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Shantaram D, Hoyd R, Blaszczak AM, Antwi L, Jalilvand A, Wright VP, Liu J, Smith AJ, Bradley D, Lafuse W, Liu Y, Williams NF, Snyder O, Wheeler C, Needleman B, Brethauer S, Noria S, Renton D, Perry KA, Nagareddy P, Wozniak D, Mahajan S, Rana PSJB, Pietrzak M, Schlesinger LS, Spakowicz DJ, Hsueh WA. Obesity-associated microbiomes instigate visceral adipose tissue inflammation by recruitment of distinct neutrophils. Nat Commun 2024; 15:5434. [PMID: 38937454 PMCID: PMC11211470 DOI: 10.1038/s41467-024-48935-5] [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: 12/05/2022] [Accepted: 05/17/2024] [Indexed: 06/29/2024] Open
Abstract
Neutrophils are increasingly implicated in chronic inflammation and metabolic disorders. Here, we show that visceral adipose tissue (VAT) from individuals with obesity contains more neutrophils than in those without obesity and is associated with a distinct bacterial community. Exploring the mechanism, we gavaged microbiome-depleted mice with stool from patients with and without obesity during high-fat or normal diet administration. Only mice receiving high-fat diet and stool from subjects with obesity show enrichment of VAT neutrophils, suggesting donor microbiome and recipient diet determine VAT neutrophilia. A rise in pro-inflammatory CD4+ Th1 cells and a drop in immunoregulatory T cells in VAT only follows if there is a transient spike in neutrophils. Human VAT neutrophils exhibit a distinct gene expression pattern that is found in different human tissues, including tumors. VAT neutrophils and bacteria may be a novel therapeutic target for treating inflammatory-driven complications of obesity, including insulin resistance and colon cancer.
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Affiliation(s)
- Dharti Shantaram
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Rebecca Hoyd
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Alecia M Blaszczak
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Linda Antwi
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Anahita Jalilvand
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Valerie P Wright
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Joey Liu
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Alan J Smith
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - David Bradley
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - William Lafuse
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
| | - YunZhou Liu
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Nyelia F Williams
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Owen Snyder
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Caroline Wheeler
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Bradley Needleman
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Stacy Brethauer
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Sabrena Noria
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - David Renton
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Kyle A Perry
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Prabha Nagareddy
- Department of Internal Medicine, Cardiovascular Section University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, OK, 73117, USA
| | - Daniel Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
| | - Sahil Mahajan
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
| | - Pranav S J B Rana
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Larry S Schlesinger
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Daniel J Spakowicz
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA.
| | - Willa A Hsueh
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA.
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2
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Torrey EF. Did the human genome project affect research on Schizophrenia? Psychiatry Res 2024; 333:115691. [PMID: 38219345 DOI: 10.1016/j.psychres.2023.115691] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024]
Abstract
The Human Genome Project was undertaken primarily to discover genetic causes and better treatments for human diseases. Schizophrenia was targeted since three of the project`s principal architects had a personal interest and also because, based on family, adoption, and twin studies, schizophrenia was widely believed to be a genetic disorder. Extensive studies using linkage analysis, candidate genes, genome wide association studies [GWAS], copy number variants, exome sequencing and other approaches have failed to identify causal genes. Instead, they identified almost 300 single nucleotide polymorphisms [SNPs] associated with altered risks of developing schizophrenia as well as some rare variants associated with increased risk in a small number of individuals. Risk genes play a role in the clinical expression of most diseases but do not cause the disease in the absence of other factors. Increasingly, observers question whether schizophrenia is strictly a genetic disorder. Beginning in 1996 NIMH began shifting its research resources from clinical studies to basic research based on the promise of the Human Genome Project. Consequently, three decades later NIMH's genetics investment has yielded almost nothing clinically useful for individuals currently affected. It is time to review NIMH`s schizophrenia research portfolio.
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Main CR, Tyler R, Huerta S. Microbial Source Tracking in the Love Creek Watershed, Delaware (USA). Dela J Public Health 2021; 7:22-31. [PMID: 34467176 PMCID: PMC8352542 DOI: 10.32481/djph.2021.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Fecal contamination of waterways in Delaware pose an ongoing problem for environmental and public health. For monitoring efforts, Enterococcus has been widely adopted by the state to indicate the presence of fecal matter from warm-blooded animals and to establish Primary and Secondary Contact Recreation criteria. In this study, we examined sites within the Love Creek watershed, a tributary of the Rehoboth bay, using next-generation sequencing and SourceTracker to determine sources of potential fecal contamination and compared to bacterial communities to chemical and nutrient concentrations. Microbial community from fecal samples of ten different types of animals and one human sample were used to generate a fecal library for community-based microbial source tracking. Orthophosphate and total dissolved solids were among the major factors associated with community composition. SourceTracker analysis of the monthly samples from the Love Creek watershed indicated the majority of the microbial community were attributed to "unknown" sources, i.e. wildlife. Those that attribute to known sources were primarily domestic animals, i.e. cat and dog. These results suggest that at the state level these methods are capable of giving the start for source tracking as a means to understanding bacterial contamination.
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Affiliation(s)
- Christopher R Main
- Environmental Laboratory Section, Division of Water, Delaware Department of Natural Resources and Environmental Control
| | - Robin Tyler
- Environmental Laboratory Section, Division of Water, Delaware Department of Natural Resources and Environmental Control
| | - Sergio Huerta
- Laboratory Director, Public Health and Environmental Laboratories, State of Delaware
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Groenenboom AE, Shindano J, Cheepa N, Smid EJ, Schoustra SE. Microbial population dynamics during traditional production of Mabisi, a spontaneous fermented milk product from Zambia: a field trial. World J Microbiol Biotechnol 2020; 36:184. [PMID: 33191438 PMCID: PMC7667141 DOI: 10.1007/s11274-020-02957-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/03/2020] [Indexed: 11/29/2022]
Abstract
Mabisi is a fermented milk product, traditionally produced in a calabash by uncontrolled fermentation. Due to high costs and a reduced availability of calabashes, nowadays plastic containers are also used for Mabisi production. However, the effect of this change in production practice on the properties of the product has not been documented. Therefore, we aimed at determining the effect of fermentation vessels and types of back-slopping on acidification and microbial communities during fermentation. A series of fifteen experiments using two types of fermentation vessels (plastic buckets and calabashes) in combination with different types of back-slopping (no back-slopping, passive back-slopping, and active back-slopping) were set up at a field site in rural Zambia. In each of the fifteen fermentations we analysed acidification rate of traditional Mabisi fermentation and bacterial diversity over time. No significant difference was found in terms of microbial diversity during and at the end of fermentation between fermentations performed in buckets or previously used calabashes. Bacterial communities in general decreased in diversity over time, where the drop in pH correlated with a decrease in Shannon Index. In case of active back-slopping, the pH drop started right after inoculation while in the no back-slopping and passive back-slopping fermentations, there was a clear lag phase before acidification started. All experimental series resulted in a microbial community dominated by Lactococcus lactis and a Shannon Index, as a measure for diversity, between 0.6 and 2.0. The use of plastic buckets for Mabisi fermentation can be a valuable alternative to the use of calabashes as this study showed no biological and physico-chemical differences between Mabisi resulting from both fermentation vessels, although the reason for perceived differences should be further investigated.
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Affiliation(s)
- Anneloes E Groenenboom
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands
- Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - John Shindano
- Department of Food Science and Nutrition, University of Zambia, Lusaka, Zambia
| | | | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Sijmen E Schoustra
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands.
- Department of Food Science and Nutrition, University of Zambia, Lusaka, Zambia.
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Zwirzitz B, Wetzels SU, Dixon ED, Stessl B, Zaiser A, Rabanser I, Thalguter S, Pinior B, Roch FF, Strachan C, Zanghellini J, Dzieciol M, Wagner M, Selberherr E. The sources and transmission routes of microbial populations throughout a meat processing facility. NPJ Biofilms Microbiomes 2020; 6:26. [PMID: 32651393 PMCID: PMC7351959 DOI: 10.1038/s41522-020-0136-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/11/2020] [Indexed: 02/02/2023] Open
Abstract
Microbial food spoilage is responsible for a considerable amount of waste and can cause food-borne diseases in humans, particularly in immunocompromised individuals and children. Therefore, preventing microbial food spoilage is a major concern for health authorities, regulators, consumers, and the food industry. However, the contamination of food products is difficult to control because there are several potential sources during production, processing, storage, distribution, and consumption, where microorganisms come in contact with the product. Here, we use high-throughput full-length 16S rRNA gene sequencing to provide insights into bacterial community structure throughout a pork-processing plant. Specifically, we investigated what proportion of bacteria on meat are presumptively not animal-associated and are therefore transferred during cutting via personnel, equipment, machines, or the slaughter environment. We then created a facility-specific transmission map of bacterial flow, which predicted previously unknown sources of bacterial contamination. This allowed us to pinpoint specific taxa to particular environmental sources and provide the facility with essential information for targeted disinfection. For example, Moraxella spp., a prominent meat spoilage organism, which was one of the most abundant amplicon sequence variants (ASVs) detected on the meat, was most likely transferred from the gloves of employees, a railing at the classification step, and the polishing tunnel whips. Our results suggest that high-throughput full-length 16S rRNA gene sequencing has great potential in food monitoring applications.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria.
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria.
| | - Stefanie U Wetzels
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Emmanuel D Dixon
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Beatrix Stessl
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Andreas Zaiser
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Isabel Rabanser
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Sarah Thalguter
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Beate Pinior
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Franz-Ferdinand Roch
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Cameron Strachan
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Jürgen Zanghellini
- Department of Analytical Chemistry, University of Vienna, 1010, Vienna, Austria
| | - Monika Dzieciol
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Martin Wagner
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Technopark 1C, 3430, Tulln, Austria
| | - Evelyne Selberherr
- Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
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6
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McGhee JJ, Rawson N, Bailey BA, Fernandez-Guerra A, Sisk-Hackworth L, Kelley ST. Meta-SourceTracker: application of Bayesian source tracking to shotgun metagenomics. PeerJ 2020; 8:e8783. [PMID: 32231882 PMCID: PMC7100590 DOI: 10.7717/peerj.8783] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/21/2020] [Indexed: 11/20/2022] Open
Abstract
Background Microbial source tracking methods are used to determine the origin of contaminating bacteria and other microorganisms, particularly in contaminated water systems. The Bayesian SourceTracker approach uses deep-sequencing marker gene libraries (16S ribosomal RNA) to determine the proportional contributions of bacteria from many potential source environments to a given sink environment simultaneously. Since its development, SourceTracker has been applied to an extensive diversity of studies, from beach contamination to human behavior. Methods Here, we demonstrate a novel application of SourceTracker to work with metagenomic datasets and tested this approach using sink samples from a study of coastal marine environments. Source environment metagenomes were obtained from metagenomics studies of gut, freshwater, marine, sand and soil environments. As part of this effort, we implemented features for determining the stability of source proportion estimates, including precision visualizations for performance optimization, and performed domain-specific source-tracking analyses (i.e., Bacteria, Archaea, Eukaryota and viruses). We also applied SourceTracker to metagenomic libraries generated from samples collected from the International Space Station (ISS). Results SourceTracker proved highly effective at predicting the composition of known sources using shotgun metagenomic libraries. In addition, we showed that different taxonomic domains sometimes presented highly divergent pictures of environmental source origins for both the coastal marine and ISS samples. These findings indicated that applying SourceTracker to separate domains may provide a deeper understanding of the microbial origins of complex, mixed-source environments, and further suggested that certain domains may be preferable for tracking specific sources of contamination.
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Affiliation(s)
- Jordan J McGhee
- Bioinformatics and Medical Informatics Program, San Diego State University, San Diego, CA, United States of America
| | - Nick Rawson
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
| | - Barbara A Bailey
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
| | - Antonio Fernandez-Guerra
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Current affiliation: Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Laura Sisk-Hackworth
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, United States of America
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Luna JC, Zamora A, Hernández-Arango N, Muñoz-Sánchez D, Pinzón MI, Cortés-Vecino JA, Lora-Suarez F, Gómez-Marín JE. Food safety assessment and risk for toxoplasmosis in school restaurants in Armenia, Colombia. Parasitol Res 2019; 118:3449-3457. [PMID: 31659453 DOI: 10.1007/s00436-019-06473-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/24/2019] [Indexed: 12/01/2022]
Abstract
We assessed the risk for toxoplasmosis in 10 school restaurants in Armenia (Quindio, Colombia). We analyzed the presence of Toxoplasma gondii DNA in the food, water, and living and inert surfaces of school restaurants, and we correlated these findings with the results of food safety inspection scores and with the prevalence of specific anti-T. gondii antibodies in children who ate at these restaurants. Of the 213 samples, 6.1% were positive using PCR to test for T. gondii DNA. Positive samples were found in meat, water, cucumber, guava juice, inert surfaces, and living surfaces. In 60% (6/10) of the public school restaurants, there was at least one PCR T. gondii-positive sample. In 311 serum samples from children who attended the restaurants, 101 (33%) were positive for IgG and 12 (3.9%) for IgM anti-T. gondii. The median of the compound score for the fulfillment of inspection for food safety conditions was of 60.7% (range 50-72). Higher T. gondii PCR positivity in surfaces, food, or water at each restaurant was correlated with lower inspection scores for water supply and water storage conditions. Lower scores in physical infrastructure and disinfection procedures and higher scores in furniture were correlated with a higher prevalence of IgG anti-T. gondii in children who ate at those restaurants. Inspection scores can identify restaurants with a higher risk for the presence of T. gondii.
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Affiliation(s)
- Julio César Luna
- Grupo Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Facultad de Ciencias de la Salud, Universidad del Quindio, Avenida Bolivar 12N, Armenia, Quindio, Colombia
| | | | - Natalia Hernández-Arango
- Grupo Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Facultad de Ciencias de la Salud, Universidad del Quindio, Avenida Bolivar 12N, Armenia, Quindio, Colombia
| | - Deicy Muñoz-Sánchez
- Grupo Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Facultad de Ciencias de la Salud, Universidad del Quindio, Avenida Bolivar 12N, Armenia, Quindio, Colombia
| | - Magda Ivonne Pinzón
- Facultad de Ciencias Agroindustriales, Universidad del Quindío, Armenia, Colombia
| | - Jesús Alfredo Cortés-Vecino
- Laboratorio de Parasitología Veterinaria, Grupo de Parasitología Veterinaria, Departamento de Salud Animal, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Fabiana Lora-Suarez
- Grupo Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Facultad de Ciencias de la Salud, Universidad del Quindio, Avenida Bolivar 12N, Armenia, Quindio, Colombia
| | - Jorge Enrique Gómez-Marín
- Grupo Parasitología Molecular (GEPAMOL), Centro de Investigaciones Biomédicas, Facultad de Ciencias de la Salud, Universidad del Quindio, Avenida Bolivar 12N, Armenia, Quindio, Colombia.
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Fermented cereal-based Munkoyo beverage: Processing practices, microbial diversity and aroma compounds. PLoS One 2019; 14:e0223501. [PMID: 31639127 PMCID: PMC6805097 DOI: 10.1371/journal.pone.0223501] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/23/2019] [Indexed: 01/28/2023] Open
Abstract
Fermented cereal-based foods play a crucial role in attaining food and nutrition security for resource-poor populations in sub-Saharan Africa. These products are widely produced by spontaneous fermentation using of cereal grains as raw material. They have a unique taste and flavour, are rich sources of energy and their non-alcoholic nature makes them ideal for consumption by the entire population, including children. Lactic acid bacteria dominate the fermentation process and lead to a low pH of around 4, which suppresses the growth of pathogenic bacteria, thereby increasing the shelf-life and safety of the food. Knowledge about processing practices, consumption patterns and bacterial communities is essential to regulate processing and design appropriate mixes of micro-organisms to produce starter cultures for commercial production of standard-quality fermented foods that meet desired quality characteristics. In four regions of Zambia, we surveyed processing practices and consumption patterns of a spontaneously fermented cereal-based beverage called Munkoyo, commonly produced in Zambia and the Democratic Republic of Congo. Variations in processing practices exist in cooking time of the unfermented maize porridge and time allowed for fermentation. Consumption is mainly at household level and the product is considered as an energy drink. Characterisation of the bacterial communities of over 90 samples with 16S amplicon sequencing on DNA extracted from the entire bacterial community revealed six dominant families, namely Streptococcaceae, Leuconostocaceae, Enterobacteriaceae, Lactabacillales, Bacillaceae and Aeromonadaceae, and a Shannon index of up to 1.18 with an effective number of 3.44 bacterial species. Bacterial communities that underlie the fermentation in Munkoyo differ in their composition for the different regions using common processing steps, suggesting that different combinations of bacteria can be used to achieve successful Munkoyo fermentation. Analysis of aroma profiles in 15 different samples from two different Provinces showed that aldehydes, esters, organic acids, alkanes, alkenes and alcohols dominated.
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Chen C, He R, Cheng Z, Han M, Zha Y, Yang P, Yao Q, Zhou H, Zhong C, Ning K. The Seasonal Dynamics and the Influence of Human Activities on Campus Outdoor Microbial Communities. Front Microbiol 2019; 10:1579. [PMID: 31354673 PMCID: PMC6636667 DOI: 10.3389/fmicb.2019.01579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/25/2019] [Indexed: 02/01/2023] Open
Abstract
Large-scale campus resembles a small “semi-open community,” harboring disturbances from the exchanges of people and vehicles, wherein stressors such as temperature and population density differ among the ground surfaces of functional partitions. Therefore, it represents a special ecological niche for the study on microbial ecology in the process of urbanization. In this study, we investigated outdoor microbial communities in four campuses in Wuhan, China. We obtained 284 samples from 55 sampling sites over six seasons, as well as their matching climatic and environmental records. The structure of campus outdoor microbial communities which influenced by multiple climatic factors featured seasonality. The dispersal influence of human activities on microbial communities also contributed to this seasonal pattern non-negligibly. However, despite the microbial composition alteration in response to multiple stressors, the overall predicted function of campus outdoor microbial communities remained stable across campuses. The spatial–temporal dynamic patterns on campus outdoor microbial communities and its predicted functions have bridged the gap between microbial and macro-level ecosystems, and provided hints toward a better understanding of the effects of climatic factors and human activities on campus micro-environments.
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Affiliation(s)
- Chaoyun Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ruiqiao He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangyu Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yuguo Zha
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Yao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Zhou
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Chaofang Zhong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-Imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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10
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Patterns of protist diversity associated with raw sewage in New York City. ISME JOURNAL 2019; 13:2750-2763. [PMID: 31289345 PMCID: PMC6794324 DOI: 10.1038/s41396-019-0467-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/28/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022]
Abstract
Protists are ubiquitous components of terrestrial and aquatic environments, as well as animal and human microbiomes. Despite this, little is known about protists in urban environments. The ~7400-mile sewer system of New York City (NYC) collects human waste from ~8 million human inhabitants as well as from animals, street runoff, and groundwater, providing an ideal system to study these microbes. We used 18S rRNA amplicon sequencing and shotgun metagenomic sequencing to profile raw sewage microbial communities. Raw sewage samples were collected over a 12-month period from 14 treatment plants of the five NYC boroughs, and compared with samples from other environments including soil, stormwater, and sediment. Sewage contained a diverse protist community dominated by free-living clades, and communities were highly differentiated across environments. Seasonal differences in protist composition were observed; however, network analysis and functional profiling demonstrated that sewage communities were robust and functionally consistent. Protists typically associated with human and animal guts or feces were frequently detected. Abundance of these parasites varied significantly both spatially and temporally, suggesting that spikes could reflect trends in the source population. This underscores sewage as a valuable model system for monitoring patterns in urban microbes and provides a baseline protist metagenome of NYC.
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11
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Aguirre AA, Longcore T, Barbieri M, Dabritz H, Hill D, Klein PN, Lepczyk C, Lilly EL, McLeod R, Milcarsky J, Murphy CE, Su C, VanWormer E, Yolken R, Sizemore GC. The One Health Approach to Toxoplasmosis: Epidemiology, Control, and Prevention Strategies. ECOHEALTH 2019; 16:378-390. [PMID: 30945159 PMCID: PMC6682582 DOI: 10.1007/s10393-019-01405-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 06/02/2023]
Abstract
One Health is a collaborative, interdisciplinary effort that seeks optimal health for people, animals, plants, and the environment. Toxoplasmosis, caused by Toxoplasma gondii, is an intracellular protozoan infection distributed worldwide, with a heteroxenous life cycle that practically affects all homeotherms and in which felines act as definitive reservoirs. Herein, we review the natural history of T. gondii, its transmission and impacts in humans, domestic animals, wildlife both terrestrial and aquatic, and ecosystems. The epidemiology, prevention, and control strategies are reviewed, with the objective of facilitating awareness of this disease and promoting transdisciplinary collaborations, integrative research, and capacity building among universities, government agencies, NGOs, policy makers, practicing physicians, veterinarians, and the general public.
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Affiliation(s)
- A Alonso Aguirre
- Department of Environmental Science and Policy, George Mason University, 4400 University Dr. MSN: 5F2, Fairfax, VA, 22030-4400, USA.
| | - Travis Longcore
- Spatial Sciences Institute, University of Southern California, 3616 Trousdale Parkway, AHF B55, Los Angeles, CA, 90089, USA
| | - Michelle Barbieri
- NMFS/PIFSC/PSD/Hawaiian Monk Seal Research Program, 1845 Wasp Boulevard, Building 176, Honolulu, HI, 96818, USA
| | - Haydee Dabritz
- Community Health Branch, Yolo County Health & Human Services Agency, 137 N Cottonwood St, Woodland, CA, 95695, USA
| | - Dolores Hill
- U.S. Department of Agriculture, Center Road Building 307-C Room 134, BARC East, Beltsville, MD, 20705, USA
| | - Patrice N Klein
- United States Department of Agriculture Forest Service, 201 14th Street, SW, Washington, DC, 20250, USA
| | | | - Emily L Lilly
- Virginia Military Institute, 303D Maury-Brooke Hall, Lexington, VA, 24450, USA
| | - Rima McLeod
- The University of Chicago, AMB N310, (MC 2114) 5841 South Maryland Avenue, Chicago, IL, 60637, USA
| | | | - Caroline E Murphy
- The Wildlife Society, 425 Barlow Place, Suite 200, Bethesda, MD, 20814, USA
| | - Chunlei Su
- M409 Walters Life Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Elizabeth VanWormer
- University of Nebraska-Lincoln, 406 Hardin Hall, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | - Robert Yolken
- Stanley Neurovirology Laboratory, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Grant C Sizemore
- American Bird Conservancy, 4301 Connecticut Ave., NW, Suite 451, Washington, DC, 20008, USA
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12
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Groenenboom AE, Parker ME, de Vries A, de Groot S, Zobrist S, Mansen K, Milani P, Kort R, Smid EJ, Schoustra SE. Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal. PLoS One 2019; 14:e0215658. [PMID: 31075124 PMCID: PMC6510411 DOI: 10.1371/journal.pone.0215658] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/07/2019] [Indexed: 11/19/2022] Open
Abstract
Spontaneously fermented food products contain a complex, natural microbial community with potential probiotic activity. The addition of a health-promoting, probiotic bacterium to these products ensures the delivery of that probiotic activity to consumers. Here, we assess the microbial community of a traditional Senegalese milk product produced by spontaneous fermentation, called lait caillé. We produced the lait caillé in a traditional way and added a probiotic starter containing Lactobacillus rhamnosus yoba 2012 to the traditional process. We found various species that are known for their ability to ferment milk, including species from the genera Lactobacillus, Acetobacter, Lactococcus, and Streptococcus. Our results show that the addition of L. rhamnosus to the inoculum, can result in detectable levels of this strain in the final product, ranging between 0.2 and 1 percent of the total bacterial population. Subsequent rounds of fermentation using passive back-slopping without the addition of new L. rhamnosus led to a loss of this strain from the community of fermenting bacteria. Our results suggest that the addition of probiotic strains at every fermentation cycle can enrich the existing complex communities of traditionally fermented lait caillé while traditional bacterial strains remain dominant in the bacterial communities.
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Affiliation(s)
- Anneloes E. Groenenboom
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
- * E-mail:
| | | | | | - Suzette de Groot
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands
| | | | | | | | - Remco Kort
- Microbiology and Systems Biology, TNO, Amsterdam, The Netherlands
- Yoba for Life Foundation, Amsterdam, The Netherlands
- Department of Molecular Cell Biology, VU University Amsterdam, Amsterdam, The Netherlands
- ARTIS-Micropia, Amsterdam, The Netherlands
| | - Eddy J. Smid
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Sijmen E. Schoustra
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands
- Department of Food Science and Nutrition, University of Zambia, Lusaka, Zambia
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13
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Groenenboom AE, Smid EJ, Schoustra SE. Robust sampling and preservation of DNA for microbial community profiling in field experiments. BMC Res Notes 2019; 12:159. [PMID: 30902062 PMCID: PMC6429817 DOI: 10.1186/s13104-019-4187-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/13/2019] [Indexed: 11/10/2022] Open
Abstract
Objective Stabilising samples of microbial communities for DNA extraction without access to laboratory equipment can be a challenging task. In this paper we propose a method using filter paper disks for the preservation of DNA from diverse microbial communities which are found in a fermented milk product. Results Small adaptations to the DNA extraction method used for liquid fermented milk delivered DNA of sufficient amounts and quality to be used for later analyses, e.g. full community 16S amplicon sequencing. The microbial community structure obtained via the filter paper method showed sufficient resemblance to the structure obtain via the traditional DNA extraction from the liquid milk sample. This method can therefore successfully be used to analyse diverse microbial communities from fermented milk products from remote areas. Electronic supplementary material The online version of this article (10.1186/s13104-019-4187-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anneloes E Groenenboom
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands. .,Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Sijmen E Schoustra
- Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands.,Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, Lusaka, Zambia
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14
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Alves LDF, Westmann CA, Lovate GL, de Siqueira GMV, Borelli TC, Guazzaroni ME. Metagenomic Approaches for Understanding New Concepts in Microbial Science. Int J Genomics 2018; 2018:2312987. [PMID: 30211213 PMCID: PMC6126073 DOI: 10.1155/2018/2312987] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/21/2018] [Accepted: 07/29/2018] [Indexed: 12/15/2022] Open
Abstract
Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such as disease susceptibility, immunological response, and social and nutritional behaviors. In this context, metagenomics has established a powerful framework for understanding the intricate connections between human societies and microbial communities, ultimately allowing for the optimization of both human health and productivity. Thus, we have shifted from the old concept of microbes as harmful organisms to a broader panorama, in which the signal of the relationship between humans and microbes is flexible and directly dependent on our own decisions and practices. In parallel, metagenomics has also been playing a major role in the prospection of "hidden" genetic features and the development of biotechnological applications, through the discovery of novel genes, enzymes, pathways, and bioactive molecules with completely new or improved biochemical functions. Therefore, this review highlights the major milestones over the last three decades of metagenomics, providing insights into both its potentialities and current challenges.
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Affiliation(s)
- Luana de Fátima Alves
- Department of Biochemistry, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Cauã Antunes Westmann
- Department of Cell Biology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Gabriel Lencioni Lovate
- Department of Biochemistry, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Tiago Cabral Borelli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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15
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Corvelo A, Clarke WE, Robine N, Zody MC. taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time. Genome Res 2018; 28:751-758. [PMID: 29588360 PMCID: PMC5932614 DOI: 10.1101/gr.225276.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 03/21/2018] [Indexed: 01/15/2023]
Abstract
High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classification tool. Using a combination of simulated and real metagenomics data sets, we demonstrate that taxMaps is more sensitive and more precise than widely used taxonomic classifiers and is capable of delivering classification accuracy comparable to that of BLASTN, but at up to three orders of magnitude less computational cost.
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Affiliation(s)
- André Corvelo
- New York Genome Center, New York, New York 10013, USA
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16
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Microbial Diversity and Putative Opportunistic Pathogens in Dishwasher Biofilm Communities. Appl Environ Microbiol 2018; 84:AEM.02755-17. [PMID: 29330184 PMCID: PMC5812945 DOI: 10.1128/aem.02755-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 12/18/2022] Open
Abstract
Extreme habitats are not only limited to natural environments, but also exist in manmade systems, for instance, household appliances such as dishwashers. Limiting factors, such as high temperatures, high and low pHs, high NaCl concentrations, presence of detergents, and shear force from water during washing cycles, define microbial survival in this extreme system. Fungal and bacterial diversity in biofilms isolated from rubber seals of 24 different household dishwashers was investigated using next-generation sequencing. Bacterial genera such as Pseudomonas, Escherichia, and Acinetobacter, known to include opportunistic pathogens, were represented in most samples. The most frequently encountered fungal genera in these samples belonged to Candida, Cryptococcus, and Rhodotorula, also known to include opportunistic pathogenic representatives. This study showed how specific conditions of the dishwashers impact the abundance of microbial groups and investigated the interkingdom and intrakingdom interactions that shape these biofilms. The age, usage frequency, and hardness of incoming tap water of dishwashers had significant impact on bacterial and fungal community compositions. Representatives of Candida spp. were found at the highest prevalence (100%) in all dishwashers and are assumed to be one of the first colonizers in recently purchased dishwashers. Pairwise correlations in tested microbiomes showed that certain bacterial groups cooccur, as did the fungal groups. In mixed bacterial-fungal biofilms, early adhesion, contact, and interactions were vital in the process of biofilm formation, where mixed complexes of bacteria and fungi could provide a preliminary biogenic structure for the establishment of these biofilms. IMPORTANCE Worldwide demand for household appliances, such as dishwashers and washing machines, is increasing, as is the number of immunocompromised individuals. The harsh conditions in household dishwashers should prevent the growth of most microorganisms. However, our research shows that persisting polyextremotolerant groups of microorganisms in household appliances are well established under these unfavorable conditions and supported by the biofilm mode of growth. The significance of our research is in identifying the microbial composition of biofilms formed on dishwasher rubber seals, how diverse abiotic conditions affect microbiota, and which key microbial members were represented in early colonization and contamination of dishwashers, as these appliances can present a source of domestic cross-contamination that leads to broader medical impacts.
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17
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Shamarina D, Stoyantcheva I, Mason CE, Bibby K, Elhaik E. Communicating the promise, risks, and ethics of large-scale, open space microbiome and metagenome research. MICROBIOME 2017; 5:132. [PMID: 28978331 PMCID: PMC5628477 DOI: 10.1186/s40168-017-0349-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/20/2017] [Indexed: 05/07/2023]
Abstract
The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining largely unknown until the late seventeenth century with the works of van Leeuwenhoek and Kircher. Despite our improved understanding regarding microorganisms, the general public are apt to think of diseases rather than of the majority of harmless or beneficial species that inhabit our bodies and the built and natural environment. As long as microbiome research was confined to labs, the public's exposure to microbiology was limited. The recent launch of global microbiome surveys, such as the Earth Microbiome Project and MetaSUB (Metagenomics and Metadesign of Subways and Urban Biomes) project, has raised ethical, financial, feasibility, and sustainability concerns as to the public's level of understanding and potential reaction to the findings, which, done improperly, risk negative implications for ongoing and future investigations, but done correctly, can facilitate a new vision of "smart cities." To facilitate improved future research, we describe here the major concerns that our discussions with ethics committees, community leaders, and government officials have raised, and we expound on how to address them. We further discuss ethical considerations of microbiome surveys and provide practical recommendations for public engagement.
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Affiliation(s)
- Daria Shamarina
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Iana Stoyantcheva
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN UK
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021 USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY 10021 USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021 USA
| | - Kyle Bibby
- University of Notre Dame Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dameᅟ, IN 46556 USA
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN UK
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18
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Teasdale MD, Fiddyment S, Vnouček J, Mattiangeli V, Speller C, Binois A, Carver M, Dand C, Newfield TP, Webb CC, Bradley DG, Collins MJ. The York Gospels: a 1000-year biological palimpsest. ROYAL SOCIETY OPEN SCIENCE 2017. [PMID: 29134095 DOI: 10.5061/dryad.1p390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.
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Affiliation(s)
- Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Jiří Vnouček
- BioArCh, University of York, York YO10 5DD, UK
- Department of Preservation, The Royal Library, København K DK-1016, Denmark
| | | | | | - Annelise Binois
- Department of Archaeology, University of Paris 1 Panthéon-Sorbonne, 3 rue Michelet, 75006 Paris, France
| | - Martin Carver
- Department of Archaeology, University of York, York YO10 5DD, UK
| | - Catherine Dand
- Borthwick Institute for Archives, University of York, York YO10 5DD, UK
| | - Timothy P Newfield
- Departments of History and Biology, Georgetown University, 37th and O Streets NW, ICC 600, Washington, DC 20057, USA
| | | | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew J Collins
- BioArCh, University of York, York YO10 5DD, UK
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
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19
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Teasdale MD, Fiddyment S, Vnouček J, Mattiangeli V, Speller C, Binois A, Carver M, Dand C, Newfield TP, Webb CC, Bradley DG, Collins MJ. The York Gospels: a 1000-year biological palimpsest. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170988. [PMID: 29134095 PMCID: PMC5666278 DOI: 10.1098/rsos.170988] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/22/2017] [Indexed: 05/10/2023]
Abstract
Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.
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Affiliation(s)
- Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Authors for correspondence: Matthew D. Teasdale e-mail: ;
| | - Sarah Fiddyment
- BioArCh, University of York, York YO10 5DD, UK
- Authors for correspondence: Sarah Fiddyment e-mail:
| | - Jiří Vnouček
- BioArCh, University of York, York YO10 5DD, UK
- Department of Preservation, The Royal Library, København K DK-1016, Denmark
| | | | | | - Annelise Binois
- Department of Archaeology, University of Paris 1 Panthéon-Sorbonne, 3 rue Michelet, 75006 Paris, France
| | - Martin Carver
- Department of Archaeology, University of York, York YO10 5DD, UK
| | - Catherine Dand
- Borthwick Institute for Archives, University of York, York YO10 5DD, UK
| | - Timothy P. Newfield
- Departments of History and Biology, Georgetown University, 37th and O Streets NW, ICC 600, Washington, DC 20057, USA
| | | | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew J. Collins
- BioArCh, University of York, York YO10 5DD, UK
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
- Authors for correspondence: Matthew J. Collins e-mail:
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20
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McIntyre ABR, Ounit R, Afshinnekoo E, Prill RJ, Hénaff E, Alexander N, Minot SS, Danko D, Foox J, Ahsanuddin S, Tighe S, Hasan NA, Subramanian P, Moffat K, Levy S, Lonardi S, Greenfield N, Colwell RR, Rosen GL, Mason CE. Comprehensive benchmarking and ensemble approaches for metagenomic classifiers. Genome Biol 2017; 18:182. [PMID: 28934964 PMCID: PMC5609029 DOI: 10.1186/s13059-017-1299-7] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/16/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. RESULTS In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages. CONCLUSIONS This study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.
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Affiliation(s)
- Alexa B R McIntyre
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
- School of Medicine, New York Medical College, Valhalla, NY, 10595, USA
| | - Robert J Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA, 95120, USA
| | - Elizabeth Hénaff
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Samuel S Minot
- One Codex, Reference Genomics, San Francisco, CA, 94103, USA
| | - David Danko
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Sofia Ahsanuddin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA
| | - Scott Tighe
- University of Vermont, Burlington, VT, 05405, USA
| | - Nur A Hasan
- CosmosID, Inc, Rockville, MD, 20850, USA
- Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies (UMIACS), College Park, MD, 20742, USA
| | | | | | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Nick Greenfield
- One Codex, Reference Genomics, San Francisco, CA, 94103, USA
| | - Rita R Colwell
- CosmosID, Inc, Rockville, MD, 20850, USA
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gail L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, 19104, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, 10021, USA.
- The Feil Family Brain and Mind Research Institute, New York, NY, 10065, USA.
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Maritz JM, Sullivan SA, Prill RJ, Aksoy E, Scheid P, Carlton JM. Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City. PLoS One 2017; 12:e0175527. [PMID: 28384336 PMCID: PMC5383295 DOI: 10.1371/journal.pone.0175527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/27/2017] [Indexed: 12/25/2022] Open
Abstract
Background Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with—and potential exchange of—microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Results Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency. Conclusions We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes.
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Affiliation(s)
- Julia M. Maritz
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Steven A. Sullivan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Robert J. Prill
- Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, California, United States of America
| | - Emre Aksoy
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Paul Scheid
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
| | - Jane M. Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States of America
- * E-mail:
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