus a much lower diversity than those in cold tap and shower water. The paradoxical results (i.e., diversity increased with water temperature, but hot tap water bacterial community was less diverse) were presumably because (1) other environmental factors made hot tap water bacterial community less diverse, (2) the diversity of bacterial communities in all types of water samples increased with water temperature, and (3) the first draw samples of hot tap water could have a comparable or even lower temperature than shower water samples and the second draw samples of cold tap water. In both a three-dimensional Non-metric multidimensional scaling ordination plot and a phylogenetic dendrogram, the samples of cold tap and shower water cluster and are separate from hot tap water samples (p < 0.05). In summary, the bacterial community in hot tap water in the simulated PPS had a distinct structure from and a much lower diversity than those in cold tap and shower water.

show abstract

“…Microbial biogeography has been documented in diverse aquatic ecosystems and on various spatial scales (Roeselers et al, 2015; Liu et al, 2018). Numerous studies revealed a remarkable heterogeneity (i.e., variations) in bacterial abundance (Liu et al, 2013; Siles and Margesin, 2016), metabolic activities (Chao et al, 2015; Charlop-Powers et al, 2015), or microbiomes (Stanish et al, 2016; Boers et al, 2018). Interestingly, this heterogeneity was not attributed to distance per se , but mainly to spatial differences in environmental factors (Hou et al, 2017; Langenheder et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Small-Scale Heterogeneity in Drinking Water Biofilms

et al. 2019

View full text Add to dashboard Cite

Biofilm heterogeneity has been characterized on various scales for both natural and engineered ecosystems. This heterogeneity has been attributed to spatial differences in environmental factors. Understanding their impact on localized biofilm heterogeneity in building plumbing systems is important for both management and representative sampling strategies. We assessed heterogeneity within the confined engineered ecosystem of a shower hose by high-resolution sampling (200 individual biofilm sections per hose) on varying scales (μm to m). We postulated that a biofilm grown on a single material under uniform conditions should be homogeneous in its structure, bacterial numbers, and community composition. A biofilm grown for 12 months under controlled laboratory conditions, showed homogeneity on large-scale. However, some small-scale heterogeneity was clearly observed. For example, biofilm thickness of cm-sections varied up to 4-fold, total cell concentrations (TCC) 3-fold, and relative abundance of dominant taxa up to 5-fold. A biofilm grown under real (i.e., uncontrolled) use conditions developed considerably more heterogeneity in all variables which was attributed to more discontinuity in environmental conditions. Interestingly, biofilm communities from both hoses showed comparably low diversity, with <400 taxa each, and only three taxa accounting for 57%, respectively, 73% of the community. This low diversity was attributed to a strong selective pressure, originating in migrating carbon from the flexible hoses as major carbon source. High-resolution sampling strategy enabled detailed analysis of spatial heterogeneity within an individual drinking water biofilm. This study gives insight into biofilm structure and community composition on cm-to m-scale and is useful for decision-making on sampling strategies in biofilm research and monitoring.

show abstract

Monitoring of microbial dynamics in a drinking water distribution system using the culture-free, user-friendly, MYcrobiota platform

Cited by 14 publications

References 34 publications

Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory

Understanding and overcoming the pitfalls and biases of next-generation sequencing (NGS) methods for use in the routine clinical microbiological diagnostic laboratory

The Bacterial Community Diversity of Bathroom Hot Tap Water Was Significantly Lower Than That of Cold Tap and Shower Water

Small-Scale Heterogeneity in Drinking Water Biofilms

Contact Info

Product

Resources

About