1
|
Royer C, Patin NV, Jesser KJ, Peña-Gonzalez A, Hatt JK, Trueba G, Levy K, Konstantinidis KT. Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections. mBio 2024; 15:e0342223. [PMID: 38488359 PMCID: PMC11005377 DOI: 10.1128/mbio.03422-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 04/11/2024] Open
Abstract
Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance. IMPORTANCE Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.
Collapse
Affiliation(s)
- C. Royer
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - N. V. Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - K. J. Jesser
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - A. Peña-Gonzalez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotà, Colombia
| | - J. K. Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G. Trueba
- Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - K. Levy
- Department of Environmental and Occupational Health, University of Washington, Seattle, Washington, USA
| | - K. T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
2
|
Lindner BG, Gerhardt K, Feistel DJ, Rodriguez-R LM, Hatt JK, Konstantinidis KT. A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection. Int J Food Microbiol 2024; 410:110488. [PMID: 38035404 DOI: 10.1016/j.ijfoodmicro.2023.110488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/15/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized. In this review, we summarize ongoing developments in metagenomic sequence analysis that facilitate its wider application to pathogen detection. We examine theoretical frameworks for estimating the limit of detection for a particular level of sequencing effort, current approaches for achieving species and strain analytical resolution, and discuss some relevant modern tools for these tasks. While these recent advances are significant and establish metagenomics as a powerful tool to provide insights not easily attained by culture-based approaches, metagenomics is unlikely to emerge as a widespread, routine monitoring tool in the near future due to its inherently high detection limits, cost, and inability to easily distinguish between viable and non-viable cells. Instead, metagenomics seems best poised for applications involving special circumstances otherwise challenging for culture-based and molecular (e.g., PCR-based) approaches such as the de novo detection of novel pathogens, cases of co-infection by more than one pathogen, and situations where it is important to assess the genomic composition of the pathogenic population(s) and/or its impact on the indigenous microbiome.
Collapse
Affiliation(s)
- Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kenji Gerhardt
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Dorian J Feistel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Luis M Rodriguez-R
- Department of Microbiology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| |
Collapse
|
3
|
Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG, Venter SN, Orellana LH, Amann R, Rossello-Mora R, Konstantinidis KT. An ANI gap within bacterial species that advances the definitions of intra-species units. mBio 2024; 15:e0269623. [PMID: 38085031 PMCID: PMC10790751 DOI: 10.1128/mbio.02696-23] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/03/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings.
Collapse
Affiliation(s)
- Luis M. Rodriguez-R
- Department of Microbiology, and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Roth E. Conrad
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tomeu Viver
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Dorian J. Feistel
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Blake G. Lindner
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ramon Rossello-Mora
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
4
|
Viver T, Conrad RE, Rodriguez-R LM, Ramírez AS, Venter SN, Rocha-Cárdenas J, Llabrés M, Amann R, Konstantinidis KT, Rossello-Mora R. Towards estimating the number of strains that make up a natural bacterial population. Nat Commun 2024; 15:544. [PMID: 38228587 PMCID: PMC10791622 DOI: 10.1038/s41467-023-44622-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with four-fold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.
Collapse
Affiliation(s)
- Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Roth E Conrad
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Luis M Rodriguez-R
- Department of Microbiology, and Digital Science Center (DiSC), Universität of Innsbruck, Innsbruck, Austria
| | - Ana S Ramírez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jairo Rocha-Cárdenas
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | - Mercè Llabrés
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
| |
Collapse
|
5
|
Jesser KJ, Trueba G, Konstantinidis KT, Levy K. Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador. Gut Microbes 2023; 15:2281010. [PMID: 37992406 PMCID: PMC10730187 DOI: 10.1080/19490976.2023.2281010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/05/2023] [Indexed: 11/24/2023] Open
Abstract
A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea. The factors responsible for the development of diarrhea symptoms, or lack thereof, remain unclear. Here, we used DEC isolate genome and whole stool microbiome data from a case-control study of diarrhea in Ecuador to examine factors associated with diarrhea symptoms accompanying DEC carriage. We investigated i) pathogen abundance, ii) gut microbiome characteristics, and iii) strain-level pathogen characteristics from DEC infections with diarrhea symptoms (symptomatic infections) and without diarrhea symptoms (asymptomatic infections). We also included data from individuals with and without diarrhea who were not infected with DEC (uninfected cases and controls). i) E. coli relative abundance in the gut microbiome was highly variable, but higher on-average in individuals with symptomatic compared to asymptomatic DEC infections. Similarly, the number and relative abundances of virulence genes in the gut were higher in symptomatic than asymptomatic DEC infections. ii) Measures of microbiome diversity were similar regardless of diarrhea symptoms or DEC carriage. Proteobacterial families that have been described as pathobionts were enriched in symptomatic infections and uninfected cases, whereas potentially beneficial taxa, including the Bacteroidaceae and Bifidobacteriaceae, were more abundant in individuals without diarrhea. An analysis of high-level gene functions recovered in metagenomes revealed that genes that were differentially abundant by diarrhea and DEC infection status were more abundant in symptomatic than asymptomatic DEC infections. iii) DEC isolates from symptomatic versus asymptomatic individuals showed no significant differences in virulence or accessory gene content, and there was no phylogenetic signal associated with diarrhea symptoms. Together, these data suggest signals that distinguish symptomatic from asymptomatic DEC infections. In particular, the abundance of E. coli, the virulence gene content of the gut microbiome, and the taxa present in the gut microbiome have an apparent role.
Collapse
Affiliation(s)
- Kelsey J Jesser
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| |
Collapse
|
6
|
Maguire M, Ramachandran P, Tallent S, Mammel MK, Brown EW, Allard MW, Musser SM, González-Escalona N. Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producing Escherichia coli in enriched agricultural water. Front Microbiol 2023; 14:1221668. [PMID: 37720160 PMCID: PMC10500926 DOI: 10.3389/fmicb.2023.1221668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/04/2023] [Indexed: 09/19/2023] Open
Abstract
Culture-independent metagenomic sequencing of enriched agricultural water could expedite the detection and virulotyping of Shiga toxin-producing Escherichia coli (STEC). We previously determined the limits of a complete, closed metagenome-assembled genome (MAG) assembly and of a complete, fragmented MAG assembly for O157:H7 in enriched agricultural water using long reads (Oxford Nanopore Technologies, Oxford), which were 107 and 105 CFU/ml, respectively. However, the nanopore assemblies did not have enough accuracy to be used in Single Nucleotide Polymorphism (SNP) phylogenies and cannot be used for the precise identification of an outbreak STEC strain. The present study aimed to determine the limits of detection and assembly for STECs in enriched agricultural water by Illumina MiSeq sequencing technology alone, followed by establishing the limit of hybrid assembly with nanopore long-read sequencing using three different hybrid assemblers (SPAdes, Unicycler, and OPERA-MS). We also aimed to generate a genome with enough accuracy to be used in a SNP phylogeny. The classification of MiSeq and nanopore sequencing identified the same highly abundant species. Using the totality of the MiSeq output and a precision metagenomics approach in which the E. coli reads are binned before assembly, the limit of detection and assembly of STECs by MiSeq were determined to be 105 and 107 CFU/ml, respectively. While a complete, closed MAG could not be generated at any concentration, a complete, fragmented MAG was produced using the SPAdes assembler with an STEC concentration of at least 107 CFU/ml. At this concentration, hybrid assembled contigs aligned to the nanopore-assembled genome could be accurately placed in a neighbor-joining tree. The MiSeq limit of detection and assembly was less sensitive than nanopore sequencing, which was likely due to factors including the small starting material (50 vs. 1 μg) and the dilution of the library loaded on the cartridge. This pilot study demonstrates that MiSeq sequencing requires higher coverage in precision metagenomic samples; however, with sufficient concentration, STECs can be characterized and phylogeny can be accurately determined.
Collapse
Affiliation(s)
- Meghan Maguire
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, MD, United States
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, MD, United States
| | - Sandra Tallent
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, MD, United States
| | - Mark K. Mammel
- Office of Applied Research and Safety Assessment, Food and Drug Administration, College Park, MD, United States
| | - Eric W. Brown
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, MD, United States
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, MD, United States
| | - Steven M. Musser
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, MD, United States
| | - Narjol González-Escalona
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, MD, United States
| |
Collapse
|
7
|
Campos-Madueno EI, Aldeia C, Sendi P, Endimiani A. Escherichia ruysiae May Serve as a Reservoir of Antibiotic Resistance Genes across Multiple Settings and Regions. Microbiol Spectr 2023; 11:e0175323. [PMID: 37318364 PMCID: PMC10434276 DOI: 10.1128/spectrum.01753-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023] Open
Abstract
Gut colonization with multidrug-resistant Enterobacterales (MDR-Ent) has reached worrisome levels worldwide. In this context, Escherichia ruysiae is a recently described species mostly found in animals. However, its spread and impact on humans is poorly understood. A stool sample from a healthy individual living in India was screened for the presence of MDR-Ent using culture-based methods. Colonies were routinely identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and phenotypically characterized by broth microdilution. Illumina and Nanopore whole-genome sequencing (WGS) platforms were implemented to generate a complete assembly. E. ruysiae genomes deposited in international databases were used for a core genome phylogenetic analysis. An extended-spectrum β-lactamase (ESBL)-producing E. coli strain (S1-IND-07-A) was isolated from the stool. WGS confirmed that S1-IND-07-A was indeed E. ruysiae, belonged to sequence type 5792 (ST5792), core genome (cg) ST89059, serotype O13/O129-:H56-like, clade IV phylogroup, and possessed five virulence factors. A copy of blaCTX-M-15 and five other antimicrobial resistance genes (ARGs) were detected in a conjugative IncB/O/K/Z plasmid. A database search identified 70 further E. ruysiae strains from 16 countries (44, 15, and 11 strains isolated from animals, the environment, and humans, respectively). The core genome phylogeny revealed five major STs: ST6467, ST8084, ST2371, ST9287, and ST5792. Three out of the seventy strains possessed important ARGs: OTP1704 (blaCTX-M-14; ST6467), SN1013-18 (blaCTX-M-15; ST5792), and CE1758 (blaCMY-2; ST7531). These strains were of human, environmental, and wild animal origin, respectively. E. ruysiae may acquire clinically important ARGs and transmit them to other species. Due to its zoonotic potential, further efforts are needed to improve routine detection and surveillance across One Health settings. IMPORTANCE Escherichia ruysiae is a recently described species of the cryptic clades III and IV of the genus Escherichia and is commonly found in animals and the environment. This work highlights the zoonotic potential of E. ruysiae, as it has been shown to colonize the human intestinal tract. Importantly, E. ruysiae may be associated with conjugative plasmids carrying clinically relevant antibiotic resistance genes. Therefore, it is important to closely monitor this species. Overall, this study highlights the need for improved identification of Escherichia species and continued surveillance of zoonotic pathogens in One Health settings.
Collapse
Affiliation(s)
- Edgar I. Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| |
Collapse
|
8
|
Ngugi DK, Salcher MM, Andrei AS, Ghai R, Klotz F, Chiriac MC, Ionescu D, Büsing P, Grossart HP, Xing P, Priscu JC, Alymkulov S, Pester M. Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes. SCIENCE ADVANCES 2023; 9:eadc9392. [PMID: 36724220 PMCID: PMC9891703 DOI: 10.1126/sciadv.adc9392] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.
Collapse
Affiliation(s)
- David Kamanda Ngugi
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Corresponding author.
| | - Michaela M. Salcher
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Adrian-Stefan Andrei
- Microbial Evogenomics Lab, Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Rohit Ghai
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Franziska Klotz
- Department of Biology, University of Konstanz, D-78457 Constance, Germany
| | - Maria-Cecilia Chiriac
- Institute of Hydrobiology, Biology Center CAS, Na Sádkách 7, 37005 České Budejovice, Czech Republic
| | - Danny Ionescu
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
| | - Petra Büsing
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, D-12587 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, D-14469 Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Free University, D-14195 Berlin, Germany
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - John C. Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, 334 Leon Johnson Hall, Bozeman, MT 59717, USA
| | - Salmor Alymkulov
- Institute of Physics, National Academy of Sciences of Kyrgyz Republic, Chui Avenue, 265-a, Bishkek 720071, Kyrgyzstan
| | - Michael Pester
- Leibniz Institute DSMZ–German Collection of Cell Microorganisms and Cell Cultures GmbH, D-38124 Braunschweig, Germany
- Institute of Microbiology, Technical University of Braunschweig, D-38108 Braunschweig, Germany
| |
Collapse
|
9
|
Ni W, Jiao X, Zou H, Jing M, Xia M, Zhu S, Li L. Gut microbiome alterations in ICU patients with enteral nutrition-related diarrhea. Front Microbiol 2022; 13:1051687. [DOI: 10.3389/fmicb.2022.1051687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/02/2022] [Indexed: 11/23/2022] Open
Abstract
Enteral Nutrition-related Diarrhea (END) is an extremely common complication in Intensive Care Unit (ICU) patients. However, it is currently unclear whether the patient’s gut microbiota is disturbed. Our study aimed to explore the characteristics of gut microbiota changes in END patients. We divided ICU patients into no-END group (n = 7) and END group (n = 7) according to whether they had END, then stool samples were collected separately. The V3-V4 region of stool bacterial 16S rRNA gene was amplified by PCR and sequenced on an Illumina MiSeq PE300 platform. Microbiome data obtained by quality control were analyzed, including microbial community composition, diversity and gene function prediction.The results showed that the dominant gut microbiota in ICU patients who were given total enteral nutrition were Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. Bacterial richness and diversity in END patients were all significantly lower than those in no-END patients. In addition, END caused significant changes in bacterial composition. LEfSe found 34 biomarkers represented by Bacteroidetes and Subdoligranulum in the no-END group as well as 11 biomarkers represented by Enterococcus and Klebsiella in the END group. Finally, through PICRUST function prediction, we found that diarrhea led to abnormal changes in numerous KEGG pathways mainly related to immunity and metabolism. In short, ICU patients with END have severe gut dysbiosis, and our study provides a reliable experimental basis for the patient’s microbiota therapy.
Collapse
|
10
|
Kim M, Rodriguez-R LM, Hatt JK, Kayali O, Nalá R, Dunlop AL, Brennan PA, Corwin E, Smith AK, Brown J, Konstantinidis KT. Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling. ISME COMMUNICATIONS 2022; 2:74. [PMID: 37938667 PMCID: PMC9723681 DOI: 10.1038/s43705-022-00154-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 07/05/2023]
Abstract
The infant gut microbiome has lifelong implications on health and immunity but there is still limited understanding of the microbiome differences and similarities between children in low- and middle-income countries (LMICs) vs. high-income countries (HICs). Here, we describe and compare the microbiome profile of children aged under 48 months in two urban areas: Maputo, Mozambique and Atlanta, USA using shotgun metagenomics. The gut microbiome of American children showed distinct development, characterized by higher alpha diversity after infancy, compared to the same age group of African children, and the microbiomes clustered separately based on geographic location or age. The abundances of antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly higher in Maputo children, driven primarily by several primary and opportunistic pathogens. Most notably, about 50% of Maputo children under the age of two were positive for enterotoxigenic (ETEC) and typical enteropathogenic (EPEC) Escherichia coli diagnostic genes while none of the Atlanta age-matched children showed such a positive signal. In contrast, commensal species such as Phocaeicola vulgatus and Bacteroides caccae were more abundant in Atlanta, potentially reflecting diets rich in animal protein and susceptibility to inflammatory diseases. Overall, our results suggest that the different environments characterizing the two cities have significant, distinctive signatures on the microbiota of children and its development over time. Lack of safe water, sanitation, and hygiene (WASH) conditions and/or unsafe food sources may explain the higher enteric pathogen load among children in Maputo.
Collapse
Affiliation(s)
- Minjae Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80523, USA
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, 6020, Innsbruck, Tyrol, Austria
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Osman Kayali
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Rassul Nalá
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Anne L Dunlop
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, 30332, USA
| | | | - Elizabeth Corwin
- School of Nursing, Columbia University, New York, NY, 10032, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, North, Carolina, NC, 27599, USA.
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| |
Collapse
|
11
|
Zhu K, Suttner B, Knee J, Capone D, Moe CL, Stauber CE, Konstantinidis KT, Wallach TE, Pickering AJ, Brown J. Elevated Fecal Mitochondrial DNA from Symptomatic Norovirus Infections Suggests Potential Health Relevance of Human Mitochondrial DNA in Fecal Source Tracking. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2022; 9:543-550. [PMID: 35719858 PMCID: PMC9202355 DOI: 10.1021/acs.estlett.2c00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
An end goal of fecal source tracking (FST) is to provide information on risk of transmission of waterborne illnesses associated with fecal contamination. Ideally, concentrations of FST markers in ambient waters would reflect exposure risk. Human mtDNA is an FST marker that is exclusively human in origin and may be elevated in feces of individuals experiencing gastrointestinal inflammation. In this study, we examined whether human mtDNA is elevated in fecal samples from individuals with symptomatic norovirus infections using samples from the United States (US), Mozambique, and Bangladesh. We quantified hCYTB484 (human mtDNA) and HF183/BacR287 (human-associated Bacteroides) FST markers using droplet digital polymerase chain reaction. We observed the greatest difference in concentrations of hCYTB484 when comparing samples from individuals with symptomatic norovirus infections versus individuals without norovirus infections or diarrhea symptoms: log10 increase of 1.42 in US samples (3,820% increase, p-value = 0.062), 0.49 in Mozambique (308% increase, p-value = 0.061), and 0.86 in Bangladesh (648% increase, p-value = 0.035). We did not observe any trends in concentrations of HF183/BacR287 in the same samples. These results suggest concentrations of fecal mtDNA may increase during symptomatic norovirus infection and that mtDNA in environmental samples may represent an unambiguously human source-tracking marker that correlates with enteric pathogen exposure risk.
Collapse
Affiliation(s)
- Kevin
J. Zhu
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Brittany Suttner
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jackie Knee
- Department
of Disease Control, London School of Hygiene
and Tropical Medicine, London WC1E 7HT,United Kingdom
| | - Drew Capone
- Department
of Environmental Sciences and Engineering, Gillings School of Global
Public Health, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| | - Christine L. Moe
- Center
for Global Safe Water, Sanitation, and Hygiene, Rollins School of
Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Christine E. Stauber
- Department
of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, Georgia 30302, United States
| | - Kostas T. Konstantinidis
- School
of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Thomas E. Wallach
- Division
of Pediatric Gastroenterology, SUNY Downstate
Health Sciences University, Brooklyn, New York 11203, United States
| | - Amy J. Pickering
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Joe Brown
- Department
of Environmental Sciences and Engineering, Gillings School of Global
Public Health, University of North Carolina
at Chapel Hill, Chapel
Hill, North Carolina 27599, United States
| |
Collapse
|
12
|
James WA, Ogunrinde E, Wan Z, Kamen DL, Oates J, Gilkeson GS, Jiang W. A Distinct Plasma Microbiome But Not Gut Microbiome in Patients With Systemic Lupus Erythematosus Compared to Healthy Individuals. J Rheumatol 2022; 49:592-597. [PMID: 35169056 PMCID: PMC9364828 DOI: 10.3899/jrheum.210952] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE Blood microbiome has been analyzed in cancer patients using machine learning. We aimed to study whether the plasma microbiome represents the microbial community in the gut among patients with systemic lupus erythematosus (SLE) and healthy controls (HCs). METHODS Paired plasma and stool samples from female patients with SLE and female HCs were assessed for microbiome composition by microbial 16S ribosomal RNA sequencing. RESULTS Decreased microbial alpha diversity in stool compared to plasma and distinct plasma and gut beta diversity were found in both HCs and patients with SLE. No difference in gut microbial diversity was found; however, plasma alpha diversity was decreased in patients with SLE compared to HCs. The predominant bacteria differed between plasma and stool in both groups. Although the predominant plasma and stool genus bacteria were similar in patients with SLE and HCs, some were clearly different. CONCLUSION Compared to the gut, the plasma microbiome contained distinct community and greater heterogeneity, indicating that the predominant circulating microbiome may originate from sites (eg, oral or skin) other than the gastrointestinal tract. The decreased plasma but not gut alpha diversity in patients with SLE compared to HCs implies an altered plasma microbiome in SLE, which may be important for systemic immune perturbations and SLE disease pathogenesis.
Collapse
Affiliation(s)
- Warren A James
- W.A. James, MD, College of Medicine, Medical University of South Carolina
| | - Elizabeth Ogunrinde
- E. Ogunrinde, PhD, Z. Wan, MS, Department of Microbiology and Immunology, Medical University of South Carolina
| | - Zhuang Wan
- E. Ogunrinde, PhD, Z. Wan, MS, Department of Microbiology and Immunology, Medical University of South Carolina
| | - Diane L Kamen
- D.L. Kamen, MD, J. Oates, Director and Endowed Chair, MD, Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, and Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina
| | - Jim Oates
- D.L. Kamen, MD, J. Oates, Director and Endowed Chair, MD, Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, and Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina
| | - Gary S Gilkeson
- G.S. Gilkeson, MD, Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, and Staff Physician, Ralph H. Johnson VA Medical Center;
| | - Wei Jiang
- W. Jiang, MD, Department of Microbiology and Immunology, and Division of Infectious Diseases, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA.
| |
Collapse
|
13
|
A longitudinal study of dominant E. coli lineages and antimicrobial Resistance in the gut of children living in an upper middle-income country. J Glob Antimicrob Resist 2022; 29:136-140. [PMID: 35283334 PMCID: PMC9232985 DOI: 10.1016/j.jgar.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
|
14
|
Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool. Microorganisms 2022; 10:microorganisms10020441. [PMID: 35208895 PMCID: PMC8880012 DOI: 10.3390/microorganisms10020441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/29/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information. Here, we evaluated shotgun metagenomics to assess the detection of common enteric bacterial pathogens in stool. We sequenced 304 stool specimens from 285 patients alongside routine diagnostic testing for Salmonella spp., Campylobacter spp., Shigella spp., and shiga-toxin producing Escherichia coli. Five analytical approaches were assessed for pathogen detection: microbiome profiling, Kraken2, MetaPhlAn, SRST2, and KAT-SECT. Among analysis tools and databases compared, KAT-SECT analysis provided the best sensitivity and specificity for all pathogens tested compared to culture (91.2% and 96.2%, respectively). Where metagenomics detected a pathogen in culture-negative specimens, standard PCR was positive 85% of the time. The cost of metagenomics is approaching the current combined cost of PCR, reflex culture, and whole genome sequencing for pathogen detection and subtyping. As cost, speed, and analytics for single-approach metagenomics improve, it may be more routinely applied in clinical and public health laboratories.
Collapse
|
15
|
Gerhardt K, Ruiz-Perez CA, Rodriguez-R LM, Conrad RE, Konstantinidis KT. RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity. FRONTIERS IN BIOINFORMATICS 2022; 1:826701. [PMID: 36303791 PMCID: PMC9580866 DOI: 10.3389/fbinf.2021.826701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/28/2021] [Indexed: 11/14/2022] Open
Abstract
Mapping of short metagenomic (or metatranscriptomic) read data to reference isolate or single-cell genomes or metagenome-assembled genomes (MAGs) to assess microbial population relative abundance and/or structure represents an essential task of many studies across environmental and clinical settings. The filtering for the quality of the read match and assessment of read mapping results are frequently performed without visual aids or with the assistance of visualizations produced through ad-hoc, in-house approaches. Here, we introduce RecruitPlotEasy, a fully automated, user-friendly pipeline for these purposes that integrates statistical approaches to quantify intra-population sequence and gene-content diversity and identify co-occurring relative populations in the sample. Hence, RecruitPlotEasy should also greatly facilitate population genetics studies. RecruitPlotEasy is implemented in Python and R languages and is freely available open source software under the Artistic License 2.0 from https://github.com/KGerhardt/RecruitPlotEasy.
Collapse
Affiliation(s)
- Kenji Gerhardt
- School of Biological Sciences, Atlanta, GA, United States
- Center for Bioinformatics and Computational Genomics, Atlanta, GA, United States
| | - Carlos A. Ruiz-Perez
- School of Biological Sciences, Atlanta, GA, United States
- Center for Bioinformatics and Computational Genomics, Atlanta, GA, United States
| | - Luis M. Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | | | - Konstantinos T. Konstantinidis
- School of Biological Sciences, Atlanta, GA, United States
- Center for Bioinformatics and Computational Genomics, Atlanta, GA, United States
- Ocean Science & Engineering, Atlanta, GA, United States
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
- *Correspondence: Konstantinos T. Konstantinidis,
| |
Collapse
|
16
|
Diarrheal disease and gut microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:149-177. [DOI: 10.1016/bs.pmbts.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
17
|
Zorrilla F, Buric F, Patil KR, Zelezniak A. metaGEM: reconstruction of genome scale metabolic models directly from metagenomes. Nucleic Acids Res 2021; 49:e126. [PMID: 34614189 PMCID: PMC8643649 DOI: 10.1093/nar/gkab815] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 08/05/2021] [Accepted: 09/28/2021] [Indexed: 01/11/2023] Open
Abstract
Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozorrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species communities directly from metagenomes. The pipeline automates all steps from the extraction of context-specific prokaryotic GEMs from MAGs to community level flux balance analysis (FBA) simulations. To demonstrate the capabilities of metaGEM, we analyzed 483 samples spanning lab culture, human gut, plant-associated, soil, and ocean metagenomes, reconstructing over 14,000 GEMs. We show that GEMs reconstructed from metagenomes have fully represented metabolism comparable to isolated genomes. We demonstrate that metagenomic GEMs capture intraspecies metabolic diversity and identify potential differences in the progression of type 2 diabetes at the level of gut bacterial metabolic exchanges. Overall, metaGEM enables FBA-ready metabolic model reconstruction directly from metagenomes, provides a resource of metabolic models, and showcases community-level modeling of microbiomes associated with disease conditions allowing generation of mechanistic hypotheses.
Collapse
Affiliation(s)
- Francisco Zorrilla
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Filip Buric
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Kiran R Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Aleksej Zelezniak
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| |
Collapse
|
18
|
Lee GO, Eisenberg JNS, Uruchima J, Vasco G, Smith SM, Van Engen A, Victor C, Reynolds E, MacKay R, Jesser KJ, Castro N, Calvopiña M, Konstantinidis KT, Cevallos W, Trueba G, Levy K. Gut microbiome, enteric infections and child growth across a rural-urban gradient: protocol for the ECoMiD prospective cohort study. BMJ Open 2021; 11:e046241. [PMID: 34686548 PMCID: PMC8543627 DOI: 10.1136/bmjopen-2020-046241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION The functional consequences of the bacterial gut microbiome for child health are not well understood. Characteristics of the early child gut microbiome may influence the course of enteric infections, and enteric infections may change the composition of the gut microbiome, all of which may have long-term implications for child growth and development. METHODS AND ANALYSIS We are conducting a community-based birth cohort study to examine interactions between gut microbiome conditions and enteric infections, and how environmental conditions affect the development of the gut microbiome. We will follow 360 newborns from 3 sites along a rural-urban gradient in northern coastal Ecuador, characterising enteric infections and gut microbial communities in the children every 3 to 6 months over their first 2 years of life. We will use longitudinal regression models to assess the correlation between environmental conditions and gut microbiome diversity and presence of specific taxa, controlling for factors that are known to be associated with the gut microbiome, such as diet. From 6 to 12 months of age, we will collect weekly stool samples to compare microbiome conditions in diarrhoea stools versus stools from healthy children prior to, during and after acute enteric infections, using principal-coordinate analysis and other multivariate statistical methods. ETHICS AND DISSEMINATION Ethics approvals have been obtained from Emory University and the Universidad San Francisco de Quito institutional review boards. The findings will be disseminated through conference presentations and peer-reviewed journals.
Collapse
Affiliation(s)
- Gwenyth O Lee
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Joseph N S Eisenberg
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jessica Uruchima
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Gabriela Vasco
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Shanon M Smith
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Amanda Van Engen
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Courtney Victor
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Elise Reynolds
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Rebecca MacKay
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Kelsey J Jesser
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, Seattle, Washington, USA
| | - Nancy Castro
- Carrera de Nutrición y Dietética, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Manuel Calvopiña
- Carrera de Medicina, Universidad de Las Americas Facultad de Ciencias de la Salud, Quito, Pichincha, Ecuador
| | | | - William Cevallos
- Instituto de Biomedicina, Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, Seattle, Washington, USA
| |
Collapse
|
19
|
Shi Q, Zhang J, Wang J, Du L, Shi Z, Xu M, Luo Y. Homologous Escherichia coli Identified in Cerebrospinal Fluid and Bloodstream. Front Cell Infect Microbiol 2021; 11:674235. [PMID: 34568083 PMCID: PMC8461209 DOI: 10.3389/fcimb.2021.674235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/11/2021] [Indexed: 11/29/2022] Open
Abstract
Background Escherichia coli is an opportunistic bacterium that causes a wide range of diseases, such as bloodstream infection and central nervous system infection. The traditional culture-based method to detect E. coli usually takes more than 2 days. The object of this study is to explore the value of metagenomic next-generation sequencing (mNGS) in identifying E. coli from human cerebrospinal fluid. In addition, we investigated the infection source of E. coli through whole genome sequencing and phylogenetic analysis. Methods We combined a clinical example to analyze the function of mNGS in pathogen detection from cerebrospinal fluid. NextSeq 550Dx platform was applied for mNGS. Next, whole genome sequencing was performed to obtain the genomic characterization of E. coli. Furthermore, we screened 20 E. coli strains from the National Center for Biotechnology Information and conducted a phylogenetic analysis. Results A middle-aged patient who attended our hospital was diagnosed with craniopharyngioma and received surgery. The patient had recurrent fever and persistent lethargy after surgery. Cerebrospinal fluid culture firstly failed to grow the bacteria. Next the cerebrospinal fluid sample was detected by mNGS and the sequence readings of E. coli were identified. Later, E. coli was reported via the second cerebrospinal fluid culture, certifying the result of mNGS. Moreover, we also cultured carbapenem-resistant E. coli from the patient’s bloodstream. Through whole genome sequencing and phylogenetic analysis, we found that the E. coli isolated from cerebrospinal fluid and the bloodstream was 100% homologous, indicating the E. coli central nervous system infection was originated from the bloodstream. Conclusion Metagenomic next-generation sequencing is a valuable tool to identify the pathogens from cerebrospinal fluid, and seeking the infection source is of great significance in clinical diagnosis and treatment. Furthermore, carbapenem-resistant E. coli is a serious problem as the cause of bloodstream infection and central nervous system infection, and effective and adequate measures to prevent and control the present circumstance are urgent.
Collapse
Affiliation(s)
- Qingmiao Shi
- Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinghui Wang
- Department of Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lijuan Du
- Department of Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhaoyang Shi
- Department of Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Min Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yonggang Luo
- Department of Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
20
|
Abstract
PURPOSE OF REVIEW Several types of Escherichia coli cause acute diarrhea in humans and are responsible for a large burden of disease globally. The purpose of this review is to summarize diarrheagenic Escherichia coli (DEC) pathotype definitions and discuss existing and emerging molecular, genomic, and gut microbiome methods to detect, define, and study DEC pathotypes. RECENT FINDINGS DEC pathotypes are currently diagnosed by molecular detection of unique virulence genes. However, some pathotypes have defied coherent molecular definitions because of imperfect gene targets, and pathotype categories are complicated by hybrid strains and isolation of pathotypes from asymptomatic individuals. Recent progress toward more efficient, sensitive, and multiplex DEC pathotype detection has been made using emerging PCR-based technologies. Genomics and gut microbiome detection methods continue to advance rapidly and are contributing to a better understanding of DEC pathotype diversity and functional potential. SUMMARY DEC pathotype categorizations and detection methods are useful but imperfect. The implementation of molecular and sequence-based methods and well designed epidemiological studies will continue to advance understanding of DEC pathotypes. Additional emphasis is needed on sequencing DEC genomes from regions of the world where they cause the most disease and from the pathotypes that cause the greatest burden of disease globally.
Collapse
|
21
|
Madeira CL, Menezes O, Park D, Jog KV, Hatt JK, Gavazza S, Krzmarzick MJ, Sierra-Alvarez R, Spain JC, Konstantinidis KT, Field JA. Bacteria Make a Living Breathing the Nitroheterocyclic Insensitive Munitions Compound 3-Nitro-1,2,4-triazol-5-one (NTO). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5806-5814. [PMID: 33835790 DOI: 10.1021/acs.est.0c07161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The nitroheterocyclic 3-nitro-1,2,4-triazol-5-one (NTO) is an ingredient of insensitive explosives increasingly used by the military, becoming an emergent environmental pollutant. Cometabolic biotransformation of NTO occurs in mixed microbial cultures in soils and sludges with excess electron-donating substrates. Herein, we present the unusual energy-yielding metabolic process of NTO respiration, in which the NTO reduction to 3-amino-1,2,4-triazol-5-one (ATO) is linked to the anoxic acetate oxidation to CO2 by a culture enriched from municipal anaerobic digester sludge. Cell growth was observed simultaneously with NTO reduction, whereas the culture was unable to grow in the presence of acetate only. Extremely low concentrations (0.06 mg L-1) of the uncoupler carbonyl cyanide m-chlorophenyl hydrazone inhibited NTO reduction, indicating that the process was linked to respiration. The ultimate evidence of NTO respiration was adenosine triphosphate production due to simultaneous exposure to NTO and acetate. Metagenome sequencing revealed that the main microorganisms (and relative abundances) were Geobacter anodireducens (89.3%) and Thauera sp. (5.5%). This study is the first description of a nitroheterocyclic compound being reduced by anaerobic respiration, shedding light on creative microbial processes that enable bacteria to make a living reducing NTO.
Collapse
Affiliation(s)
- Camila L Madeira
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Osmar Menezes
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, Pernambuco 50740-530, Brazil
| | - Doyoung Park
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Kalyani V Jog
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Savia Gavazza
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, Pernambuco 50740-530, Brazil
| | - Mark J Krzmarzick
- School of Civil and Environmental Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Jim C Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, Pensacola, Florida 32514, United States
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Jim A Field
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| |
Collapse
|
22
|
Soto-Girón MJ, Peña-Gonzalez A, Hatt JK, Montero L, Páez M, Ortega E, Smith S, Cevallos W, Trueba G, Konstantinidis KT, Levy K. Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. Am J Trop Med Hyg 2021; 104:2275-2285. [PMID: 33872206 DOI: 10.4269/ajtmh.20-0831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with, ADD supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.
Collapse
Affiliation(s)
- Maria J Soto-Girón
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Angela Peña-Gonzalez
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Janet K Hatt
- 2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Lorena Montero
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maritza Páez
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Estefania Ortega
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Shanon Smith
- 4School of Public Health, University of Washington, Seattle, Washington
| | - William Cevallos
- 5Centro de Biomedicina, Universidad Central del Ecuador, Quito, Ecuador
| | - Gabriel Trueba
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T Konstantinidis
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Karen Levy
- 4School of Public Health, University of Washington, Seattle, Washington
| |
Collapse
|
23
|
The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample. Appl Environ Microbiol 2021; 87:AEM.02593-20. [PMID: 33452027 DOI: 10.1128/aem.02593-20] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/06/2021] [Indexed: 12/24/2022] Open
Abstract
The recovery of metagenome-assembled genomes (MAGs) from metagenomic data has recently become a common task for microbial studies. The strengths and limitations of the underlying bioinformatics algorithms are well appreciated by now based on performance tests with mock data sets of known composition. However, these mock data sets do not capture the complexity and diversity often observed within natural populations, since their construction typically relies on only a single genome of a given organism. Further, it remains unclear if MAGs can recover population-variable genes (those shared by >10% but <90% of the members of the population) as efficiently as core genes (those shared by >90% of the members). To address these issues, we compared the gene variabilities of pathogenic Escherichia coli isolates from eight diarrheal samples, for which the isolate was the causative agent, against their corresponding MAGs recovered from the companion metagenomic data set. Our analysis revealed that MAGs with completeness estimates near 95% captured only 77% of the population core genes and 50% of the variable genes, on average. Further, about 5% of the genes of these MAGs were conservatively identified as missing in the isolate and were of different (non-Enterobacteriaceae) taxonomic origin, suggesting errors at the genome-binning step, even though contamination estimates based on commonly used pipelines were only 1.5%. Therefore, the quality of MAGs may often be worse than estimated, and we offer examples of how to recognize and improve such MAGs to sufficient quality by (for instance) employing only contigs longer than 1,000 bp for binning.IMPORTANCE Metagenome assembly and the recovery of metagenome-assembled genomes (MAGs) have recently become common tasks for microbiome studies across environmental and clinical settings. However, the extent to which MAGs can capture the genes of the population they represent remains speculative. Current approaches to evaluating MAG quality are limited to the recovery and copy number of universal housekeeping genes, which represent a small fraction of the total genome, leaving the majority of the genome essentially inaccessible. If MAG quality in reality is lower than these approaches would estimate, this could have dramatic consequences for all downstream analyses and interpretations. In this study, we evaluated this issue using an approach that employed comparisons of the gene contents of MAGs to the gene contents of isolate genomes derived from the same sample. Further, our samples originated from a diarrhea case-control study, and thus, our results are relevant for recovering the virulence factors of pathogens from metagenomic data sets.
Collapse
|
24
|
Patin NV, Peña-Gonzalez A, Hatt JK, Moe C, Kirby A, Konstantinidis KT. The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study. mBio 2020; 11:e02634-20. [PMID: 33203758 PMCID: PMC7683401 DOI: 10.1128/mbio.02634-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/16/2020] [Indexed: 12/11/2022] Open
Abstract
Norovirus infections take a heavy toll on worldwide public health. While progress has been made toward understanding host responses to infection, the role of the gut microbiome in determining infection outcome is unknown. Moreover, data are lacking on the nature and duration of the microbiome response to norovirus infection, which has important implications for diagnostics and host recovery. Here, we characterized the gut microbiomes of subjects enrolled in a norovirus challenge study. We analyzed microbiome features of asymptomatic and symptomatic individuals at the genome (population) and gene levels and assessed their response over time in symptomatic individuals. We show that the preinfection microbiomes of subjects with asymptomatic infections were enriched in Bacteroidetes and depleted in Clostridia relative to the microbiomes of symptomatic subjects. These compositional differences were accompanied by differences in genes involved in the metabolism of glycans and sphingolipids that may aid in host resilience to infection. We further show that microbiomes shifted in composition following infection and that recovery times were variable among human hosts. In particular, Firmicutes increased immediately following the challenge, while Bacteroidetes and Proteobacteria decreased over the same time. Genes enriched in the microbiomes of symptomatic subjects, including the adenylyltransferase glgC, were linked to glycan metabolism and cell-cell signaling, suggesting as-yet unknown roles for these processes in determining infection outcome. These results provide important context for understanding the gut microbiome role in host susceptibility to symptomatic norovirus infection and long-term health outcomes.IMPORTANCE The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.
Collapse
Affiliation(s)
- N V Patin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - A Peña-Gonzalez
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - C Moe
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - A Kirby
- Waterborne Disease Prevention Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - K T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
25
|
Goddard FB, Ban R, Barr DB, Brown J, Cannon J, Colford JM, Eisenberg JNS, Ercumen A, Petach H, Freeman MC, Levy K, Luby SP, Moe C, Pickering AJ, Sarnat JA, Stewart J, Thomas E, Taniuchi M, Clasen T. Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11673-11691. [PMID: 32813503 PMCID: PMC7547864 DOI: 10.1021/acs.est.0c02421] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 05/06/2023]
Abstract
Infections with enteric pathogens impose a heavy disease burden, especially among young children in low-income countries. Recent findings from randomized controlled trials of water, sanitation, and hygiene interventions have raised questions about current methods for assessing environmental exposure to enteric pathogens. Approaches for estimating sources and doses of exposure suffer from a number of shortcomings, including reliance on imperfect indicators of fecal contamination instead of actual pathogens and estimating exposure indirectly from imprecise measurements of pathogens in the environment and human interaction therewith. These shortcomings limit the potential for effective surveillance of exposures, identification of important sources and modes of transmission, and evaluation of the effectiveness of interventions. In this review, we summarize current and emerging approaches used to characterize enteric pathogen hazards in different environmental media as well as human interaction with those media (external measures of exposure), and review methods that measure human infection with enteric pathogens as a proxy for past exposure (internal measures of exposure). We draw from lessons learned in other areas of environmental health to highlight how external and internal measures of exposure can be used to more comprehensively assess exposure. We conclude by recommending strategies for advancing enteric pathogen exposure assessments.
Collapse
Affiliation(s)
- Frederick
G. B. Goddard
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Radu Ban
- Bill and
Melinda Gates Foundation, Seattle, Washington 98109, United States
| | - Dana Boyd Barr
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Joe Brown
- School of
Civil and Environmental Engineering, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Jennifer Cannon
- Centers
for Disease Control and Prevention Foundation, Atlanta, Georgia 30308, United States
| | - John M. Colford
- Division
of Epidemiology and Biostatistics, School of Public Health, University of California−Berkeley, Berkeley, California 94720, United States
| | - Joseph N. S. Eisenberg
- Department
of Epidemiology, University of Michigan
School of Public Health, Ann Arbor, Michigan 48109, United States
| | - Ayse Ercumen
- Department
of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Helen Petach
- U.S. Agency
for International Development, Washington, DC 20004, United States
| | - Matthew C. Freeman
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Karen Levy
- Department
of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Stephen P. Luby
- Division
of Infectious Diseases and Geographic Medicine, Stanford University, California 94305, United States
| | - Christine Moe
- Center
for
Global Safe Water, Sanitation and Hygiene, Rollins School of Public
Health, Emory University, Atlanta, Georgia 30322, United States
| | - Amy J. Pickering
- Department
of Civil and Environmental Engineering, School of Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Jeremy A. Sarnat
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Jill Stewart
- Department
of Environmental Sciences and Engineering, Gillings School of Global
Public Health, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Evan Thomas
- Mortenson
Center in Global Engineering, University
of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Mami Taniuchi
- Division
of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Thomas Clasen
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
26
|
|
27
|
Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med 2020; 12:71. [PMID: 32791981 PMCID: PMC7427293 DOI: 10.1186/s13073-020-00765-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and “culturomics” technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.
Collapse
Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
28
|
Rossello-Mora R, Konstantinidis KT, Sutcliffe I, Whitman W. Opinion: Response to concerns about the use of DNA sequences as types in the nomenclature of prokaryotes. Syst Appl Microbiol 2020; 43:126070. [PMID: 32081606 DOI: 10.1016/j.syapm.2020.126070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Abstract
In the current Opinion we respond to the major concerns by Bisgaard et al. (2019) and Overmann et al. (2019) and conclude that the adoption of sequences as types for the names of prokaryotes will allow for improvements of the taxonomic framework, increased stability of names derived from robust phylogenomic methods, and enable a full circumscription of the microbial world rather than just the cultivated minority.
Collapse
Affiliation(s)
- Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Bacterial Diversity, IMEDEA (CSIC-UIB), 07190 Esporles, Balearic Islands, Spain.
| | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Iain Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - William Whitman
- Department of Microbiology, University of Georgia, Athens, GA, USA
| |
Collapse
|
29
|
Konstantinidis KT, Rosselló‐Móra R, Amann R. Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy. Environ Microbiol 2020; 22:819-822. [DOI: 10.1111/1462-2920.14934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology Atlanta GA USA
| | - Ramon Rosselló‐Móra
- Marine Microbiology Group, Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC‐UIB) E‐07190 Esporles Spain
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology D‐28359 Bremen Germany
| |
Collapse
|