A comparative analysis of drinking water employing metagenomics

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Abstract

The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can now be determined more accurately and analyzed in significantly greater detail, providing comprehensive understanding of the microbial community of drinking water applicable to public health. In this study, shotgun metagenomic analysis was performed to determine the microbiological content of drinking water and to provide a preliminary assessment of tap, drinking fountain, sparkling natural mineral, and non-mineral bottled water. Predominant bacterial species detected were members of the phyla Actinobacteria and Proteobacteria, notably the genera Alishewanella, Salmonella, and Propionibacterium in non-carbonated non-mineral bottled water, Methyloversatilis and Methylibium in sparkling natural mineral water, and Mycobacterium and Afipia in tap and drinking fountain water. Fecal indicator bacteria, i.e., Escherichia coli or enterococci, were not detected in any samples examined in this study. Bacteriophages and DNA encoding a few virulence-associated factors were detected but determined to be present only at low abundance. Antibiotic resistance markers were detected only at abundance values below our threshold of confidence. DNA of opportunistic plant and animal pathogens was identified in some samples and these included bacteria ( Mycobacterium spp.), protozoa ( Acanthamoeba mauritaniensis and Acanthamoeba palestinensis), and fungi ( Melampsora pinitorqua and Chryosporium queenslandicum). Archaeal DNA ( Candidatus Nitrosoarchaeum) was detected only in sparkling natural mineral water. This preliminary study reports the complete microbiome (bacteria, viruses, fungi, and protists) of selected types of drinking water employing whole-genome high-throughput sequencing and bioinformatics. Investigation into activity and function of the organisms detected is in progress.

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US Immigration Westernizes the Human Gut Microbiome

Pajau Vangay, Abigail Johnson, Tonya Ward … (2018)

Many United States immigrant populations develop metabolic diseases post-immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of U.S. immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the U.S., including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 U.S.-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the U.S. is associated with immediate loss of gut microbiome diversity and function, in which U.S.-associated strains and functions displace native strains and functions. These effects increase with duration of U.S. residence, and are compounded by obesity and across generations.

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Water Microbiology. Bacterial Pathogens and Water

João P. S. Cabral (2010)

Water is essential to life, but many people do not have access to clean and safe drinking water and many die of waterborne bacterial infections. In this review a general characterization of the most important bacterial diseases transmitted through water—cholera, typhoid fever and bacillary dysentery—is presented, focusing on the biology and ecology of the causal agents and on the diseases’ characteristics and their life cycles in the environment. The importance of pathogenic Escherichia coli strains and emerging pathogens in drinking water-transmitted diseases is also briefly discussed. Microbiological water analysis is mainly based on the concept of fecal indicator bacteria. The main bacteria present in human and animal feces (focusing on their behavior in their hosts and in the environment) and the most important fecal indicator bacteria are presented and discussed (focusing on the advantages and limitations of their use as markers). Important sources of bacterial fecal pollution of environmental waters are also briefly indicated. In the last topic it is discussed which indicators of fecal pollution should be used in current drinking water microbiological analysis. It was concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. Routine basic microbiological analysis of drinking water should be carried out by assaying the presence of Escherichia coli by culture methods. Whenever financial resources are available, fecal coliform determinations should be complemented with the quantification of enterococci. More studies are needed in order to check if ammonia is reliable for a preliminary screening for emergency fecal pollution outbreaks. Financial resources should be devoted to a better understanding of the ecology and behavior of human and animal fecal bacteria in environmental waters.

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Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases

Heather Armstrong, Misagh Alipour, Rosica Valcheva … (2019)

Background Inflammatory bowel diseases (IBD) are a group of complex and multifactorial disorders with unknown etiology. Chronic intestinal inflammation develops against resident intestinal bacteria in genetically susceptible hosts. We hypothesized that host intestinal immunoglobulin (Ig) G can be used to identify bacteria involved in IBD pathogenesis. Results IgG-bound and -unbound microorganisms were collected from 32 pediatric terminal ileum aspirate washes during colonoscopy [non-IBD (n = 10), Crohn disease (n = 15), and ulcerative colitis (n = 7)], and composition was assessed using the Illumina MiSeq platform. In vitro analysis of invasive capacity was evaluated by fluorescence in situ hybridization and gentamicin invasion assay; immune activation was measured by qPCR. Despite considerable inter-individual variations, IgG binding favored specific and unique mucosa-associated species in pediatric IBD patients. Burkholderia cepacia, Flavonifractor plautii, and Rumminococcus sp. demonstrated increased IgG binding, while Pseudomonas ST29 demonstrated reduced IgG binding, in IBD. In vitro validation confirmed that B. cepacia, F. plautii, and Rumminococcus display invasive potential while Pseudomonas protogens did not. Conclusion Using IgG as a marker of pathobionts in larger patient cohorts to identify microbes and elucidate their role in IBD pathogenesis will potentially underpin new strategies to facilitate development of novel, targeted diagnostic, and therapeutic approaches. Interestingly, this method can be used beyond the scope of this manuscript to evaluate altered gut pathobionts in a number of diseases associated with altered microbiota including arthritis, obesity, diabetes mellitus, alcoholic liver disease, cirrhosis, metabolic syndrome, and carcinomas. Electronic supplementary material The online version of this article (10.1186/s40168-018-0604-3) contains supplementary material, which is available to authorized users.

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Author and article information

Contributors

Kyle D. Brumfield:

ORCID: http://orcid.org/0000-0002-3234-3337

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing

Nur A. Hasan: Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SoftwareRole: SupervisionRole: ValidationRole: Writing – review & editing

Menu B. Leddy:

ORCID: http://orcid.org/0000-0001-7250-0088

Role: ConceptualizationRole: MethodologyRole: SupervisionRole: Writing – review & editing

Joseph A. Cotruvo: Role: ConceptualizationRole: MethodologyRole: SupervisionRole: Writing – review & editing

Shah M. Rashed: Role: ConceptualizationRole: Data curationRole: MethodologyRole: Writing – review & editing

Rita R. Colwell:

ORCID: http://orcid.org/0000-0001-5432-1502

Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – review & editing

Anwar Huq: Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing

Christopher Staley: Role: Editor

Journal

Journal ID (nlm-ta): PLoS One

Journal ID (iso-abbrev): PLoS ONE

Journal ID (publisher-id): plos

Journal ID (pmc): plosone

Title: PLoS ONE

Publisher: Public Library of Science (San Francisco, CA USA )

ISSN (Electronic): 1932-6203

Publication date (Electronic): 9 April 2020

Publication date Collection: 2020

Volume: 15

Issue: 4

Electronic Location Identifier: e0231210

Affiliations

[1 ] Maryland Pathogen Research Institute, University of Maryland, MD, College Park, United States of America

[2 ] University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States of America

[3 ] CosmosID Inc., Rockville, MD, United States of America

[4 ] Essential Environmental and Engineering Systems, Huntington Beach, CA, United States of America

[5 ] Joseph Cotruvo and Associates LLC, Washington, DC, United States of America

University of Minnesota Twin Cities, UNITED STATES

Author notes

Competing Interests: The authors declare the follow potential conflicts of interest with respect to the research, authorship and/or publication of this article: RRC is the founder of CosmosID, Inc., Rockville, MD and also a Professor at the University of Maryland; NAH and SMR are employees of CosmosID, Inc., Rockville, MD; JAC is the founder of Joseph Cotruvo and Associates LLC, Washington, DC; MBL is an employee of Essential Environmental and Engineering Systems, Huntington Beach, CA. The specific roles of these authors are articulated in the ‘author contributions’ section. This does not alter our adherence to PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors ( https://journals.plos.org/plosone/s/competing-interests).

* E-mail: huq@ 123456umd.edu

Author information

Kyle D. Brumfield http://orcid.org/0000-0002-3234-3337

Menu B. Leddy http://orcid.org/0000-0001-7250-0088

Rita R. Colwell http://orcid.org/0000-0001-5432-1502

Article

Publisher ID: PONE-D-19-27859

DOI: 10.1371/journal.pone.0231210

PMC ID: 7145143

PubMed ID: 32271799

SO-VID: b9863794-4fa1-4944-922b-c4620777e4c4

License:

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

History

Date received : 4 October 2019

Date accepted : 18 March 2020

Page count

Figures: 6, Tables: 4, Pages: 27

Funding

Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;

Award ID: 1742869

Award Recipient : Anwar Huq

Research reported in this publication was funded by the National Science Foundation (NSF, https://nsf.gov) through the EAGER, COLLABORATIVE RESEARCH program under award number 1742869 [NAH, RRC, AH]. Support in the form of partial salaries for authors was provided from NSF to the University of Maryland, College Park, MD [KDB, AH], CosmosID Inc., Rockville, MD [NAH, SMR], Joseph Cotruvo and Associates LLC, Washington, DC [JAC], and Essential Environmental and Engineering Systems, Huntington Beach, CA [MBL]. The funding agency had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The content is solely the responsibility of the authors and does not necessarily represent the official views of funding agencies. The specific roles of these authors are articulated in the ‘author contributions’ section.

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Data Availability Ion Torrent metagenomic sequencing data for all samples, after respectively removing P. pnomenusa spiked sequences, are deposited in the NCBI Sequence Read Archive database under BioProject PRJNA575040. Additionally, this project establishes a new NCBI Taxonomy ID for sequencing reads associated with the drinking water metagenome as 2651591.

A comparative analysis of drinking water employing metagenomics

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Most cited references 82

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Water Microbiology. Bacterial Pathogens and Water

Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases

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