1
|
Evaluating Methods of Preserving Aquatic Invertebrates for Microbiome Analysis. Microorganisms 2022; 10:microorganisms10040811. [PMID: 35456860 PMCID: PMC9032454 DOI: 10.3390/microorganisms10040811] [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] [Received: 01/23/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
Research on the microbiomes of animals has increased substantially within the past decades. More recently, microbial analyses of aquatic invertebrates have become of increased interest. The storage method used while collecting aquatic invertebrates has not been standardized throughout the scientific community, and the effects of common storage methods on the microbial composition of the organism is unknown. Using crayfish and dragonfly nymphs collected from a natural pond and crayfish maintained in an aquarium, the effects of two common storage methods, preserving in 95% ethanol and freezing at −20 °C, on the invertebrate bacterial microbiome was evaluated. We found that the bacterial community was conserved for two sample types (gut and exoskeleton) of field-collected crayfish stored either in ethanol or frozen, as was the gut microbiome of aquarium crayfish. However, there were significant differences between the bacterial communities found on the exoskeleton of aquarium crayfish stored in ethanol compared to those that were frozen. Dragonfly nymphs showed significant differences in gut microbial composition between species, but the microbiome was conserved between storage methods. These results demonstrate that preserving field-collected specimens of aquatic invertebrates in 95% ethanol is likely to be a simple and effective sample preservation method for subsequent gut microbiome analysis but is less reliable for the external microbiome.
Collapse
|
2
|
Johny TK, Puthusseri RM, Bhat SG. Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome. Arch Microbiol 2021; 204:87. [PMID: 34961896 DOI: 10.1007/s00203-021-02675-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/27/2021] [Accepted: 12/07/2021] [Indexed: 01/08/2023]
Abstract
Fish gut microbiota, encompassing a colossal reserve of microbes represents a dynamic ecosystem, influenced by a myriad of environmental and host factors. The current study presents a comprehensive insight into Sardinella longiceps gut microbiome using whole metagenome shotgun sequencing. Taxonomic profiling identified the predominance of phylum Proteobacteria, comprising of Photobacterium, Vibrio and Shewanella sp. Functional annotation revealed the dominance of Clustering based subsystems, Carbohydrate, and Amino acids and derivatives. Analysis of Virulence, disease and defense subsystem identified genes conferring resistance to antibiotics and toxic compounds, like multidrug resistance efflux pumps and resistance genes for fluoroquinolones and heavy metals like cobalt, zinc, cadmium and copper. The presence of overlapping genetic mechanisms of resistance to antibiotics and heavy metals, like the efflux pumps is a serious cause of concern as it is likely to aggravate co-selection pressure, leading to an increased dissemination of these resistance genes to fish and humans.
Collapse
Affiliation(s)
- Tina Kollannoor Johny
- Department of Biotechnology, Cochin University of Science and Technology, Kalamassery, Cochin, Kerala, 682022, India
| | - Rinu Madhu Puthusseri
- Department of Biotechnology, Cochin University of Science and Technology, Kalamassery, Cochin, Kerala, 682022, India
| | - Sarita Ganapathy Bhat
- Department of Biotechnology, Cochin University of Science and Technology, Kalamassery, Cochin, Kerala, 682022, India.
| |
Collapse
|
3
|
Milan M, Maroso F, Dalla Rovere G, Carraro L, Ferraresso S, Patarnello T, Bargelloni L, Cardazzo B, Fariselli P. Tracing seafood at high spatial resolution using NGS-generated data and machine learning: Comparing microbiome versus SNPs. Food Chem 2019; 286:413-420. [PMID: 30827626 DOI: 10.1016/j.foodchem.2019.02.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/16/2019] [Accepted: 02/11/2019] [Indexed: 11/25/2022]
Abstract
Developing reliable tools to trace food origin represents a major goal for producers and control authorities. Here, we test the hypothesis whether NGS-generated data could provide a reliable tool to ensure seafood traceability. As a test case, we used the Manila clam Ruditapes philippinarum, a bivalve mollusk of high commercial interest with worldwide distribution, collected in the Venice lagoon sites subjected to prohibition of clam harvesting because of chemical contamination as well as in authorized clam harvesting areas. The results obtained demonstrated that the geographic origin of Manila clam may be more accurately determined basing on microbiome data than single nucleotide polymorphisms. In particular, combining microbiome data with machine-learning techniques, we provide the experimental evidence that it is possible to trace the clam place of origin at high spatial resolution. Considering its low cost and portability, NGS-analysis of microbiome data might represent a cost-effective, high-resolution tool for reliable food traceability.
Collapse
Affiliation(s)
- Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy.
| | - Francesco Maroso
- Departamento de Zoología, Genética y Antropología Física, Facultad de Veterinaria, Universidade de Santiago de Compostela, 27002 Lugo, Spain
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Lisa Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy
| | - Barbara Cardazzo
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| | - Piero Fariselli
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy
| |
Collapse
|
4
|
Rodrigues PA, Ferrari RG, Conte-Junior CA. Application of molecular tools to elucidate the microbiota of seafood. J Appl Microbiol 2018; 124:1347-1365. [PMID: 29345036 DOI: 10.1111/jam.13701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 12/19/2022]
Abstract
The aim of this review is to present the methodologies currently applied to identify microbiota and pathogens transmitted to humans through seafood consumption, focusing on molecular techniques and pointing out their importance, advantages, disadvantages and applicability. Knowledge of available techniques allows researchers to identify which technique best fits their expectations. With such discernment, it will be possible to infer which disadvantages will be present and, therefore, not interfering with the final result. Two methodologies can be employed for this purpose, dependent and independent cultures. However, the dependent culture has certain limitations that can be solved through the independent cultivation techniques, such as PCR, PFGE and NGS, especially through the sequencing of the 16S rRNA region, providing a complete view of microbial diversity. These have revolutionized microbiological knowledge, mainly because they allow for the identification of uncultivable micro-organisms, which represent a substantial portion of total micro-organisms, making it possible to elucidate not yet described taxa which may display pathogenic potential, besides quantifying microbial communities, microbiota genetics, translated proteins and produced metabolites. In addition, transcriptomic and metabolomic techniques also allow for the evaluation of possible impacts that microbial communities may create in their environment, as well as the determination of potential pathogenicity to humans.
Collapse
Affiliation(s)
- P A Rodrigues
- Department of Food Technology, Faculty of Veterinary, Molecular & Analytical Laboratory Center, Universidade Federal Fluminense, Niterói, Brazil
| | - R G Ferrari
- Department of Food Technology, Faculty of Veterinary, Molecular & Analytical Laboratory Center, Universidade Federal Fluminense, Niterói, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - C A Conte-Junior
- Department of Food Technology, Faculty of Veterinary, Molecular & Analytical Laboratory Center, Universidade Federal Fluminense, Niterói, Brazil.,Chemistry Institute, Food Science Program, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Health Quality Control, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| |
Collapse
|
5
|
Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, Lauder A, Sherrill-Mix S, Chehoud C, Kelsen J, Conrad M, Collman RG, Baldassano R, Bushman FD, Bittinger K. Optimizing methods and dodging pitfalls in microbiome research. MICROBIOME 2017; 5:52. [PMID: 28476139 PMCID: PMC5420141 DOI: 10.1186/s40168-017-0267-5] [Citation(s) in RCA: 338] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/21/2017] [Indexed: 05/09/2023]
Abstract
Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors.
Collapse
Affiliation(s)
- Dorothy Kim
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Casey E. Hofstaedter
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Erik Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Abigail Lauder
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Christel Chehoud
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Máire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Ronald G. Collman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Robert Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104 USA
| |
Collapse
|
6
|
Davis EM. Gene Sequence Analyses of the Healthy Oral Microbiome in Humans and Companion Animals. J Vet Dent 2016; 33:97-107. [DOI: 10.1177/0898756416657239] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
It has long been accepted that certain oral bacterial species are responsible for the development of periodontal disease. However, the focus of microbial and immunological research is shifting from studying the organisms associated with disease to examining the indigenous microbial inhabitants that are present in health. Microbiome refers to the aggregate genetic material of all microorganisms living in, or on, a defined habitat. Recent developments in gene sequence analysis have enabled detection and identification of bacteria from polymicrobial samples, including subgingival plaque. Diversity surveys utilizing this technology have demonstrated that bacterial culture techniques have vastly underestimated the richness and diversity of microorganisms in vivo, since only certain bacteria grow in vitro. Surveys using gene sequence analysis have demonstrated that the healthy oral microbiome is composed of an unexpectedly high number of diverse species, including putative pathogens. These findings support the view that coevolution microorganisms and macroscopic hosts has occurred in which certain microorganisms have adapted to survive in the oral cavity and host immune tolerance has allowed the establishment of a symbiotic relationship in which both parties receive benefits (mutualism). This review describes gene sequence analysis as an increasingly common, culture-independent tool for detecting bacteria in vivo and describes the results of recent oral microbiome diversity surveys of clinically healthy humans, dogs, and cats. Six bacterial phyla consistently dominated the healthy oral microbiome of all 3 host species. Previous hypotheses on etiology of periodontitis are reviewed in light of new scientific findings. Finally, the consideration that clinically relevant periodontal disease occurs when immune tolerance of the symbiotic oral microbiome is altered to a proinflammatory response will be discussed.
Collapse
Affiliation(s)
- Eric M. Davis
- Animal Dental Specialists of Upstate New York, Fayetteville, NY, USA
| |
Collapse
|
7
|
Halpin AL, de Man TJB, Kraft CS, Perry KA, Chan AW, Lieu S, Mikell J, Limbago BM, McDonald LC. Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention. Am J Infect Control 2016; 44:830-6. [PMID: 26905790 DOI: 10.1016/j.ajic.2016.01.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 12/18/2015] [Accepted: 01/04/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Composition and diversity of intestinal microbial communities (microbiota) are generally accepted as a risk factor for poor outcomes; however, we cannot yet use this information to prevent adverse outcomes. METHODS Stool was collected from 8 long-term acute care hospital patients experiencing diarrhea and 2 fecal microbiota transplant donors; 16S rDNA V1-V2 hypervariable regions were sequenced. Composition and diversity of each sample were described. Stool was also tested for Clostridium difficile, vancomycin-resistant enterococci (VRE), and carbapenem-resistant Enterobacteriaceae. Associations between microbiota diversity and demographic and clinical characteristics, including antibiotic use, were analyzed. RESULTS Antibiotic exposure and Charlson Comorbidity Index were inversely correlated with diversity (Spearman = -0.7). Two patients were positive for VRE; both had microbiomes dominated by Enterococcus faecium, accounting for 67%-84% of their microbiome. CONCLUSIONS Antibiotic exposure correlated with diversity; however, other environmental and host factors not easily obtainable in a clinical setting are also known to impact the microbiota. Therefore, direct measurement of microbiome disruption by sequencing, rather than reliance on surrogate markers, might be most predictive of adverse outcomes. If and when microbiome characterization becomes a standard diagnostic test, improving our understanding of microbiome dynamics will allow for interpretation of results to improve patient outcomes.
Collapse
Affiliation(s)
- Alison Laufer Halpin
- Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA.
| | - Tom J B de Man
- Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA
| | - K Allison Perry
- Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Austin W Chan
- Division of Infectious Diseases, Duke University, Durham, NC
| | - Sung Lieu
- Department of Medicine, Emory University, Atlanta, GA
| | | | - Brandi M Limbago
- Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - L Clifford McDonald
- Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| |
Collapse
|
8
|
|
9
|
d’Avila-Levy CM, Boucinha C, Kostygov A, Santos HLC, Morelli KA, Grybchuk-Ieremenko A, Duval L, Votýpka J, Yurchenko V, Grellier P, Lukeš J. Exploring the environmental diversity of kinetoplastid flagellates in the high-throughput DNA sequencing era. Mem Inst Oswaldo Cruz 2015; 110:956-65. [PMID: 26602872 PMCID: PMC4708014 DOI: 10.1590/0074-02760150253] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/01/2015] [Indexed: 12/12/2022] Open
Abstract
The class Kinetoplastea encompasses both free-living and parasitic species from a wide range of hosts. Several representatives of this group are responsible for severe human diseases and for economic losses in agriculture and livestock. While this group encompasses over 30 genera, most of the available information has been derived from the vertebrate pathogenic genera Leishmaniaand Trypanosoma. Recent studies of the previously neglected groups of Kinetoplastea indicated that the actual diversity is much higher than previously thought. This article discusses the known segment of kinetoplastid diversity and how gene-directed Sanger sequencing and next-generation sequencing methods can help to deepen our knowledge of these interesting protists.
Collapse
Affiliation(s)
- Claudia Masini d’Avila-Levy
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Estudos
Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
| | - Carolina Boucinha
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Estudos
Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
| | - Alexei Kostygov
- University of Ostrava, Life Science Research Centre, Ostrava, Czech
Republic
- Russian Academy of Sciences, Zoological Institute, Laboratory of
Molecular Systematics, St Petersburg, Russia
| | - Helena Lúcia Carneiro Santos
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Estudos
Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
| | - Karina Alessandra Morelli
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Estudos
Integrados em Protozoologia, Coleção de Protozoários, Rio de Janeiro, RJ, Brasil
- Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto
Alcântara Gomes, Departamento de Ecologia, Rio de Janeiro, RJ, Brasil
| | | | - Linda Duval
- Sorbonne Universités, Muséum National d’Histoire Naturelle, Centre
National de la Recherche Scientifique, Unité Molécules de Communication et Adaptation
des Microorganisme, Unités Mixte de Recherche 7245, Paris, France
| | - Jan Votýpka
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre,
České Budejovice, Czech Republic
- Charles University, Faculty of Science, Department of Parasitology,
Prague, Czech Republic
| | - Vyacheslav Yurchenko
- University of Ostrava, Life Science Research Centre, Ostrava, Czech
Republic
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre,
České Budejovice, Czech Republic
| | - Philippe Grellier
- Sorbonne Universités, Muséum National d’Histoire Naturelle, Centre
National de la Recherche Scientifique, Unité Molécules de Communication et Adaptation
des Microorganisme, Unités Mixte de Recherche 7245, Paris, France
| | - Julius Lukeš
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre,
České Budejovice, Czech Republic
- University of South Bohemia, Faculty of Sciences, České Budejovice,
Czech Republic
- Canadian Institute for Advanced Research, Toronto, Canada
| |
Collapse
|
10
|
Galloway D, Danziger-Isakov L, Goldschmidt M, Hemmelgarn T, Courter J, Nathan JD, Alonso M, Tiao G, Fei L, Kocoshis S. Incidence of bloodstream infections in small bowel transplant recipients receiving selective decontamination of the digestive tract: A single-center experience. Pediatr Transplant 2015; 19:722-9. [PMID: 26332092 PMCID: PMC4837460 DOI: 10.1111/petr.12583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/15/2015] [Indexed: 12/13/2022]
Abstract
Pediatric patients undergoing small bowel transplantation are susceptible to postoperative CLABSI. SDD directed against enteric microbes is a strategy for reducing CLABSI. We hypothesized that SDD reduces the frequency of CLABSI, infections outside the bloodstream, and allograft rejection during the first 30 days following transplant. A retrospective chart review of 38 pediatric small bowel transplant recipients at CCHMC from 2003 to 2011 was conducted. SDD antimicrobials were oral colistin, tobramycin, and amphotericin B. The incidence of CLABSI, infections outside the bloodstream, and rejection episodes were compared between study periods. The incidence of CLABSI did not differ between study periods (6.9 CLABSI vs. 4.6 CLABSI per 1000 catheter days; p = 0.727), but gram positives and Candida predominated in the first 30 days. Incidence of bacterial infections outside the bloodstream did not differ (p = 0.227). Rejection occurred more frequently during the first month following transplant (p = 0.302). SDD does not alter the incidence of CLABSI, bacterial infections outside the bloodstream, or allograft rejection in the immediate 30 days post-transplantation. However, SDD does influence CLABSI organism types (favoring gram positives and Candida) and Candidal infections outside the bloodstream.
Collapse
Affiliation(s)
- David Galloway
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Lara Danziger-Isakov
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Monique Goldschmidt
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Trina Hemmelgarn
- Division of Pharmacy, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Joshua Courter
- Division of Pharmacy, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Jaimie D. Nathan
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Maria Alonso
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Greg Tiao
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Lin Fei
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Samuel Kocoshis
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| |
Collapse
|
11
|
Zepeda Mendoza ML, Sicheritz-Pontén T, Gilbert MTP. Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. Brief Bioinform 2015; 16:745-58. [PMID: 25673291 PMCID: PMC4570204 DOI: 10.1093/bib/bbv001] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/16/2014] [Indexed: 01/19/2023] Open
Abstract
DNA-based taxonomic and functional profiling is widely used for the characterization of organismal communities across a rapidly increasing array of research areas that include the role of microbiomes in health and disease, biomonitoring, and estimation of both microbial and metazoan species richness. Two principal approaches are currently used to assign taxonomy to DNA sequences: DNA metabarcoding and metagenomics. When initially developed, each of these approaches mandated their own particular methods for data analysis; however, with the development of high-throughput sequencing (HTS) techniques they have begun to share many aspects in data set generation and processing. In this review we aim to define the current characteristics, goals and boundaries of each field, and describe the different software used for their analysis. We argue that an appreciation of the potential and limitations of each method can help underscore the improvements required by each field so as to better exploit the richness of current HTS-based data sets.
Collapse
|
12
|
Proctor CR, Hammes F. Drinking water microbiology — from measurement to management. Curr Opin Biotechnol 2015; 33:87-94. [DOI: 10.1016/j.copbio.2014.12.014] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 12/14/2014] [Accepted: 12/16/2014] [Indexed: 01/02/2023]
|
13
|
UCHIHASHI M, BERGIN IL, BASSIS CM, HASHWAY SA, CHAI D, BELL JD. Influence of age, reproductive cycling status, and menstruation on the vaginal microbiome in baboons (Papio anubis). Am J Primatol 2015; 77:563-78. [PMID: 25676781 PMCID: PMC4458466 DOI: 10.1002/ajp.22378] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 12/18/2022]
Abstract
The vaginal microbiome is believed to influence host health by providing protection from pathogens and influencing reproductive outcomes such as fertility and gestational length. In humans, age-associated declines in diversity of the vaginal microbiome occur in puberty and persist into adulthood. Additionally, menstruation has been associated with decreased microbial community stability. Adult female baboons, like other non-human primates (NHPs), have a different and highly diverse vaginal microbiome compared to that of humans, which is most commonly dominated by Lactobacillus spp. We evaluated the influence of age, reproductive cycling status (cycling vs. non-cycling) and menstruation on the vaginal microbiome of 38 wild-caught, captive female olive baboons (Papio anubis) by culture-independent sequencing of the V3-V5 region of the bacterial 16S rRNA gene. All baboons had highly diverse vaginal microbial communities. Adult baboons had significantly lower microbial diversity in comparison to subadult baboons, which was attributable to decreased relative abundance of minor taxa. No significant differences were detected based on cycling state or menstruation. Predictive metagenomic analysis showed uniformity in relative abundance of metabolic pathways regardless of age, cycle stage, or menstruation, indicating conservation of microbial community functions. This study suggests that selection of an optimal vaginal microbial community occurs at puberty. Since decreased diversity occurs in both baboons and humans at puberty, this may reflect a general strategy for selection of adult vaginal microbial communities. Comparative evaluation of vaginal microbial community development and composition may elucidate mechanisms of community formation and function that are conserved across host species or across microbial community types. These findings have implications for host health, evolutionary biology, and microbe-host ecosystems.
Collapse
Affiliation(s)
- M. UCHIHASHI
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan
| | - I. L. BERGIN
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan
| | - C. M. BASSIS
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - S. A. HASHWAY
- Research Animal Resources, University of Minnesota, Minneapolis, Minnesota
| | - D. CHAI
- Institute of Primate Research, National Museums of Kenya, Nairobi, Kenya
| | - J. D. BELL
- Reproductive Sciences Program, University of Michigan, Ann Arbor, Michigan
- Program on Women's Healthcare Effectiveness Research, Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
14
|
Chandler JA, Liu RM, Bennett SN. RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi. Front Microbiol 2015; 6:185. [PMID: 25852655 PMCID: PMC4371751 DOI: 10.3389/fmicb.2015.00185] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/19/2015] [Indexed: 01/09/2023] Open
Abstract
Mosquitoes, most often recognized for the microbial agents of disease they may carry, harbor diverse microbial communities that include viruses, bacteria, and fungi, collectively called the microbiota. The composition of the microbiota can directly and indirectly affect disease transmission through microbial interactions that could be revealed by its characterization in natural populations of mosquitoes. Furthermore, the use of shotgun metagenomic sequencing (SMS) approaches could allow the discovery of unknown members of the microbiota. In this study, we use RNA SMS to characterize the microbiota of seven individual mosquitoes (species include Culex pipiens, Culiseta incidens, and Ochlerotatus sierrensis) collected from a variety of habitats in California, USA. Sequencing was performed on the Illumina HiSeq platform and the resulting sequences were quality-checked and assembled into contigs using the A5 pipeline. Sequences related to single stranded RNA viruses of the Bunyaviridae and Rhabdoviridae were uncovered, along with an unclassified genus of double-stranded RNA viruses. Phylogenetic analysis finds that in all three cases, the closest relatives of the identified viral sequences are other mosquito-associated viruses, suggesting widespread host-group specificity among disparate viral taxa. Interestingly, we identified a Narnavirus of fungi, also reported elsewhere in mosquitoes, that potentially demonstrates a nested host-parasite association between virus, fungi, and mosquito. Sequences related to 8 bacterial families and 13 fungal families were found across the seven samples. Bacillus and Escherichia/Shigella were identified in all samples and Wolbachia was identified in all Cx. pipiens samples, while no single fungal genus was found in more than two samples. This study exemplifies the utility of RNA SMS in the characterization of the natural microbiota of mosquitoes and, in particular, the value of identifying all microbes associated with a specific host.
Collapse
Affiliation(s)
- James Angus Chandler
- Department of Microbiology, California Academy of Sciences San Francisco, CA, USA
| | - Rachel M Liu
- Department of Microbiology, California Academy of Sciences San Francisco, CA, USA
| | - Shannon N Bennett
- Department of Microbiology, California Academy of Sciences San Francisco, CA, USA
| |
Collapse
|
15
|
Handley JA, Shi Z, Park SH, Dawoud TM, Kwon YM, Ricke SC. Salmonella and the Potential Role for Methods to Develop Microbial Process Indicators on Chicken Carcasses. Food Saf (Tokyo) 2015. [DOI: 10.1016/b978-0-12-800245-2.00006-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
16
|
Massart S, Olmos A, Jijakli H, Candresse T. Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus Res 2014; 188:90-6. [PMID: 24717426 DOI: 10.1016/j.virusres.2014.03.029] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 12/17/2022]
Abstract
The ability to provide a fast, inexpensive and reliable diagnostic for any given viral infection is a key parameter in efforts to fight and control these ubiquitous pathogens. The recent developments of high-throughput sequencing (also called Next Generation Sequencing - NGS) technologies and bioinformatics have drastically changed the research on viral pathogens. It is now raising a growing interest for virus diagnostics. This review provides a snapshot vision on the current use and impact of high throughput sequencing approaches in plant virus characterization. More specifically, this review highlights the potential of these new technologies and their interplay with current protocols in the future of molecular diagnostic of plant viruses. The current limitations that will need to be addressed for a wider adoption of high-throughput sequencing in plant virus diagnostics are thoroughly discussed.
Collapse
Affiliation(s)
- Sebastien Massart
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-BioTech, Passage des déportés, 2, 5030 Gembloux, Belgium.
| | - Antonio Olmos
- Centro de Protección Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, 46113 Moncada, Valencia, Spain
| | - Haissam Jijakli
- Laboratory of Phytopathology, University of Liège, Gembloux Agro-BioTech, Passage des déportés, 2, 5030 Gembloux, Belgium
| | - Thierry Candresse
- UMR 1332 de Biologie du fruit et Pathologie, INRA, CS20032, 33882 Villenave d'Ornon cedex, France; UMR 1332 de Biologie du fruit et Pathologie, Université de Bordeaux, CS20032, 33882 Villenave d'Ornon cedex, France
| |
Collapse
|
17
|
Wang K, Li H, Yuan Y, Etheridge A, Zhou Y, Huang D, Wilmes P, Galas D. The complex exogenous RNA spectra in human plasma: an interface with human gut biota? PLoS One 2012; 7:e51009. [PMID: 23251414 PMCID: PMC3519536 DOI: 10.1371/journal.pone.0051009] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 10/29/2012] [Indexed: 11/19/2022] Open
Abstract
Human plasma has long been a rich source for biomarker discovery. It has recently become clear that plasma RNA molecules, such as microRNA, in addition to proteins are common and can serve as biomarkers. Surveying human plasma for microRNA biomarkers using next generation sequencing technology, we observed that a significant fraction of the circulating RNA appear to originate from exogenous species. With careful analysis of sequence error statistics and other controls, we demonstrated that there is a wide range of RNA from many different organisms, including bacteria and fungi as well as from other species. These RNAs may be associated with protein, lipid or other molecules protecting them from RNase activity in plasma. Some of these RNAs are detected in intracellular complexes and may be able to influence cellular activities under invitro conditions. These findings raise the possibility that plasma RNAs of exogenous origin may serve as signaling molecules mediating for example the human-microbiome interaction and may affect and/or indicate the state of human health.
Collapse
Affiliation(s)
- Kai Wang
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail: (KW); (DG); (PW)
| | - Hong Li
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Yue Yuan
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Alton Etheridge
- Institute for Systems Biology, Seattle, Washington, United States of America
- Pacific Northwest Diabetes Research, Seattle, Washington, United States of America
| | - Yong Zhou
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - David Huang
- Institute for Systems Biology, Seattle, Washington, United States of America
- Pacific Northwest Diabetes Research, Seattle, Washington, United States of America
| | - Paul Wilmes
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg City, Luxembourg
- * E-mail: (KW); (DG); (PW)
| | - David Galas
- Institute for Systems Biology, Seattle, Washington, United States of America
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg City, Luxembourg
- Pacific Northwest Diabetes Research, Seattle, Washington, United States of America
- * E-mail: (KW); (DG); (PW)
| |
Collapse
|
18
|
Trimble WL, Keegan KP, D'Souza M, Wilke A, Wilkening J, Gilbert J, Meyer F. Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. BMC Bioinformatics 2012; 13:183. [PMID: 22839106 PMCID: PMC3526449 DOI: 10.1186/1471-2105-13-183] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 07/13/2012] [Indexed: 11/17/2022] Open
Abstract
Background Gene prediction algorithms (or gene callers) are an essential tool for analyzing shotgun nucleic acid sequence data. Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume of data by identifying the most likely reading frame for a fragment, permitting the out-of-frame translations to be ignored. In this study we evaluate five widely used ab initio gene-calling algorithms—FragGeneScan, MetaGeneAnnotator, MetaGeneMark, Orphelia, and Prodigal—for accuracy on short (75–1000 bp) fragments containing sequence error from previously published artificial data and “real” metagenomic datasets. Results While gene prediction tools have similar accuracies predicting genes on error-free fragments, in the presence of sequencing errors considerable differences between tools become evident. For error-containing short reads, FragGeneScan finds more prokaryotic coding regions than does MetaGeneAnnotator, MetaGeneMark, Orphelia, or Prodigal. This improved detection of genes in error-containing fragments, however, comes at the cost of much lower (50%) specificity and overprediction of genes in noncoding regions. Conclusions Ab initio gene callers offer a significant reduction in the computational burden of annotating individual nucleic acid reads and are used in many metagenomic annotation systems. For predicting reading frames on raw reads, we find the hidden Markov model approach in FragGeneScan is more sensitive than other gene prediction tools, while Prodigal, MGA, and MGM are better suited for higher-quality sequences such as assembled contigs.
Collapse
Affiliation(s)
- William L Trimble
- Computation Institute, University of Chicago, Chicago, IL 60637, USA.
| | | | | | | | | | | | | |
Collapse
|
19
|
Hallinan J. Data mining for microbiologists. J Microbiol Methods 2012. [DOI: 10.1016/b978-0-08-099387-4.00002-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
|