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SanchesTrevizol J, Dionizio A, Delgado AQ, Ventura TMO, da Silva Ribeiro CF, Rabelo Buzalaf N, Bosqueiro JR, Buzalaf MAR. Optimized protocol for shotgun label-free proteomic analysis of pancreatic islets. Biol Methods Protoc 2024; 9:bpae003. [PMID: 38405023 PMCID: PMC10893585 DOI: 10.1093/biomethods/bpae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/27/2024] Open
Abstract
Pancreatic islets are crucial in diabetes research. Consequently, this protocol aims at optimizing both the protein-extraction process and the proteomic analysis via shotgun methods for pancreatic islets. Six protocols were tested, combining three types of chemical extraction with two mechanical extraction methods. Furthermore, two protocols incorporated a surfactant to enhance enzymatic cleavage. The steps involved extraction and concentration of protein, protein quantification, reduction, alkylation, digestion, purification and desalination, sample concentration to ∼1 µl, and proteomic analysis using the mass spectrometer. The most effective protocol involves either a milder chemical extraction paired with a more intensive mechanical process, or a more robust chemical extraction paired with a gentle mechanical process, tailored to the sample's characteristics. Additionally, it was observed that the use of a surfactant proved ineffective for these types of samples. Protocol 5 was recently used with success to examine metabolic changes in pancreatic islets of non-obese diabetic mice exposed to low doses of fluoride ions (F-) and the primary pathways altered by the treatment.
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Affiliation(s)
- Juliana SanchesTrevizol
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - Aline Dionizio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | | | | | | | - Nathalia Rabelo Buzalaf
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, Brazil
| | - José Roberto Bosqueiro
- Department of Physical Education, Faculty of Science, São Paulo State University, Bauru, São Paulo, Brazil
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Zeber-Lubecka N, Kulecka M, Jagiełło-Gruszfeld A, Dąbrowska M, Kluska A, Piątkowska M, Bagińska K, Głowienka M, Surynt P, Tenderenda M, Mikula M, Ostrowski J. Breast cancer but not the menopausal status is associated with small changes of the gut microbiota. Front Oncol 2024; 14:1279132. [PMID: 38327745 PMCID: PMC10848918 DOI: 10.3389/fonc.2024.1279132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/03/2024] [Indexed: 02/09/2024] Open
Abstract
Background Possible relationships between gut dysbiosis and breast cancer (BC) development and progression have been previously reported. However, the results of these metagenomics studies are inconsistent. Our study involved 88 patients diagnosed with breast cancer and 86 cancer-free control women. Participants were divided into groups based on their menopausal status. Fecal samples were collected from 47 and 41 pre- and postmenopausal newly diagnosed breast cancer patients and 51 and 35 pre- and postmenopausal controls, respectively. In this study, we performed shotgun metagenomic analyses to compare the gut microbial community between pre- and postmenopausal BC patients and the corresponding controls. Results Firstly, we identified 12, 64, 158, and 455 bacterial taxa on the taxonomy level of phyla, families, genera, and species, respectively. Insignificant differences of the Shannon index and β-diversity were found at the genus and species levels between pre- and postmenopausal controls; the differences concerned only the Chao index at the species level. No differences in α-diversity indexes were found between pre- and postmenopausal BC patients, although β-diversity differed these subgroups at the genus and species levels. Consistently, only the abundance of single taxa differed between pre- and postmenopausal controls and cases, while the abundances of 14 and 23 taxa differed or tended to differ between premenopausal cases and controls, and between postmenopausal cases and controls, respectively. There were similar differences in the distribution of enterotypes. Of 460 bacterial MetaCyc pathways discovered, no pathways differentiated pre- and postmenopausal controls or BC patients, while two and one pathways differentiated cases from controls in the pre- and postmenopausal subgroups, respectively. Conclusion While our findings did not reveal an association of changes in the overall microbiota composition and selected taxa with the menopausal status in cases and controls, they confirmed differences of the gut microbiota between pre- and postmenopausal BC patients and the corresponding controls. However, these differences were less extensive than those described previously.
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Affiliation(s)
- Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Jagiełło-Gruszfeld
- Department of Breast Cancer & Reconstructive Surgery, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Katarzyna Bagińska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Głowienka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Piotr Surynt
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Tenderenda
- Department of Oncological Surgery and Neuroendocrine Tumors, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
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3
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Ramon E, Obón-Santacana M, Khannous-Lleiffe O, Saus E, Gabaldón T, Guinó E, Bars-Cortina D, Ibáñez-Sanz G, Rodríguez-Alonso L, Mata A, García-Rodríguez A, Moreno V. Performance of a Shotgun Prediction Model for Colorectal Cancer When Using 16S rRNA Sequencing Data. Int J Mol Sci 2024; 25:1181. [PMID: 38256252 PMCID: PMC10816515 DOI: 10.3390/ijms25021181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Colorectal cancer (CRC), the third most common cancer globally, has shown links to disturbed gut microbiota. While significant efforts have been made to establish a microbial signature indicative of CRC using shotgun metagenomic sequencing, the challenge lies in validating this signature with 16S ribosomal RNA (16S) gene sequencing. The primary obstacle is reconciling the differing outputs of these two methodologies, which often lead to divergent statistical models and conclusions. In this study, we introduce an algorithm designed to bridge this gap by mapping shotgun-derived taxa to their 16S counterparts. This mapping enables us to assess the predictive performance of a shotgun-based microbiome signature using 16S data. Our results demonstrate a reduction in performance when applying the 16S-mapped taxa in the shotgun prediction model, though it retains statistical significance. This suggests that while an exact match between shotgun and 16S data may not yet be feasible, our approach provides a viable method for comparative analysis and validation in the context of CRC-associated microbiome research.
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Affiliation(s)
- Elies Ramon
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
| | - Mireia Obón-Santacana
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Olfat Khannous-Lleiffe
- Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), 08028 Barcelona, Spain
| | - Elisabet Guinó
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - David Bars-Cortina
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
| | - Gemma Ibáñez-Sanz
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- Gastroenterology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Lorena Rodríguez-Alonso
- Gastroenterology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Alfredo Mata
- Digestive System Service, Moisés Broggi Hospital, 08970 Sant Joan Despí, Spain
| | - Ana García-Rodríguez
- Endoscopy Unit, Digestive System Service, Viladecans Hospital-IDIBELL, 08840 Viladecans, Spain
| | - Victor Moreno
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona (UB), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
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4
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Shwed PS, Bernatchez S, Leveque G. Draft genome sequences of biofuel production microalgae Auxenochlorella protothecoides and Chlorella sorokiniana. Microbiol Resour Announc 2024; 13:e0044023. [PMID: 38032237 DOI: 10.1128/mra.00440-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/14/2023] [Indexed: 12/01/2023] Open
Abstract
Green microalgae are used in biofuel production. To contribute to the knowledge of the Chlorellaceae family, the de novo assembled draft genome sequences of Auxenochlorella protothecoides Kruger and Chlorella sorokiniana Shihira and Krauss are presented.
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Affiliation(s)
- P S Shwed
- Environmental and Radiation Health Sciences Directorate, Healthy Environments and Consumer Safety Branch , Ottawa, Canada
| | - S Bernatchez
- Biotechnology Section, New Substances Control and Assessment Bureau, Health Canada , Ottawa, Canada
| | - G Leveque
- Canadian Centre for Computational Genomics (C3G), McGill University , Montréal, Canada
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Gafarova E, Kuracji D, Sogomonyan K, Gorokhov I, Polev D, Zubova E, Golikova E, Granovitch A, Maltseva A. Gut Bacteriomes and Ecological Niche Divergence: An Example of Two Cryptic Gastropod Species. Biology (Basel) 2023; 12:1521. [PMID: 38132347 PMCID: PMC10740740 DOI: 10.3390/biology12121521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Symbiotic microorganisms may provide their hosts with abilities critical to their occupation of microhabitats. Gut (intestinal) bacterial communities aid animals to digest substrates that are either innutritious or toxic, as well as support their development and physiology. The role of microbial communities associated with sibling species in the hosts' adaptation remains largely unexplored. In this study, we examined the composition and plasticity of the bacteriomes in two sibling intertidal gastropod species, Littorina fabalis and L. obtusata, which are sympatric but differ in microhabitats. We applied 16S rRNA gene metabarcoding and shotgun sequencing to describe associated microbial communities and their spatial and temporal variation. A significant drop in the intestinal bacteriome diversity was revealed during the cold season, which may reflect temperature-related metabolic shifts and changes in snail behavior. Importantly, there were significant interspecies differences in the gut bacteriome composition in summer but not in autumn. The genera Vibrio, Aliivibrio, Moritella and Planktotalea were found to be predominantly associated with L. fabalis, while Granulosicoccus, Octadecabacter, Colwellia, Pseudomonas, Pseudoalteromonas and Maribacter were found to be mostly associated with L. obtusata. Based on these preferential associations, we analyzed the metabolic pathways' enrichment. We hypothesized that the L. obtusata gut bacteriome contributes to decomposing algae and detoxifying polyphenols produced by fucoids. Thus, differences in the sets of associated bacteria may equip their closely phylogenetically related hosts with a unique ability to occupy specific micro-niches.
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Affiliation(s)
- Elizaveta Gafarova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Dmitrii Kuracji
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Karina Sogomonyan
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ivan Gorokhov
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Dmitrii Polev
- Department of Epidemiology, St. Petersburg Pasteur Institute, Mira Street 14, 197101 St. Petersburg, Russia;
| | - Ekaterina Zubova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Elena Golikova
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Andrey Granovitch
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
| | - Arina Maltseva
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia; (D.K.); (E.Z.); (A.G.)
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Teyssier C, Rogier O, Claverol S, Gautier F, Lelu-Walter MA, Duruflé H. Comprehensive Organ-Specific Profiling of Douglas Fir ( Pseudotsuga menziesii) Proteome. Biomolecules 2023; 13:1400. [PMID: 37759800 PMCID: PMC10526743 DOI: 10.3390/biom13091400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The Douglas fir (Pseudotsuga menziesii) is a conifer native to North America that has become increasingly popular in plantations in France due to its many advantages as timber: rapid growth, quality wood, and good adaptation to climate change. Tree genetic improvement programs require knowledge of a species' genetic structure and history and the development of genetic markers. The very slow progress in this field, for Douglas fir as well as the entire genus Pinus, can be explained using the very large size of their genomes, as well as by the presence of numerous highly repeated sequences. Proteomics, therefore, provides a powerful way to access genomic information of otherwise challenging species. Here, we present the first Douglas fir proteomes acquired using nLC-MS/MS from 12 different plant organs or tissues. We identified 3975 different proteins and quantified 3462 of them, then examined the distribution of specific proteins across plant organs/tissues and their implications in various molecular processes. As the first large proteomic study of a resinous tree species with organ-specific profiling, this short note provides an important foundation for future genomic annotations of conifers and other trees.
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Affiliation(s)
| | - Odile Rogier
- INRAE, ONF, BioForA, UMR 0588, 45075 Orleans, France
| | - Stéphane Claverol
- Plateforme de Protéomique, Université de Bordeaux, 33405 Bordeaux, France
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Skotniczny M, Satora P. Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum. Int J Mol Sci 2023; 24. [PMID: 36902287 DOI: 10.3390/ijms24054853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.
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8
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Li G, Shi Q, He Y, Zhu J, Zhong M, Tong L, Li H, Nie Y, Li Y. Screening of Candidate Effectors from Magnaporthe oryzae by In Vitro Secretomic Analysis. Int J Mol Sci 2023; 24. [PMID: 36834598 DOI: 10.3390/ijms24043189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Magnaporthe oryzae is the causal agent of rice blast, one of the most serious diseases of rice worldwide. Secreted proteins play essential roles during a M. oryzae-rice interaction. Although much progress has been made in recent decades, it is still necessary to systematically explore M. oryzae-secreted proteins and to analyze their functions. This study employs a shotgun-based proteomic analysis to investigate the in vitro secretome of M. oryzae by spraying fungus conidia onto the PVDF membrane to mimic the early stages of infection, during which 3315 non-redundant secreted proteins were identified. Among these proteins, 9.6% (319) and 24.7% (818) are classified as classically or non-classically secreted proteins, while the remaining 1988 proteins (60.0%) are secreted through currently unknown secretory pathway. Functional characteristics analysis show that 257 (7.8%) and 90 (2.7%) secreted proteins are annotated as CAZymes and candidate effectors, respectively. Eighteen candidate effectors are selected for further experimental validation. All 18 genes encoding candidate effectors are significantly up- or down-regulated during the early infection process. Sixteen of the eighteen candidate effectors cause the suppression of BAX-mediated cell death in Nicotiana benthamiana by using an Agrobacterium-mediated transient expression assay, suggesting their involvement in pathogenicity related to secretion effectors. Our results provide high-quality experimental secretome data of M. oryzae and will expand our knowledge on the molecular mechanisms of M. oryzae pathogenesis.
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Usyk M, Peters BA, Karthikeyan S, McDonald D, Sollecito CC, Vazquez-Baeza Y, Shaffer JP, Gellman MD, Talavera GA, Daviglus ML, Thyagarajan B, Knight R, Qi Q, Kaplan R, Burk RD. Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies. Cell Rep Methods 2023; 3:100391. [PMID: 36814836 PMCID: PMC9939430 DOI: 10.1016/j.crmeth.2022.100391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/28/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023]
Abstract
In a large cohort of 1,772 participants from the Hispanic Community Health Study/Study of Latinos with overlapping 16SV4 rRNA gene (bacterial amplicon), ITS1 (fungal amplicon), and shotgun sequencing data, we demonstrate that 16SV4 amplicon sequencing and shotgun metagenomics offer the same level of taxonomic accuracy for bacteria at the genus level even at shallow sequencing depths. In contrast, for fungal taxa, we did not observe meaningful agreements between shotgun and ITS1 amplicon results. Finally, we show that amplicon and shotgun data can be harmonized and pooled to yield larger microbiome datasets with excellent agreement (<1% effect size variance across three independent outcomes) using pooled amplicon/shotgun data compared to pure shotgun metagenomic analysis. Thus, there are multiple approaches to study the microbiome in epidemiological studies, and we provide a demonstration of a powerful pooling approach that will allow researchers to leverage the massive amount of amplicon sequencing data generated over the last two decades.
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Affiliation(s)
- Mykhaylo Usyk
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
- Department of Epidemiology and Population Health, NYU School of Medicine, New York, NY, USA
| | - Brandilyn A. Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Christopher C. Sollecito
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Yoshiki Vazquez-Baeza
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Justin P. Shaffer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marc D. Gellman
- Department of Psychology, University of Miami, Miami, FL, USA
| | - Gregory A. Talavera
- Division of Health Promotion and Behavioral Science, San Diego State University, San Diego, CA, USA
| | - Martha L. Daviglus
- Department of Medicine, University of Illinois-Chicago, Chicago, IL, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis, MN, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Departments of Computer Science and Engineering, and Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, NYU School of Medicine, New York, NY, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, NYU School of Medicine, New York, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert D. Burk
- Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Departments of Microbiology & Immunology, and Obstetrics, Gynecology & Women’s Health, Albert Einstein College of Medicine, Bronx, NY, USA
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Dhariwal A, Haugli Bråten LC, Sturød K, Salvadori G, Bargheet A, Åmdal H, Junges R, Berild D, Zwart JA, Storheim K, Petersen FC. Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome. Gut Microbes 2023; 15:2157200. [PMID: 36576106 PMCID: PMC9809947 DOI: 10.1080/19490976.2022.2157200] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The collateral impact of antibiotics on the microbiome has attained increasing attention. However, the ecological consequences of long-term antibiotic exposure on the gut microbiome, including antibiotic resistance, are still limited. Here, we investigated long-term exposure effects to amoxicillin on the human gut microbiome and resistome. Fecal samples were collected from 20 patients receiving 3-months of amoxicillin or placebo treatment as part of a Norwegian multicenter clinical trial on chronic low back pain (AIM study). Samples were collected at baseline, last day of treatment, and 9 months after antibiotic cessation. The abundance and diversity of microbial and resistome composition were characterized using whole shotgun and functional metagenomic sequencing data. While the microbiome profiles of placebo subjects were stable over time, discernible changes in diversity and overall microbiome composition were observed after amoxicillin treatment. In particular, health-associated short-chain fatty acid producing species significantly decreased in proportion. However, these changes were short-lived as the microbiome showed overall recovery 9 months post-treatment. On the other hand, exposure to long-term amoxicillin was associated with an increase in total antimicrobial resistance gene load and diversity of antimicrobial resistance genes, with persistent changes even at 9 months post-treatment. Additionally, beta-lactam resistance was the most affected antibiotic class, suggesting a targeted response to amoxicillin, although changes at the gene level varied across individuals. Overall, our results suggest that the impact of prolonged amoxicillin exposure was more explicit and long-lasting in the fecal resistome than in microbiome composition. Such information is relevant for designing rational administration guidelines for antibiotic therapies.
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Affiliation(s)
- Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Lars Christian Haugli Bråten
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital HF, Oslo, Norway
| | - Kjersti Sturød
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Gabriela Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Ahmed Bargheet
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Heidi Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Dag Berild
- Department of Infectious Diseases, Oslo University Hospital HF, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - John-Anker Zwart
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital HF, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kjersti Storheim
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital HF, Oslo, Norway,Department of Physiotherapy, Faculty of Health Science, Oslo Metropolitan University, Oslo, Norway
| | - Fernanda Cristina Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway,CONTACT Fernanda Cristina Petersen Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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Huang MY, Wang WY, Liang ZZ, Huang YC, Yi Y, Niu FX. Enhancing the Production of Pinene in Escherichia coli by Using a Combination of Shotgun, Product-Tolerance and I-SceI Cleavage Systems. Biology (Basel) 2022; 11:biology11101484. [PMID: 36290388 PMCID: PMC9598909 DOI: 10.3390/biology11101484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/23/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022]
Abstract
Simple Summary The limit screening method (LMS method) and product-tolerance engineering was proposed and applied. AcrB, flgFG, motB and ndk were found to be associated with an enhanced tolerance of E. coli to pinene. Using the I-SceI cleavage system, the promoters of acrB, flgFG, and ndk genes were replaced with P37, and pinene production was eventually increased 2.1 times. In general, a combination of shotgun, product-tolerance, and I-SceI cleavage systems provides a more convenient and efficient way of enhancing the synthesis of target products in a host strain. Abstract Tolerance breeding through genetic engineering, sequence and omics analyses, and gene identification processes are widely used to synthesize biofuels. The majority of related mechanisms have been shown to yield endogenous genes with high expression. However, the process was time-consuming and labor-intensive, meaning there is a need to address the problems associated with the low-throughput screening method and significant time and money consumption. In this study, a combination of the limit screening method (LMS method) and product-tolerance engineering was proposed and applied. The Escherichia coli MG1655 genomic DNA library was constructed using the shotgun method. Then, the cultures were incubated at concentrations of 0.25%, 0.5%, 0.75% and 1.0% of pinene with different inhibitory effects. Finally, the genes acrB, flgFG, motB and ndk were found to be associated with the enhanced tolerance of E. coli to pinene. Using the I-SceI cleavage system, the promoters of acrB, flgFG and ndk genes were replaced with P37. The final strain increased the production of pinene from glucose by 2.1 times.
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Affiliation(s)
- Ming-Yue Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
- Department of Basic Medicine, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Wei-Yang Wang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Zhen-Zhen Liang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Yu-Chen Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
| | - Yi Yi
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
- Correspondence: (Y.Y.); (F.-X.N.)
| | - Fu-Xing Niu
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Liuzhou 545006, China
- Correspondence: (Y.Y.); (F.-X.N.)
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12
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Rubin IMC, Mollerup S, Broholm C, Baker A, Holm MKA, Pedersen MS, Pinholt M, Westh H, Petersen AM. Synbiotic Intervention with Lactobacilli, Bifidobacteria, and Inulin in Healthy Volunteers Increases the Abundance of Bifidobacteria but Does Not Alter Microbial Diversity. Appl Environ Microbiol 2022;:e0108722. [PMID: 36165644 DOI: 10.1128/aem.01087-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synbiotics combine probiotics and prebiotics and are being investigated for potential health benefits. In this single-group-design trial, we analyzed changes in the gut microbiome, stool quality, and gastrointestinal well-being in 15 healthy volunteers after a synbiotic intervention comprising Lacticaseibacillus rhamnosus (LGG), Lactobacillus acidophilus (LA-5), Lacticaseibacillus paracasei subsp. paracasei (L. CASEI 431), and Bifidobacterium animalis subsp. lactis BB-12 and 20 g of chicory-derived inulin powder consumed daily for 4 weeks. Fecal samples were collected at baseline and at completion of the intervention, and all participants completed a fecal diary based on the Bristol Stool Scale and recorded their gastrointestinal well-being. No adverse effects were observed after consumption of the synbiotic product, and stool consistency and frequency remained almost unchanged during the trial. Microbiome analysis of the fecal samples was achieved using shotgun sequencing followed by taxonomic profiling. No changes in alpha and beta diversity were seen after the intervention. Greater relative abundances of Bifidobacteriaceae were observed in 12 subjects, with indigenous bifidobacteria species constituting the main increase. All four probiotic organisms increased in abundance, and L. rhamnosus, B. animalis, and L. acidophilus were differentially abundant, compared to baseline. Comparison of the fecal strains to the B. animalis subsp. lactis BB-12 reference genome and the sequenced symbiotic product revealed only a few single-nucleotide polymorphisms differentiating the probiotic B. animalis subsp. lactis BB-12 from the fecal strains identified, indicating that this probiotic strain was detectable after the intervention. IMPORTANCE The effects of probiotics/synbiotics are seldom investigated in healthy volunteers; therefore, this study is important, especially considering the safety aspects of multiple probiotics together with prebiotic fiber in consumption by humans. The study explores at the potential of a synbiotic intervention with lactobacilli, bifidobacteria, and inulin in healthy volunteers and tracks the ingested probiotic strain B. animalis subsp. lactis.
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13
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Obón-Santacana M, Mas-Lloret J, Bars-Cortina D, Criado-Mesas L, Carreras-Torres R, Díez-Villanueva A, Moratalla-Navarro F, Guinó E, Ibáñez-Sanz G, Rodríguez-Alonso L, Mulet-Margalef N, Mata A, García-Rodríguez A, Duell EJ, Pimenoff VN, Moreno V. Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes. Cancers (Basel) 2022; 14:cancers14174214. [PMID: 36077748 PMCID: PMC9454621 DOI: 10.3390/cancers14174214] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/26/2022] [Accepted: 08/28/2022] [Indexed: 11/16/2022] Open
Abstract
The gut microbiome is a potential modifiable risk factor for colorectal cancer (CRC). We re-analyzed all eight previously published stool sequencing data and conducted an MWAS meta-analysis. We used cross-validated LASSO predictive models to identify a microbiome signature for predicting the risk of CRC and precancerous lesions. These models were validated in a new study, Colorectal Cancer Screening (COLSCREEN), including 156 participants that were recruited in a CRC screening context. The MWAS meta-analysis identified 95 bacterial species that were statistically significantly associated with CRC (FDR < 0.05). The LASSO CRC predictive model obtained an area under the receiver operating characteristic curve (aROC) of 0.81 (95%CI: 0.78−0.83) and the validation in the COLSCREEN dataset was 0.75 (95%CI: 0.66−0.84). This model selected a total of 32 species. The aROC of this CRC-trained model to predict precancerous lesions was 0.52 (95%CI: 0.41−0.63). We have identified a signature of 32 bacterial species that have a good predictive accuracy to identify CRC but not precancerous lesions, suggesting that the identified microbes that were enriched or depleted in CRC are merely a consequence of the tumor. Further studies should focus on CRC as well as precancerous lesions with the intent to implement a microbiome signature in CRC screening programs.
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Affiliation(s)
- Mireia Obón-Santacana
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Joan Mas-Lloret
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - David Bars-Cortina
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Lourdes Criado-Mesas
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Robert Carreras-Torres
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Digestive Diseases and Microbiota Group, Girona Biomedical Research Institute (IDIBGI), Salt, 17190 Girona, Spain
| | - Anna Díez-Villanueva
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Ferran Moratalla-Navarro
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain
| | - Elisabet Guinó
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Gemma Ibáñez-Sanz
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Gastroenterology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Lorena Rodríguez-Alonso
- Gastroenterology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Núria Mulet-Margalef
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08916 Badalona, Spain
- Badalona-Applied Research Group in Oncology, Catalan Institute of Oncology (ICO), 08916 Badalona, Spain
| | - Alfredo Mata
- Digestive System Service, Moisés Broggi Hospital, 08970 Sant Joan Despí, Spain
| | - Ana García-Rodríguez
- Endoscopy Unit, Digestive System Service, Viladecans Hospital-IDIBELL, 08840 Viladecans, Spain
| | - Eric J. Duell
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Ville Nikolai Pimenoff
- Department of Laboratory Medicine, Karolinska Institutet, 14186 Stockholm, Sweden
- Correspondence: (V.N.P.); (V.M.)
| | - Victor Moreno
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, 08007 Barcelona, Spain
- Correspondence: (V.N.P.); (V.M.)
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14
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Papadimitriou K, Anastasiou R, Georgalaki M, Bounenni R, Paximadaki A, Charmpi C, Alexandraki V, Kazou M, Tsakalidou E. Comparison of the Microbiome of Artisanal Homemade and Industrial Feta Cheese through Amplicon Sequencing and Shotgun Metagenomics. Microorganisms 2022; 10. [PMID: 35630516 DOI: 10.3390/microorganisms10051073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 01/21/2023] Open
Abstract
Feta is the most renowned protected designation of origin (PDO) white brined cheese produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on, among other factors, its overall microbial ecosystem. In this study, we employed 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing, as well as shotgun metagenomics, to investigate the microbiome of artisanal homemade and industrial Feta cheese samples from different regions of Greece, which has very rarely been investigated. 16S rDNA data suggested the prevalence of the Lactococcus genus in the homemade samples, while Streptococcus and Lactobacillus genera prevailed in the industrial control samples. Species identification deriving from shotgun metagenomics corroborated these findings, as Lactococcus lactis dominated two homemade samples while Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were found to be dominating one industrial sample. ITS data revealed a complex diversity of the yeast population among the samples analyzed. Debaryomyces, Kluyveromyces, Cutaneotrichosporon, Pichia, Candida, and Rhodotorula were the major genera identified, which were distributed in a rather arbitrary manner among the different samples. Furthermore, a number of potential metagenome-assembled genomes (MAGs) could be detected among assembled shotgun bins. The overall analysis of the shotgun metagenomics supported the presence of different foodborne pathogens in homemade samples (e.g., Staphylococcus aureus, Listeria monocytogenes, Enterobacter cloacae, and Streptococcus suis), but with low to very low abundances. Concluding, the combination of both amplicon sequencing and shotgun metagenomics allowed us to obtain an in-depth profile of the artisanal homemade Feta cheese microbiome.
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15
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Dinç M, Yalçın T, Çavuş İ, Özbilgin A. Comparative proteomic analysis of Leishmania parasites isolated from visceral and cutaneous leishmaniasis patients. Parasitology 2022; 149:298-305. [PMID: 34758895 PMCID: PMC11010476 DOI: 10.1017/s0031182021001967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/30/2021] [Accepted: 10/27/2021] [Indexed: 11/06/2022]
Abstract
Leishmaniasis is an infectious disease in which different clinical manifestations are classified into three primary forms: visceral, cutaneous and mucocutaneous. These disease forms are associated with parasite species of the protozoan genus Leishmania. For instance, Leishmania infantum and Leishmania tropica are typically linked with visceral (VL) and cutaneous (CL) leishmaniasis, respectively; however, these two species can also cause other form to a lesser extent. What is more alarming is this characteristic, which threatens current medical diagnosis and treatment, is started to be acquired by other species. Our purpose was to address this issue; therefore, gel-based and gel-free proteomic analyses were carried out on the species L. infantum to determine the proteins differentiating between the parasites caused VL and CL. In addition, L. tropica parasites representing the typical cases for CL were included. According to our results, electrophoresis gels of parasites caused to VL were distinguishable regarding the repetitive down-regulation on some specific locations. In addition, a distinct spot of an antioxidant enzyme, superoxide dismutase, was shown up only on the gels of CL samples regardless of the species. In the gel-free approach, 37 proteins that were verified with a second database search using a different search engine, were recognized from the comparison between VL and CL samples. Among them, 31 proteins for the CL group and six proteins for the VL group were determined differentially abundant. Two proteins from the gel-based analysis, pyruvate kinase and succinyl-coA:3-ketoacid-coenzyme A transferase analysis were encountered in the protein list of the CL group.
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Affiliation(s)
- Melike Dinç
- Izmir Institute of Technology, Integrated Research Centers, National Mass Spectrometry Application and Research Center, Izmir, Turkey
| | - Talat Yalçın
- Faculty of Science, Department of Chemistry, Izmir Institute of Technology, Izmir, Turkey
| | - İbrahim Çavuş
- Faculty of Medicine, Department of Parasitology, Manisa Celal Bayar University, Manisa, Turkey
| | - Ahmet Özbilgin
- Faculty of Medicine, Department of Parasitology, Manisa Celal Bayar University, Manisa, Turkey
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16
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Yan Y, Zhou B, Lee YJ, You S, Freeman MR, Yang W. BoxCar and shotgun proteomic analyses reveal molecular networks regulated by UBR5 in prostate cancer. Proteomics 2021; 22:e2100172. [PMID: 34897998 DOI: 10.1002/pmic.202100172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/12/2021] [Accepted: 12/07/2021] [Indexed: 11/08/2022]
Abstract
Prostate cancer (PC) is a major health and economic problem in industrialized countries, yet our understanding of the molecular mechanisms of PC progression and drug response remains limited. Accumulating evidence showed that certain E3 ubiquitin ligases such as SIAH2, RNF7, and SPOP play important roles in PC development and progression. However, the roles and mechanisms of other E3s in PC progression remain largely unexplored. Through an integration analysis of clinical genomic and transcriptomic profiles of PC tumors, this study identified UBR5 as a top PC-relevant E3 ubiquitin ligase whose expression levels are strongly associated with PC progression and aggressiveness. BoxCar and shotgun proteomic analyses of control and UBR5-knockdown PC3 cells complementarily identified 75 UBR5-regulated proteins. Bioinformatic analysis suggested that the 75 proteins form four molecular networks centered around FANCD2, PAF1, YY1, and LAMB3 via direct protein-protein interactions. Experimental analyses demonstrated that UBR5 associates with and downregulates two key DNA damage repair proteins (XRCC3 and FANCD2) and confers PC cell sensitivity to olaparib, a PARP inhibitor in clinical use for cancer therapy. This study represents the first application of BoxCar in PC research, provides new insights into the molecular functions of UBR5 in PC, and suggests that PC patients with UBR5-high tumors may potentially benefit from PARP inhibitor treatment.
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Affiliation(s)
- Yiwu Yan
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bo Zhou
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yeon-Joo Lee
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sungyong You
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael R Freeman
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Wei Yang
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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17
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Tarracchini C, Milani C, Longhi G, Fontana F, Mancabelli L, Pintus R, Lugli GA, Alessandri G, Anzalone R, Viappiani A, Turroni F, Mussap M, Dessì A, Cesare Marincola F, Noto A, De Magistris A, Vincent M, Bernasconi S, Picaud JC, Fanos V, Ventura M. Unraveling the Microbiome of Necrotizing Enterocolitis: Insights in Novel Microbial and Metabolomic Biomarkers. Microbiol Spectr 2021; 9:e0117621. [PMID: 34704805 DOI: 10.1128/Spectrum.01176-21] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Necrotizing enterocolitis (NEC) is among the most relevant gastrointestinal diseases affecting mostly prematurely born infants with low birth weight. While intestinal dysbiosis has been proposed as one of the possible factors involved in NEC pathogenesis, the role of the gut microbiota remains poorly understood. In this study, the gut microbiota of preterm infants was explored to highlight differences in the composition between infants affected by NEC and infants prior to NEC development. A large-scale gut microbiome analysis was performed, including 47 shotgun sequencing data sets generated in the framework of this study, along with 124 retrieved from publicly available repositories. Meta-analysis led to the identification of preterm community state types (PT-CSTs), which recur in healthy controls and NEC infants. Such analyses revealed an overgrowth of a range of opportunistic microbial species accompanying the loss of gut microbial biodiversity in NEC subjects. Moreover, longitudinal insights into preterm infants prior to NEC development indicated Clostridium neonatale and Clostridium perfringens species as potential biomarkers for predictive early diagnosis of this disease. Furthermore, functional investigation of the enzymatic reaction profiles associated with pre-NEC condition suggested DL-lactate as a putative metabolic biomarker for early detection of NEC onset. IMPORTANCE Necrotizing enterocolitis (NEC) is a severe gastrointestinal disease occurring predominantly in premature infants whose etiology is still not fully understood. In this study, the analysis of infant fecal samples through shotgun metagenomics approaches revealed a marked reduction of the intestinal (bio)diversity and an overgrowth of (opportunistic) pathogens associated with the NEC development. In particular, dissection of the infant’s gut microbiome before NEC diagnosis highlighted the potential involvement of Clostridium genus members in the progression of NEC. Remarkably, our analyses highlighted a gastrointestinal DL-lactate accumulation among NEC patients that might represent a novel potential functional biomarker for the early diagnosis of NEC.
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He Y, Zhou X, Li J, Li H, Li Y, Nie Y. In Vitro Secretome Analysis Suggests Differential Pathogenic Mechanisms between Fusarium oxysporum f. sp. cubense Race 1 and Race 4. Biomolecules 2021; 11:1353. [PMID: 34572566 PMCID: PMC8466104 DOI: 10.3390/biom11091353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
Banana Fusarium wilt, caused by the fungus pathogen Fusarium oxysporum f. sp. cubense (Foc), is a devastating disease that causes tremendous reductions in banana yield worldwide. Secreted proteins can act as pathogenicity factors and play important roles in the Foc-banana interactions. In this study, a shotgun-based proteomic approach was employed to characterize and compare the secretomes of Foc1 and Foc4 upon banana extract treatment, which detected 1183 Foc1 and 2450 Foc4 proteins. Comprehensive in silico analyses further identified 447 Foc1 and 433 Foc4 proteins in the classical and non-classical secretion pathways, while the remaining proteins might be secreted through currently unknown mechanisms. Further analyses showed that the secretomes of Foc1 and Foc4 are similar in their overall functional characteristics and share largely conserved repertoires of CAZymes and effectors. However, we also identified a number of potentially important pathogenicity factors that are differentially present in Foc1 and Foc4, which may contribute to their different pathogenicity against banana hosts. Furthermore, our quantitative PCR analysis revealed that genes encoding secreted pathogenicity factors differ significantly between Foc1 and Foc4 in their expression regulation in response to banana extract treatment. To our knowledge, this is the first experimental secretome analysis that focused on the pathogenicity mechanism in different Foc races. The results of this study provide useful resources for further exploration of the complicated pathogenicity mechanisms in Foc.
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Affiliation(s)
- Yanqiu He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Jieling Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Huaping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yunfeng Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; (Y.H.); (X.Z.); (J.L.); (H.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yanfang Nie
- College of Materials and Energy, South China Agricultural University, Guangzhou 510642, China
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19
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Multan M, Moore S, Forest-Allard É, Orde MM. Shotgun slug wads as a marker of range of fire: A case report and novel firearm testing data. J Forensic Sci 2021; 66:2521-2526. [PMID: 34309023 DOI: 10.1111/1556-4029.14814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/08/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022]
Abstract
Assessment of wound characteristics and the identification of various constituents of firearm discharge at autopsy play a key role in the determination of range of fire. In relation to wounds caused by shotguns, identification of the wad within the wound track, or of injury caused by the wad, is typically thought to suggest a fairly close range of fire. We present a case of a fatality due to a shotgun slug wound where the presence of the wad within the decedent's body was proposed by defense at criminal trial to favor accidental close range discharge during a struggle for the weapon-as opposed to the prosecution's contention of intentional firing of the weapon from a greater range and through an intermediate target. We undertook test firing of a shotgun of similar design to that which was fired during the interaction (a 12-gauge pump-action shotgun) using shotshells consistent with the slug that was recovered from the body (Winchester Super X brand), which demonstrated that the non-attached fiber wad present in this shotshell design can accompany the slug over distances of at least up to 22 feet (6.7 m) and even after transit through intermediate targets such as a vehicle headrest. These novel data provide assistance with estimation of range of fire in instances of injuries caused by shotgun slugs.
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Affiliation(s)
- Michael Multan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Shannon Moore
- Forensic Firearm and Toolmark Unit, Vancouver Police Department, Vancouver, BC, Canada
| | | | - Matthew M Orde
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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20
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Gelabert P, Sawyer S, Bergström A, Margaryan A, Collin TC, Meshveliani T, Belfer-Cohen A, Lordkipanidze D, Jakeli N, Matskevich Z, Bar-Oz G, Fernandes DM, Cheronet O, Özdoğan KT, Oberreiter V, Feeney RNM, Stahlschmidt MC, Skoglund P, Pinhasi R. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment. Curr Biol 2021; 31:3564-3574.e9. [PMID: 34256019 PMCID: PMC8409484 DOI: 10.1016/j.cub.2021.06.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/23/2021] [Accepted: 06/09/2021] [Indexed: 01/07/2023]
Abstract
Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ashot Margaryan
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas C Collin
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Tengiz Meshveliani
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Anna Belfer-Cohen
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Lordkipanidze
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Nino Jakeli
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Mareike C Stahlschmidt
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
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21
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Henriet C, Balliau T, Aimé D, Le Signor C, Kreplak J, Zivy M, Gallardo K, Vernoud V. Proteomics of developing pea seeds reveals a complex antioxidant network underlying the response to sulfur deficiency and water stress. J Exp Bot 2021; 72:2611-2626. [PMID: 33558872 DOI: 10.1093/jxb/eraa571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/19/2021] [Indexed: 05/17/2023]
Abstract
Pea is a legume crop producing protein-rich seeds and is increasingly in demand for human consumption and animal feed. The aim of this study was to explore the proteome of developing pea seeds at three key stages covering embryogenesis, the transition to seed-filling, and the beginning of storage-protein synthesis, and to investigate how the proteome was influenced by S deficiency and water stress, applied either separately or combined. Of the 3184 proteins quantified by shotgun proteomics, 2473 accumulated at particular stages, thus providing insights into the proteome dynamics at these stages. Differential analyses in response to the stresses and inference of a protein network using the whole proteomics dataset identified a cluster of antioxidant proteins (including a glutathione S-transferase, a methionine sulfoxide reductase, and a thioredoxin) possibly involved in maintaining redox homeostasis during early seed development and preventing cellular damage under stress conditions. Integration of the proteomics data with previously obtained transcriptomics data at the transition to seed-filling revealed the transcriptional events associated with the accumulation of the stress-regulated antioxidant proteins. This transcriptional defense response involves genes of sulfate homeostasis and assimilation, thus providing candidates for targeted studies aimed at dissecting the signaling cascade linking S metabolism to antioxidant processes in developing seeds.
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Affiliation(s)
- Charlotte Henriet
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Thierry Balliau
- Plateforme d'Analyse de Protéomique Paris Sud-Ouest (PAPPSO), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR Génétique Quantitative et Évolution-Le Moulon, Gif-sur-Yvette, France
| | - Delphine Aimé
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Le Signor
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Michel Zivy
- Plateforme d'Analyse de Protéomique Paris Sud-Ouest (PAPPSO), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR Génétique Quantitative et Évolution-Le Moulon, Gif-sur-Yvette, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Vanessa Vernoud
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
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22
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Sempéré G, Pétel A, Abbé M, Lefeuvre P, Roumagnac P, Mahé F, Baurens G, Filloux D. metaXplor: an interactive viral and microbial metagenomic data manager. Gigascience 2021; 10:6126034. [PMID: 33527143 PMCID: PMC7931823 DOI: 10.1093/gigascience/giab001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/13/2020] [Accepted: 01/10/2021] [Indexed: 12/02/2022] Open
Abstract
Background Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research. Results metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data. Conclusion metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.
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Affiliation(s)
- Guilhem Sempéré
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France.,South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France.,INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | - Adrien Pétel
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France
| | - Magsen Abbé
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France.,INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | | | - Philippe Roumagnac
- CIRAD, BGPI, 34398 Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Université de Montpellier, 34398 Montpellier, France
| | - Frédéric Mahé
- CIRAD, BGPI, 34398 Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Université de Montpellier, 34398 Montpellier, France
| | - Gaël Baurens
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France.,INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | - Denis Filloux
- CIRAD, BGPI, 34398 Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Université de Montpellier, 34398 Montpellier, France
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23
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Akçan R, Demircioglu D, Aydogan HC, Cavlak M, Erkan E, Demiray E, Mercan M, Rıza Tümer A. Ear as an alternative sampling site for GSR analysis following shotgun discharge. J Forensic Sci 2021; 66:1042-1047. [PMID: 33491186 DOI: 10.1111/1556-4029.14672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/16/2020] [Accepted: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Detection of GSR particles potentially indicates that a person fired a gun or somehow involved to a shooting event. GSR on the shooter's hand, face, and clothing may disappear within hours and with sweat secretion, washing or cleaning to remove evidences. Due to its anatomical properties, ears are relatively protected; therefore, we aimed to identify GSR particles on ears, to compare its anatomical parts of ears, and compare ears with common GSR sampling sites, based on firing frequency. A 12-gauge semi-automatic shotgun was used. In the 4-week study, one shot in the first week, two consecutive shots in second week, three shots in third week, and five shots in fourth week were fired by six participants. Samples were taken from MAE, CA, and AAECA of both ears and common GSR sampling sites. The characteristic 3-component structure (Pb/Sb/Ba) of the samples was analyzed by SEM/EDX. Right CA was the most suitable area for sampling, which might be attributed to posture of body during targeting. Right ear was the most suitable area to take samples from CA or MAE in 3-shot group. Besides, left AAECA in 1- and 2-shot groups and the left MAE in 5-shot group were the most suitable areas for GSR sampling. In conclusion, ear seems to be a valuable alternative for detection of GSR particles, due to its complex anatomical structure potentially preventing loss of GSR with daily cleaning. Findings suggested that crime scene investigation teams and criminal laboratory staff should consider ear as a valuable alternative for GSR detection.
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Affiliation(s)
- Ramazan Akçan
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Derya Demircioglu
- Department of Criminology, Ankara General Command of Gendarmerie, Ankara, Turkey
| | - Halit Canberk Aydogan
- Department of Forensic Medicine, Gülhane Training and Research Hospital, Ankara, Turkey
| | - Mehmet Cavlak
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Emre Erkan
- Department of Criminology, Ankara General Command of Gendarmerie, Ankara, Turkey
| | - Emirhan Demiray
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Mustafa Mercan
- Department of Criminology, Ankara General Command of Gendarmerie, Ankara, Turkey
| | - Ali Rıza Tümer
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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24
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Boscaini S, Cabrera‐Rubio R, Nychyk O, Roger Speakman J, Francis Cryan J, David Cotter P, Nilaweera KN. Age- and duration-dependent effects of whey protein on high-fat diet-induced changes in body weight, lipid metabolism, and gut microbiota in mice. Physiol Rep 2020; 8:e14523. [PMID: 32748559 PMCID: PMC7399378 DOI: 10.14814/phy2.14523] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023] Open
Abstract
Bovine whey protein has been demonstrated to exert a positive effect on energy balance, lipid metabolism, and nutrient absorption. Additionally, it affects gut microbiota configuration. Thus, whey protein is considered as good dietary candidate to prevent or ameliorate metabolic diseases, such as obesity. However, the relationship that links energy balance, metabolism, and intestinal microbial population mediated by whey protein intake remains poorly understood. In this study, we investigated the beneficial effects attributed to whey protein in the context of high-fat diet (HFD) in mice at two different ages, with short or longer durations of whey protein supplementation. Here, a 5-week dietary intervention with HFD in combination with either whey protein isolate (WPI) or the control nonwhey milk protein casein (CAS) was performed using 5-week or 10-week-old C57BL/6J mice. Notably, the younger mice had no prior history of ingestion of WPI, while older mice did. 5-week-old HFD-WPI-fed mice showed a decrease in weight gain and changes in the expression of genes within the epidydimal white adipose tissue including those encoding leptin, inflammatory marker CD68, fasting-induced adipose factor FIAF and enzymes involved in fatty acids catabolism, relative to HFD-CAS-fed mice. Differences in β-diversity and higher proportions of Lactobacillus murinus, and related functions, were evident within the gut microbiota of HFD-WPI mice. However, none of these changes were observed in mice that started the HFD dietary intervention at 10-weeks-old, with an extended period of WPI supplementation. These results suggest that the effect of whey protein on mouse body weight, adipose tissue, and intestinal parameters depends on diet duration and stage of life during which the diet is provided. In some instances, WPI influences gut microbiota composition and functional potential, which might orchestrate observed metabolic and physiological modifications.
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Affiliation(s)
- Serena Boscaini
- Food Biosciences DepartmentTeagasc Food Research Centre, MooreparkFermoyIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of Anatomy and NeuroscienceUniversity College CorkCorkIreland
| | - Raul Cabrera‐Rubio
- Food Biosciences DepartmentTeagasc Food Research Centre, MooreparkFermoyIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Oleksandr Nychyk
- Food Biosciences DepartmentTeagasc Food Research Centre, MooreparkFermoyIreland
| | - John Roger Speakman
- State Key Laboratory of Molecular Developmental BiologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- Institute of Biological and Environmental SciencesUniversity of AberdeenAberdeenScotland
| | - John Francis Cryan
- APC Microbiome IrelandUniversity College CorkCorkIreland
- Department of Anatomy and NeuroscienceUniversity College CorkCorkIreland
| | - Paul David Cotter
- Food Biosciences DepartmentTeagasc Food Research Centre, MooreparkFermoyIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
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25
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Kriek M, Monyai K, Magcwebeba TU, Du Plessis N, Stoychev SH, Tabb DL. Interrogating Fractionation and Other Sources of Variability in Shotgun Proteomes Using Quality Metrics. Proteomics 2020; 20:e1900382. [PMID: 32415754 DOI: 10.1002/pmic.201900382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/04/2020] [Indexed: 12/14/2022]
Abstract
The increasing amount of publicly available proteomics data creates opportunities for data scientists to investigate quality metrics in novel ways. QuaMeter IDFree is used to generate quality metrics from 665 RAW files and 97 WIFF files representing publicly available "shotgun" mass spectrometry datasets. These experiments are selected to represent Mycobacterium tuberculosis lysates, mouse MDSCs, and exosomes derived from human cell lines. Machine learning techniques are demonstrated to detect outliers within experiments and it is shown that quality metrics may be used to distinguish sources of variability among these experiments. In particular, the findings demonstrate that according to nested ANOVA performed on an SDS-PAGE shotgun principal component analysis, runs of fractions from the same gel regions cluster together rather than technical replicates, close temporal proximity, or even biological samples. This indicates that the individual fraction may have had a higher impact on the quality metrics than other factors. In addition, sample type, instrument type, mass analyzer, fragmentation technique, and digestion enzyme are identified as sources of variability. From a quality control perspective, the importance of study design and in particular, the run order, is illustrated in seeking ways to limit the impact of technical variability.
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Affiliation(s)
- Marina Kriek
- SATBBI (South African Tuberculosis Bioinformatics Initiative), Centre for Bioinformatics and Computational Biology, Stellenbosch University, Cape Town, 7505, South Africa.,DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, 7505, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Cape Town, 7505, South Africa.,Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 7505, South Africa
| | - Koena Monyai
- Council for Scientific and Industrial Research, Pretoria, 0001, South Africa
| | - Tandeka U Magcwebeba
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, 7505, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Cape Town, 7505, South Africa.,Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 7505, South Africa
| | - Nelita Du Plessis
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, 7505, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Cape Town, 7505, South Africa.,Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 7505, South Africa
| | - Stoyan H Stoychev
- Council for Scientific and Industrial Research, Pretoria, 0001, South Africa
| | - David L Tabb
- SATBBI (South African Tuberculosis Bioinformatics Initiative), Centre for Bioinformatics and Computational Biology, Stellenbosch University, Cape Town, 7505, South Africa.,DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Cape Town, 7505, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Cape Town, 7505, South Africa.,Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 7505, South Africa
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26
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Hlavaty L, Amley J, Root K, Avedschmidt S, Jaworski A, Sung L. The Difficulties in Assessing Wounds Created by .410 Bore Ammunition and Weapons. J Forensic Sci 2019; 65:500-507. [PMID: 31483496 DOI: 10.1111/1556-4029.14181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/28/2019] [Accepted: 08/14/2019] [Indexed: 11/30/2022]
Abstract
When interpreting firearm injuries, the distinction between gunshot wounds and shotgun wounds is important, and separation of these categories is typically straightforward. However, .410 bore firearms can make the classification difficult. Shotguns and revolvers that can fire the same .410 bore ammunition are readily available. This study investigates the soot and gunpowder deposits and pellet patterning of these two types of weapons using cartridges specially designed for .410 bore revolvers and standard birdshot pellet ammunition. For both ammunition types, the revolver had more prompt pellet dispersion and positive detection of gunpowder at greater distances compared to the shotgun. Additionally, .410 bore slugs are of similar caliber to many common bullets. In comparing the .410 bore slugs to equivalent bullets, some morphologic differences may be imparted on the skin by the slugs, but the greatest insight into the weapon remained with the retained projectiles.
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Affiliation(s)
- Leigh Hlavaty
- Wayne County Medical Examiner's Office, 1300 E. Warren Avenue, Detroit, MI.,Department of Pathology, University of Michigan, 1301 Catherine Street, Ann Arbor, MI
| | - Jeffery Amley
- Firearms and Toolmarks Identification Unit, Michigan State Police Forensic Laboratory, Lansing, MI
| | - Kelly Root
- Wayne County Medical Examiner's Office, 1300 E. Warren Avenue, Detroit, MI.,Department of Pathology, University of Michigan, 1301 Catherine Street, Ann Arbor, MI
| | - Sarah Avedschmidt
- Sacramento County Coroner's Office, 4800 Broadway Avenue, Sacramento, CA
| | - Andrea Jaworski
- Wayne County Medical Examiner's Office, 1300 E. Warren Avenue, Detroit, MI
| | - LokMan Sung
- Wayne County Medical Examiner's Office, 1300 E. Warren Avenue, Detroit, MI.,Department of Pathology, University of Michigan, 1301 Catherine Street, Ann Arbor, MI
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27
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Grützke J, Malorny B, Hammerl JA, Busch A, Tausch SH, Tomaso H, Deneke C. Fishing in the Soup - Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing. Front Microbiol 2019; 10:1805. [PMID: 31447815 PMCID: PMC6691356 DOI: 10.3389/fmicb.2019.01805] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/22/2019] [Indexed: 01/22/2023] Open
Abstract
In food safety the detection of food contaminations with pathogenic microorganisms is a race against time and often outpaced by error-prone epidemiological approaches. For evidence-based outbreak investigations fast and reliable techniques and procedures are required to identify the source of infection. Metagenomics has the potential to become a powerful tool in the field of modern food safety, since it allows the detection, identification and characterization of a broad range of pathogens in a single experiment without pre-cultivation within a couple of days. Nevertheless, sample handling, sequencing and data analysis are challenging and can introduce errors and biases into the analysis. In order to evaluate the potential of metagenomics in food safety, we generated a mock community containing DNA of foodborne bacteria. Herewith, we compare the aptitude of the two prevalent approaches - 16S rDNA amplicon sequencing and whole genome shotgun sequencing - for the detection of foodborne bacteria using different parameters during sample preparation, sequencing and data analysis. 16S rDNA sequencing did not only result in high deviations from the expected sample composition on genus and species level, but more importantly lacked the detection of several pathogenic species. While shotgun sequencing is more suitable for species detection, abundance estimation, genome assembly and species characterization, the performance can vary depending on the library preparation kit, which was confirmed for a naturally Francisella tularensis contaminated game meat sample. The application of the Nextera XT DNA Library Preparation Kit for shotgun sequencing did not only result in lower reference genome recovery and coverage, but also in distortions of the mock community composition. For data analysis, we propose a publicly available workflow for pathogen detection and characterization and demonstrate its benefits on the usability of metagenomic sequencing in food safety by analyzing an authentic metagenomic sample.
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Affiliation(s)
- Josephine Grützke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jens Andre Hammerl
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Anne Busch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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28
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Ilgisonis EV, Kopylov AT, Ponomarenko EA, Poverennaya EV, Tikhonova OV, Farafonova TE, Novikova S, Lisitsa AV, Zgoda VG, Archakov AI. Increased Sensitivity of Mass Spectrometry by Alkaline Two-Dimensional Liquid Chromatography: Deep Cover of the Human Proteome in Gene-Centric Mode. J Proteome Res 2018; 17:4258-4266. [PMID: 30354151 DOI: 10.1021/acs.jproteome.8b00754] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Currently, great interest is paid to the identification of "missing" proteins that have not been detected in any biological material at the protein level (PE1). In this paper, using the Universal Proteomic Standard sets 1 and 2 (UPS1 and UPS2, respectively) as an example, we characterized mass spectrometric approaches from the point of view of sensitivity (Sn), specificity (Sp), and accuracy (Ac). The aim of the paper was to show the utility of a mass spectra approach for protein detection. This sets consists of 48 high-purity human proteins without single aminoacid polymorphism (SAP) or post translational modification (PTM). The UPS1 set consists of the same 48 proteins at 5 pmols each, and in UPS2, proteins were grouped into 5 groups in accordance with their molar concentration, ranging from 10-11 to 10-6 M. Single peptides from the 92% and 96% of all sets of proteins could be detected in a pure solution of UPS2 and UPS1, respectively, by selected reaction monitoring with stable isotope-labeled standards (SRM-SIS). We also found that, in the presence of a biological matrix such as Escherichia coli extract or human blood plasma (HBP), SRM-SIS makes it possible to detect from 63% to 79% of proteins in the UPS2 set (sensitivity) with the highest specificity (∼100%) and an accuracy of 80% by increasing the sensitivity of shotgun and selected reaction monitoring combined with a stable-isotope-labeled peptide standard (SRM-SIS technology) by fractionating samples using reverse-phase liquid chromatography under alkaline conditions (2D-LC_alk). It is shown that this technique of sample fractionation allows the SRM-SIS to detect 98% of the single peptides from the proteins present in the pure solution of UPS2 (47 out of 48 proteins). When the extracts of E. coli or Pichia pastoris are added as biological matrixes to the UPS2, 46, and 45 out of 48 proteins (∼95%) can be detected, respectively, using the SRM-SIS combined with 2D-LC_alk. The combination of the 2D-LC_alk SRM-SIS and shotgun technologies allows us to increase the sensitivity up to 100% in the case of the proteins of the UPS2 set. The usage of that technology can be a solution for identifying the so-called "missing" proteins and, eventually, creating the deep proteome of a particular chromosome of tissue or organs. Experimental data have been deposited in the PeptideAtlas SRM Experiment Library with the dataset identifier PASS01192 and the PRIDE repository with the dataset identifier PXD007643.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Victor G Zgoda
- Institute of Biomedical Chemistry, RAS , Moscow , Russia
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Matthews C, Crispie F, Lewis E, Reid M, O’Toole PW, Cotter PD. The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency. Gut Microbes 2018; 10:115-132. [PMID: 30207838 PMCID: PMC6546327 DOI: 10.1080/19490976.2018.1505176] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Methane is generated in the foregut of all ruminant animals by the microorganisms present. Dietary manipulation is regarded as the most effective and most convenient way to reduce methane emissions (and in turn energy loss in the animal) and increase nitrogen utilization efficiency. This review examines the impact of diet on bovine rumen function and outlines what is known about the rumen microbiome. Our understanding of this area has increased significantly in recent years due to the application of omics technologies to determine microbial composition and functionality patterns in the rumen. This information can be combined with data on nutrition, rumen physiology, nitrogen excretion and/or methane emission to provide comprehensive insights into the relationship between rumen microbial activity, nitrogen utilisation efficiency and methane emission, with an ultimate view to the development of new and improved intervention strategies.
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Affiliation(s)
- Chloe Matthews
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland,Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland,Nutribio, Co. Cork,School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland,Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland,Nutribio, Co. Cork,School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Eva Lewis
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland,Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland,Nutribio, Co. Cork,School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Michael Reid
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland,Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland,Nutribio, Co. Cork,School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Paul W. O’Toole
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland,Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland,Nutribio, Co. Cork,School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Co. Cork, Ireland,Teagasc, Animal & Grassland Research and Innovation Centre, Co. Cork, Ireland, Ireland,Nutribio, Co. Cork,School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland,CONTACT Paul D. Cotter
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Affe HMDJ, Rigonato J, Nunes JMDC, Menezes M. Metagenomic Analysis of Cyanobacteria in an Oligotrophic Tropical Estuary, South Atlantic. Front Microbiol 2018; 9:1393. [PMID: 29997603 PMCID: PMC6029486 DOI: 10.3389/fmicb.2018.01393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 06/07/2018] [Indexed: 11/20/2022] Open
Abstract
This study assessed the species composition, distribution, and functional profiles of cyanobacteria in Camamu Bay, a tropical oligotrophic estuarine system on the northeast coast of Brazil, using shotgun metagenomic sequencing. Surface-water samples were evaluated in two different rainfall periods (rainy and dry seasons), at nine stations in the three hydrodynamic regions of the bay. At a fixed sampling station, on each season, samples were taken over a tidal cycle at 3-h intervals over 12 h. A total of 219 cyanobacterial taxa were identified, demonstrating a diverse community of freshwater, euryhaline, and marine cyanobacteria. The genera of greater relative abundance, Synechococcus and Prochlorococcus, corresponded to the picoplankton fraction. Although Camamu Bay has conspicuous marine characteristics, the contribution of freshwater during the rainy season caused variation in cyanobacteria community, with an increase in species richness. Due the high prevalence of Synechococcus (90% of the sequences), the functional analysis revealed only minor differences in gene content between the dry and rainy seasons. In both rainy and dry seasons, an increase in Prochlorococcus relative abundance occurred during high tide, demonstrating the tidal influence in the bay. The environmental characteristics of the bay provide niche conditions for a wide variety of cyanobacteria, including freshwater, euryhaline, and marine strains.
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Affiliation(s)
- Helen M de Jesus Affe
- Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Janaina Rigonato
- Centro de Energia Nuclear e Agricultura, Universidade de São Paulo, Piracicaba, Brazil.,CEA, Centre de Sequençage Genoscope, Institut de Biologie François Jacob, Evry, France
| | - José M de Castro Nunes
- Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Mariângela Menezes
- Laboratório de Ficologia, Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Brito MF, Auler PA, Tavares GC, Rezende CP, Almeida GMF, Pereira FL, Leal CAG, Moura ADA, Figueiredo HCP, Henry M. Label-free proteome of water buffalo (Bubalus bubalis) seminal plasma. Reprod Domest Anim 2018; 53:1243-1246. [PMID: 29888513 DOI: 10.1111/rda.13206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/04/2018] [Accepted: 04/11/2018] [Indexed: 11/30/2022]
Abstract
The study aimed to describe the Bubalus bubalis seminal plasma proteome using a label-free shotgun UDMSE approach. A total of 859 nonredundant proteins were identified across five biological replicates with stringent identification. Proteins specifically related to sperm maturation and protection, capacitation, fertilization and metabolic activity were detected in the buffalo seminal fluid. In conclusion, we provide a comprehensive proteomic profile of buffalo seminal plasma, which establishes a foundation for further studies designed to understand regulation of sperm function and discovery of novel biomarkers for fertility. MS data are available in the ProteomeXchange with identifier PXD003728.
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Affiliation(s)
- Mayara F Brito
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Patrícia A Auler
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme C Tavares
- AQUAVET - Laboratory of Aquatic Animal Diseases, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cristiana P Rezende
- AQUACEN - National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel M F Almeida
- AQUACEN - National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Felipe L Pereira
- AQUACEN - National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Carlos A G Leal
- AQUACEN - National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Henrique C P Figueiredo
- AQUACEN - National Reference Laboratory for Aquatic Animal Diseases, Ministry of Agriculture, Livestock and Food Supply, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marc Henry
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Bicalho MLS, Machado VS, Higgins CH, Lima FS, Bicalho RC. Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows. J Dairy Sci 2017; 100:3850-3862. [PMID: 28259404 DOI: 10.3168/jds.2016-12058] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/14/2017] [Indexed: 12/21/2022]
Abstract
Metritis is a uterine disease that affects 10 to 30% of all lactating dairy cows and has detrimental effects on reproductive performance, milk production, and survival. Data regarding the identity and abundance of bacterial genes governing traits such as virulence, antibiotic resistance, and stress responses could enable identification of previously unknown agents that play a role in metritis pathogenesis. Moreover, such knowledge could lead to the development of improved treatments or preventive methods. Therefore, the objectives of this study were to characterize the uterine microbial population and to differentiate, for the first time, the microbial functional diversity in cows with metritis versus healthy cows. In addition, we aimed to identify relationships between microbial genes and postpartum uterine health. Uterine swabs were collected from 24 cows within 3 to 12 d in milk; 12 cows were diagnosed with metritis and the other 12 were healthy. Metritis was defined as a watery, reddish or brownish uterine discharge having a fetid smell, and rectal temperature greater than 39.5°C. Cows with a clear and viscous uterine discharge, not fetid or mucopurulent, were classified as healthy. Microbial metagenomic DNA from uterine swab samples was subjected to whole-genome shotgun sequencing on the Illumina MiSeq platform (Illumina Inc., San Diego, CA). The MG-RAST server (metagenomic rapid annotations using subsystems technology; http://metagenomics.anl.gov/) and STAMP software (http://kiwi.cs.dal.ca/Software/STAMP) were used to detect statistically significant differences in the abundance of taxonomic and functional features between the uterine microbial metagenomes of metritic and healthy cows. Our results showed an increased abundance of Fusobacteria and Bacteroidetes in metritic cows, confirming the potential role of those 2 taxa in the pathogenesis of metritis. The MG-RAST analysis revealed a significantly higher abundance of genes for protein transport across the cytoplasmic membrane and type VI bacterial secretion systems in the metritic microbiota. Additionally, genes coding for resistance to acid stress were exclusive to the metritis microbiota, suggesting that microbial resistance to acid stress is important for microbial survival in the infected uterus. On the other hand, genes coding for adhesion molecules, bacteriocins, and antibacterial peptides were significantly associated with the uterine microbiota of healthy cows, as was tolerance to colicin E2.
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Affiliation(s)
- M L S Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - V S Machado
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - C H Higgins
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - F S Lima
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | - R C Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853.
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Wang GB, Zheng Q, Shen YW, Wu XF. Shotgun proteomic analysis of Bombyx mori brain: emphasis on regulation of behavior and development of the nervous system. Insect Sci 2016; 23:15-27. [PMID: 25504592 DOI: 10.1111/1744-7917.12195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/13/2014] [Indexed: 06/04/2023]
Abstract
The insect brain plays crucial roles in the regulation of growth and development and in all types of behavior. We used sodium dodecyl sulfate polyacrylamide gel electrophoresis and high-performance liquid chromatography - electron spray ionization tandem mass spectrometry (ESI-MS/MS) shotgun to identify the proteome of the silkworm brain, to investigate its protein composition and to understand their biological functions. A total of 2210 proteins with molecular weights in the range of 5.64-1539.82 kDa and isoelectric points in the range of 3.78-12.55 were identified. These proteins were annotated according to Gene Ontology Annotation into the categories of molecular function, biological process and cellular component. We characterized two categories of proteins: one includes behavior-related proteins involved in the regulation of behaviors, such as locomotion, reproduction and learning; the other consists of proteins related to the development or function of the nervous system. The identified proteins were classified into 283 different pathways according to KEGG analysis, including the PI3K-Akt signaling pathway which plays a crucial role in mediating survival signals in a wide range of neuronal cell types. This extensive protein profile provides a basis for further understanding of the physiological functions in the silkworm brain.
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Affiliation(s)
- Guo-Bao Wang
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Qin Zheng
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yun-Wang Shen
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Xiao-Feng Wu
- College of Animal Science, Zhejiang University, Hangzhou, China
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Coorssen JR, Yergey AL. Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses. Proteomes 2015; 3:440-53. [PMID: 28248279 DOI: 10.3390/proteomes3040440] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/21/2015] [Accepted: 11/26/2015] [Indexed: 11/17/2022] Open
Abstract
Molecular mechanisms underlying health and disease function at least in part based on the flexibility and fine-tuning afforded by protein isoforms and post-translational modifications. The ability to effectively and consistently resolve these protein species or proteoforms, as well as assess quantitative changes is therefore central to proteomic analyses. Here we discuss the pros and cons of currently available and developing analytical techniques from the perspective of the full spectrum of available tools and their current applications, emphasizing the concept of fitness-for-purpose in experimental design based on consideration of sample size and complexity; this necessarily also addresses analytical reproducibility and its variance. Data quality is considered the primary criterion, and we thus emphasize that the standards of Analytical Chemistry must apply throughout any proteomic analysis.
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Abstract
All current next-generation sequencing (NGS) platforms and applications require the sequencing library to have specific characteristics: in particular, size, size distribution, and 5' and 3' flanking sequences. This unit presents a robust protocol for converting a wide variety of input DNA samples into appropriate NGS libraries and discusses important considerations in experimental design, failure modes, and typical results.
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Affiliation(s)
- Jessica Podnar
- Genomic Sequencing and Analysis Facility, University of Texas at Austin, Austin, Texas
| | - Heather Deiderick
- Genomic Sequencing and Analysis Facility, University of Texas at Austin, Austin, Texas
| | - Scott Hunicke-Smith
- Genomic Sequencing and Analysis Facility, University of Texas at Austin, Austin, Texas
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Pedreschi R, Nørgaard J, Maquet A. Current challenges in detecting food allergens by shotgun and targeted proteomic approaches: a case study on traces of peanut allergens in baked cookies. Nutrients 2012; 4:132-50. [PMID: 22413066 DOI: 10.3390/nu4020132] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Revised: 02/08/2012] [Accepted: 02/13/2012] [Indexed: 11/16/2022] Open
Abstract
There is a need for selective and sensitive methods to detect the presence of food allergens at trace levels in highly processed food products. In this work, a combination of non-targeted and targeted proteomics approaches are used to illustrate the difficulties encountered in the detection of the major peanut allergens Ara h 1, Ara h 2 and Ara h 3 from a representative processed food matrix. Shotgun proteomics was employed for selection of the proteotypic peptides for targeted approaches via selective reaction monitoring. Peanut presence through detection of the proteotypic Ara h 3/4 peptides AHVQVVDSNGNR (m/z 432.5, 3+) and SPDIYNPQAGSLK (m/z 695.4, 2+) was confirmed and the developed method was able to detect peanut presence at trace levels (≥10 μg peanut g(-1) matrix) in baked cookies.
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Zmojdzian M, Da Ponte JP, Jagla K. Cellular components and signals required for the cardiac outflow tract assembly in Drosophila. Proc Natl Acad Sci U S A 2008; 105:2475-80. [PMID: 18250318 PMCID: PMC2268161 DOI: 10.1073/pnas.0706402105] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Indexed: 11/18/2022] Open
Abstract
Specification of cardiac primordia and formation of the Drosophila heart tube is highly reminiscent of the early steps of vertebrate heart development. We previously reported that the final morphogenesis of the Drosophila heart involves a group of nonmesodermal cells called heart-anchoring cells and a pair of derived from the pharyngeal mesoderm cardiac outflow muscles. Like the vertebrate cardiac neural crest cells, heart-anchoring cells migrate, interact with the tip of the heart, and participate in shaping the cardiac outflow tract. To better understand this process, we performed an in-depth analysis of how the Drosophila outflow tract is formed. We found that the most anterior cardioblasts that form a central outflow tract component, the funnel-shaped heart tip, do not originate from the cardiac primordium. They are initially associated with the pharyngeal cardiac outflow muscles and join the anterior aorta during outflow tract assembly. The particular morphology of the heart tip is disrupted in embryos in which heart-anchoring cells were ablated, revealing their critical role in outflow tract morphogenesis. We also demonstrate that Slit and Robo are required for directed movements of heart-anchoring cells toward the heart tip and that the cell-cell contact between the heart-anchoring cells and the ladybird-expressing cardioblasts is critically dependent on DE-cadherin Shotgun. Our observations suggest that the similarities between Drosophila and vertebrate cardiogenesis extend beyond the early developmental events.
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Affiliation(s)
- Monika Zmojdzian
- Unité Mixte de Recherche, Centre National de la Recherche Scientifique 6247-GreD, Clermont–Ferrand University, Institut National de la Santé et de la Recherche Médicale Clermont–Ferrand, 28 Place Henri Dunant, F-63000 Clermont–Ferrand, France
| | - Jean Philippe Da Ponte
- Unité Mixte de Recherche, Centre National de la Recherche Scientifique 6247-GreD, Clermont–Ferrand University, Institut National de la Santé et de la Recherche Médicale Clermont–Ferrand, 28 Place Henri Dunant, F-63000 Clermont–Ferrand, France
| | - Krzysztof Jagla
- Unité Mixte de Recherche, Centre National de la Recherche Scientifique 6247-GreD, Clermont–Ferrand University, Institut National de la Santé et de la Recherche Médicale Clermont–Ferrand, 28 Place Henri Dunant, F-63000 Clermont–Ferrand, France
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