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Ma W, An B, Xu X, Huo M, Mi K, Tian X, Kou Z, Tang A, Cheng G, Huang L. Ceftiofur in swine manure contributes to reducing pathogens and antibiotic resistance genes during composting. ENVIRONMENTAL RESEARCH 2024; 252:119033. [PMID: 38685300 DOI: 10.1016/j.envres.2024.119033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 03/14/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Aerobic composting is a common way for the disposal of feces produced in animal husbandry, and can reduce the release of antibiotic resistance genes (ARGs) from feces into the environment. In this study, we collected samples from two distinct treatments of swine manure compost with and without ceftiofur (CEF), and identified the ARGs, mobile genetic elements (MGEs), and bacterial community by metagenomic sequencing. The impacts of CEF on the bacterial community composition and fate of ARGs and MGEs were investigated. With increasing composting temperature and pH, the concentration of CEF in the manure decreased rapidly, with a degradation half-life of 1.12 d and a 100% removal rate after 10 d of aerobic composting. Metagenomics demonstrated that CEF in the manure might inhibit the growth of Firmicutes and Proteobacteria, thereby reducing some ARGs and MGEs hosted by these two bacteria, which was further confirmed by the variations of ARGs and MGEs. A further redundancy analysis suggested that pH and temperature are key environmental factors affecting ARG removal during composting, and intI1 and bacterial communities also have significant influence on ARG abundance. These results are of great significance for promoting the removal of some ARGs from animal manure by controlling some key environmental factors and the type of antibiotics used in animals.
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Affiliation(s)
- Wenjin Ma
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Boyu An
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiangyue Xu
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Meixia Huo
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Kun Mi
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiaoyuan Tian
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Ziyan Kou
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Aoran Tang
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Guyue Cheng
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China.
| | - Lingli Huang
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China.
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Achudhan AB, Kannan P, Gupta A, Saleena LM. A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data. Biochem Genet 2024; 62:621-632. [PMID: 37507643 DOI: 10.1007/s10528-023-10467-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
Metagenomics has now evolved as a promising technology for understanding the microbial population in the environment. By metagenomics, a number of extreme and complex environment has been explored for their microbial population. Using this technology, researchers have brought out novel genes and their potential characteristics, which have robust applications in food, pharmaceutical, scientific research, and other biotechnological fields. A sequencing platform can provide a sequence of microbial populations in any given environment. The sequence needs to be analysed computationally to derive meaningful information. It is presumed that only bioinformaticians with extensive computational skills can process the sequencing data till the downstream end. However, numerous open-source software and online servers are available to analyse the metagenomic data developed for a biologist with less computational skills. This review is focused on bioinformatics tools such as Galaxy, CSI-NGS portal, ANASTASIA and SHAMAN, EBI- metagenomics, IDseq, and MG-RAST for analysing metagenomic data.
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Affiliation(s)
- Arunmozhi Bharathi Achudhan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Priya Kannan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Annapurna Gupta
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Lilly M Saleena
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India.
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Raghav N, Saraswat P, Kumar S, Chaurasia A, Ranjan R. Metagenomics analysis of water samples collected from the Yamuna River of Agra city, India. World J Microbiol Biotechnol 2024; 40:113. [PMID: 38418624 DOI: 10.1007/s11274-024-03919-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Yamuna River water in Agra city of India is contaminated with toxic pollutants, including heavy metals that cause damage to the environment and human health. At present, the direct use of river water for drinking purposes and household activities lead to the direct exposure of society to the contaminants. In this study, Yamuna River water samples were collected from three different sites in Agra city during the monsoon, summer, and winter seasons. The physico-chemical parameters were estimated along with heavy metals. In physico-chemical parameter, the values found were mostly above the permissible limits. The results water samples contain high levels of cadmium, chromium, lead, and nickel above the desirable levels in most cases. The metagenomic analysis revealed that Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctobacteria were the most abundant phyla with a relative abundance of 61%, 9.34%, 5.23%, 4.64%, and 4.3%, respectively. The Comamonadaceae, the most abundant family consists of the genera involved in hydrogen oxidation, iron reduction, degraders of polycyclic aromatic hydrocarbons, and fermentation. The presence of Pseudomonas, Nitrosomonas sp., Thauera humireducens and Dechloromonas denitrificans (decomposition of sewage and organic matter) and Pseudomonas aeruginosa indicates the presence of heavy metal degrading bacteria in water sample. Functional prediction showed the presence of genes responsible for different metabolic pathways that could help developing new bioremediation strategies. The study concludes the status of water contamination, the presence of complex microbial community and suggests the futuristic use and their role in bioremediation.
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Affiliation(s)
- Nupur Raghav
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Pooja Saraswat
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Sunil Kumar
- Division of Agriculture Bioinformatics, Indian Agricultural Statistical Research Institute, Pusa, New Delhi, 110012, India
| | - Anurag Chaurasia
- Division of Crop Protection, ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, 221305, India.
| | - Rajiv Ranjan
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India.
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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Bambaradeniya TB, Magni PA, Dadour IR. A Summary of Concepts, Procedures and Techniques Used by Forensic Entomologists and Proxies. INSECTS 2023; 14:536. [PMID: 37367352 DOI: 10.3390/insects14060536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023]
Abstract
Forensic entomology is a branch of forensic science that incorporates insects as a part of solving crime. Insect-based evidence recovered at a crime scene can be used to estimate the minimum postmortem interval, determine if a carcass/corpse has been relocated, and contribute to the cause and manner of death. The current review summarises the stepwise usage of forensic entomology methods at a crime scene and in the laboratory, including specimen collection and rearing, identification, xenobiotic detection, documentation, and referencing previous research and casework. It also provides three standards for the collection of insects when attending a crime scene. The Gold standard attributes to a forensic entomologist (FE) who is likely to be well-trained attending a scene. The subsequent standards (Silver and Bronze) have been added because the authors believe that this information is currently missing in the literature. The purpose is so that an attending crime scene agent/proxy with some basic knowledge and some simple tools can recover almost all the insect information required by an FE to make the best estimation of the minimum postmortem interval.
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Affiliation(s)
- Tharindu B Bambaradeniya
- School of Medical, Molecular & Forensic Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Paola A Magni
- School of Medical, Molecular & Forensic Sciences, Murdoch University, Murdoch, WA 6150, Australia
- Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Ian R Dadour
- School of Medical, Molecular & Forensic Sciences, Murdoch University, Murdoch, WA 6150, Australia
- Source Certain, P.O. Box 1570, Wangara, WA 6947, Australia
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Dai R, Wu H, Liu G, Shen L, Geng Y, Zhang S, Zhou H, Jiang C, Gong J, Fan X, Ji C. Investigation of bacterial and fungal population structure on environmental surfaces of three medical institutions during the COVID-19 pandemic. Front Microbiol 2023; 14:1089474. [PMID: 36970696 PMCID: PMC10033641 DOI: 10.3389/fmicb.2023.1089474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/15/2023] [Indexed: 03/11/2023] Open
Abstract
ObjectivesTo evaluate the population structure of environmental bacteria and fungi in three different types of medical institutions and the potential risks due to antibiotic resistance during the coronavirus disease 2019 (COVID-19) pandemic.MethodsOne hundred twenty-six environmental surface samples were collected from three medical institutions during the COVID-19 pandemic. A total of 6,093 and 13,514 representative sequences of 16S and ITS ribosomal RNA (rRNA) were obtained by amplicon sequencing analysis. The functional prediction was performed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States tool based on the Greengenes database and the FAPROTAX database.ResultsOn environmental surfaces in three medical institutions during the COVID-19 pandemic, Firmicutes (51.6%) and Bacteroidetes (25%) were the dominant bacteria, while Ascomycota (39.4%) and Basidiomycota (14.2%) were the dominant fungi. A number of potential bacterial and fungal pathogens were successfully identified by the metagenomic approach. Furthermore, compared with the bacterial results, the fungi showed a generally closer Bray Curtis distance between samples. The overall ratio of Gram-negative bacteria to Gram-positive bacteria was about 3:7. The proportion of stress-tolerant bacteria in medical institutions A, B and C reached 88.9, 93.0 and 93.8%, respectively. Anaerobic bacteria accounted for 39.6% in outdoor environments, 77.7% in public areas, 87.9% in inpatient areas and 79.6% in restricted areas. Finally, the β-Lactam resistance pathway and polymyxin resistance pathway were revealed through functional prediction.ConclusionWe described the microbial population structure changes in three different types of medical institutions using the metagenomic approach during the COVID-19 pandemic. We found that the disinfection measures performed by three healthcare facilities may be effective on the “ESKAPE” pathogens, but less effective on fungal pathogens. Moreover, emphasis should be given to the prevention and control of β-lactam and polymyxin antibiotics resistance bacteria during the COVID-19 pandemic.
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Affiliation(s)
- Rongchen Dai
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Hanting Wu
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Linlai Shen
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuanyuan Geng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Shu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Haijian Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Canran Jiang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jie Gong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xin Fan
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- *Correspondence: Xin Fan, ; Conghua Ji,
| | - Conghua Ji
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- *Correspondence: Xin Fan, ; Conghua Ji,
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Athanasopoulou K, Adamopoulos PG, Scorilas A. Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics. Biomedicines 2023; 11:biomedicines11030827. [PMID: 36979806 PMCID: PMC10045138 DOI: 10.3390/biomedicines11030827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/26/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Over 1014 symbiotic microorganisms are present in a healthy human body and are responsible for the synthesis of vital vitamins and amino acids, mediating cellular pathways and supporting immunity. However, the deregulation of microbial dynamics can provoke diverse human diseases such as diabetes, human cancers, cardiovascular diseases, and neurological disorders. The human gastrointestinal tract constitutes a hospitable environment in which a plethora of microbes, including diverse species of archaea, bacteria, fungi, and microeukaryotes as well as viruses, inhabit. In particular, the gut microbiome is the largest microbiome community in the human body and has drawn for decades the attention of scientists for its significance in medical microbiology. Revolutions in sequencing techniques, including 16S rRNA and ITS amplicon sequencing and whole genome sequencing, facilitate the detection of microbiomes and have opened new vistas in the study of human microbiota. Especially, the flourishing fields of metagenomics and metatranscriptomics aim to detect all genomes and transcriptomes that are retrieved from environmental and human samples. The present review highlights the complexity of the gastrointestinal tract microbiome and deciphers its implication not only in cellular homeostasis but also in human diseases. Finally, a thorough description of the widely used microbiome detection methods is discussed.
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Affiliation(s)
- Konstantina Athanasopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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The Role of Quorum Sensing Molecules in Bacterial-Plant Interactions. Metabolites 2023; 13:metabo13010114. [PMID: 36677039 PMCID: PMC9863971 DOI: 10.3390/metabo13010114] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Quorum sensing (QS) is a system of communication of bacterial cells by means of chemical signals called autoinducers, which modulate the behavior of entire populations of Gram-negative and Gram-positive bacteria. Three classes of signaling molecules have been recognized, Al-1, Al-2, Al-3, whose functions are slightly different. However, the phenomenon of quorum sensing is not only concerned with the interactions between bacteria, but the whole spectrum of interspecies interactions. A growing number of research results confirm the important role of QS molecules in the growth stimulation and defense responses in plants. Although many of the details concerning the signaling metabolites of the rhizosphere microflora and plant host are still unknown, Al-1 compounds should be considered as important components of bacterial-plant interactions, leading to the stimulation of plant growth and the biological control of phytopathogens. The use of class 1 autoinducers in plants to induce beneficial activity may be a practical solution to improve plant productivity under field conditions. In addition, researchers are also interested in tools that offer the possibility of regulating the activity of autoinducers by means of degrading enzymes or specific inhibitors (QSI). Current knowledge of QS and QSI provides an excellent foundation for the application of research to biopreparations in agriculture, containing a consortia of AHL-producing bacteria and QS inhibitors and limiting the growth of phytopathogenic organisms.
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Naumova NB, Kabilov MR. About the Biodiversity of the Air Microbiome. Acta Naturae 2022; 14:50-56. [PMID: 36694900 PMCID: PMC9844089 DOI: 10.32607/actanaturae.11671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 10/27/2022] [Indexed: 01/22/2023] Open
Abstract
This brief review focuses on the properties of bioaerosols, presenting some recent results of metagenomic studies of the air microbiome performed using next-generation sequencing. The taxonomic composition and structure of the bioaerosol microbiome may display diurnal and seasonal dynamics and be dependent on meteorological events such as dust storms, showers, fogs, etc., as well as air pollution. The Proteobacteria and Ascomycota members are common dominants in bioaerosols in different troposphere layers. The microbiological composition of the lower troposphere air affects the composition and diversity of the indoor bioaerosol microbiome, and information about the latter is very important, especially during exacerbated epidemiological situations. Few studies focusing on the bioaerosol microbiome of the air above Russia urge intensification of such research.
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Affiliation(s)
- N. B. Naumova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
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Shaaban MT, Abdelhamid RM, Zayed M, Ali SM. Evaluation of a new antimicrobial agent production (RSMM C3) by using metagenomics approaches from Egyptian marine biota. BIOTECHNOLOGY REPORTS 2022; 34:e00706. [PMID: 35686002 PMCID: PMC9171440 DOI: 10.1016/j.btre.2022.e00706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 11/24/2022]
Abstract
Metagenomics technique has the ability for production of novel antimicrobial agents. Marine sediment samples from Alexandria used as a source for production of novel antimicrobial agents. Activity of the RSMM C3 antimicrobial agent was a wide spectrum towards different microorganisms. Molecular analysis and characterization of RSMM C3 antimicrobial agent ensure novelty.
Diseases and epidemics in the current days need new types of antibiotics in order to be able to eliminate them. The goal of this research is to use metagenomics to identify isolated utilitarian gene (s) as antimicrobial specialists. Collection of diverse locations from sea sediment samples from Alexandria and extraction of total DNA, restriction enzyme fragmentation, cloning into pUC19 vector, and expression of the isolated gene(s) in E. coli DH5α were all part of the process. Characterization of Antimicrobial agent was done for the best clone for antimicrobial agent's production to detect efficiency, optimum pH, thermal stability, pH stability, effect of different compounds on antimicrobial activity, and residual activity of product after preservation in room temperature. Amino acid sequence of RSMM C3 gene (1250 bp) was 72% identity with Herbaspirillum sp. The ideal temperature level of the RSMM C3 antimicrobial agent production was 36 °C. The antimicrobial agent RSMM C3′s stability was stable at -20 °Celsius for up to two months without thawing. The antibacterial agent RSMM C3 was stable at 4 °C for 14 days without loss in activity. The ideal pH level of the RSMM C3 antimicrobial agent was 6. Remain activity was gradually decreased at pH 5, 6, 6.5 and 7 (86.1, 96.9, 97.2 and 94.9%, respectively). On the other hand, residual activity was (92 and 84%) at (pH 7.5 and 8) for 8 days. The tested antimicrobial RSMM C3 was stable against 1 mM of different compounds (DMSO, Glycerol, NaCl, CaCl2, MgCl2, ZnCl2, FeSO4, MnSO4 and CuSO4). The research provides for the Metagenomics technique that has the ability for the production of novel antimicrobial agents produced by clone RSMM C3 which has a wide spectrum activity towards different microorganisms comparing to other antibiotics as Ampicillin and Tetracycline.
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Affiliation(s)
- Mohamed T Shaaban
- Botany and Microbiology Department, Menoufia University, Shebin El-Kom, Egypt
| | - Reham M Abdelhamid
- Botany and Microbiology Department, Menoufia University, Shebin El-Kom, Egypt
- Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, Alexandria, Egypt
| | - Muhammad Zayed
- Botany and Microbiology Department, Menoufia University, Shebin El-Kom, Egypt
| | - Safaa M Ali
- Department of Nucleic Acid Research, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications, Alexandria, Egypt
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Hoang MTV, Irinyi L, Hu Y, Schwessinger B, Meyer W. Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections. Front Microbiol 2022; 12:708550. [PMID: 35069461 PMCID: PMC8770865 DOI: 10.3389/fmicb.2021.708550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of the causative infectious agent is essential in the management of infectious diseases, with the ideal diagnostic method being rapid, accurate, and informative, while remaining cost-effective. Traditional diagnostic techniques rely on culturing and cell propagation to isolate and identify the causative pathogen. These techniques are limited by the ability and the time required to grow or propagate an agent in vitro and the facts that identification based on morphological traits are non-specific, insensitive, and reliant on technical expertise. The evolution of next-generation sequencing has revolutionized genomic studies to generate more data at a cheaper cost. These are divided into short- and long-read sequencing technologies, depending on the length of reads generated during sequencing runs. Long-read sequencing also called third-generation sequencing emerged commercially through the instruments released by Pacific Biosciences and Oxford Nanopore Technologies, although relying on different sequencing chemistries, with the first one being more accurate both platforms can generate ultra-long sequence reads. Long-read sequencing is capable of entirely spanning previously established genomic identification regions or potentially small whole genomes, drastically improving the accuracy of the identification of pathogens directly from clinical samples. Long-read sequencing may also provide additional important clinical information, such as antimicrobial resistance profiles and epidemiological data from a single sequencing run. While initial applications of long-read sequencing in clinical diagnosis showed that it could be a promising diagnostic technique, it also has highlighted the need for further optimization. In this review, we show the potential long-read sequencing has in clinical diagnosis of fungal infections and discuss the pros and cons of its implementation.
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Affiliation(s)
- Minh Thuy Vi Hoang
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
| | - Yiheng Hu
- Research School of Biology, Australia National University, Canberra, ACT, Australia
| | | | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Westmead, NSW, Australia
- Sydney Infectious Disease Institute, The University of Sydney, Sydney, NSW, Australia
- Westmead Hospital (Research and Education Network), Westmead, NSW, Australia
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12
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Mining marine metagenomes revealed a quorum-quenching lactonase with improved biochemical properties that inhibits the food spoilage bacteria Pseudomonas fluorescens. Appl Environ Microbiol 2021; 88:e0168021. [PMID: 34910563 DOI: 10.1128/aem.01680-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The marine environment presents great potential as a source of microorganisms that possess novel enzymes with unique activities and biochemical properties. Examples of such are the quorum-quenching (QQ) enzymes that hydrolyze bacterial quorum-sensing (QS) signaling molecules, such as N-acyl-homoserine lactones (AHLs). QS is a form of cell-to-cell communication that enables bacteria to synchronize gene expression in correlation with population density. Searching marine metagenomes for sequences homologous to an AHL lactonase from the phosphotriesterase-like lactonase (PLL) family, we identified new putative AHL lactonases (sharing 30-40% amino acid identity to a thermostable PLL member). Phylogenetic analysis indicated that these putative AHL lactonases comprise a new clade of marine enzymes in the PLL family. Following recombinant expression and purification, we verified the AHL lactonase activity for one of these proteins, named marine originated Lactonase Related Protein (moLRP). This enzyme presented greater activity and stability at a broad range of temperatures and pH, and tolerance to high salinity levels (up to 5M NaCl), as well as higher durability in bacterial culture, compared to another PLL member. The addition of purified moLRP to cultures of Pseudomonas fluorescens inhibited its extracellular protease activity, expression of the protease encoding gene, biofilm formation, and the sedimentation process in milk-based medium. These findings suggest that moLRP is adapted to the marine environment, and can potentially serve as an effective QQ enzyme, inhibiting the QS process in gram-negative bacteria involved in food spoilage. Importance Our results emphasize the potential of sequence and structure-based identification of new quorum-quenching (QQ) enzymes from environmental metagenomes, such as from the ocean, with improved stability or activity. The findings also suggest that purified QQ enzymes can present new strategies against food spoilage, in addition to their recognized involvement in inhibiting bacterial pathogen virulence factors. Future studies on the delivery and safety of enzymatic QQ strategy against bacterial food spoilage should be performed.
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13
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Kitsou K, Iliopoulou M, Spoulou V, Lagiou P, Magiorkinis G. Viral Causality of Human Cancer and Potential Roles of Human Endogenous Retroviruses in the Multi-Omics Era: An Evolutionary Epidemiology Review. Front Oncol 2021; 11:687631. [PMID: 34778024 PMCID: PMC8586426 DOI: 10.3389/fonc.2021.687631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Being responsible for almost 12% of cancers worldwide, viruses are among the oldest known and most prevalent oncogenic agents. The quality of the evidence for the in vivo tumorigenic potential of microorganisms varies, thus accordingly, viruses were classified in 4 evidence-based categories by the International Agency for Research on Cancer in 2009. Since then, our understanding of the role of viruses in cancer has significantly improved, firstly due to the emergence of high throughput sequencing technologies that allowed the “brute-force” recovery of unknown viral genomes. At the same time, multi-omics approaches unravelled novel virus-host interactions in stem-cell biology. We now know that viral elements, either exogenous or endogenous, have multiple sometimes conflicting roles in human pathophysiology and the development of cancer. Here we integrate emerging evidence on viral causality in human cancer from basic mechanisms to clinical studies. We analyze viral tumorigenesis under the scope of deep-in-time human-virus evolutionary relationships and critically comment on the evidence through the eyes of clinical epidemiology, firstly by reviewing recognized oncoviruses and their mechanisms of inducing tumorigenesis, and then by examining the potential role of integrated viruses in our genome in the process of carcinogenesis.
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Affiliation(s)
- Konstantina Kitsou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Iliopoulou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Vana Spoulou
- Immunobiology and Vaccinology Research Laboratory, First Department of Peadiatrics, "Aghia Sophia" Children's Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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14
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Bovine Milk Microbiota: Comparison among Three Different DNA Extraction Protocols To Identify a Better Approach for Bacterial Analysis. Microbiol Spectr 2021; 9:e0037421. [PMID: 34550002 PMCID: PMC8557886 DOI: 10.1128/spectrum.00374-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The bovine udder is colonized by a huge quantity of microorganisms that constitute the intramammary ecosystem, with a specific role in modulating not only udder homeostasis and mastitis susceptibility, but also the quality of the dairy products. However, generating high-quality bacterial DNA can be critical, especially starting from a complex biological matrix like milk, characterized by high fat, protein, and calcium contents. Here, bacterial DNA was recovered from a commercial ultra-high-temperature (UHT) milk sample artificially spiked with a predetermined mock community composition and from three bulk tank milk (raw milk) samples. The DNA was isolated using three different protocols to evaluate the effect of the extraction procedures on the milk microbiota composition. In the mock community experiment, the bacterial profiles generated by the three DNA extraction protocols were profoundly different, with the genera Staphylococcus, Lactobacillus, Listeria, and Salmonella underestimated by all the protocols. Only one protocol revealed values close to the expected abundances for Escherichia/Shigella spp., Bacillus spp., Enterococcus spp., and Pseudomonas spp. On the other hand, the nonspiked UHT milk sample exhibited a similar microbiota composition, revealing the prevalence of Acinetobacter spp., for all the DNA extraction protocols. For the raw milk samples, the three DNA extraction kits performed differently, revealing significant separations in both the microbial richness (alpha diversity) and composition (beta diversity). Our study highlights the presence of significant differences among these procedures, probably due to the different DNA extracting capacities and to the different properties of the milk samples, revealing that the selection of DNA extraction protocol is a critical point. IMPORTANCE The advance of high-throughput technologies has increased our knowledge of the world of microorganisms, especially of microbial populations inhabiting living animals. This study provides evidence that milk, as other complex sources, could be critical for generating high-quality DNA for microbiota analysis. In addition, it demonstrates that the microbial population highlighted by metagenomic studies changes in relation to different DNA extraction procedures, revealing that attention should be paid especially when comparing different studies.
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15
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Batlles-delaFuente A, Belmonte-Ureña LJ, Plaza-Úbeda JA, Abad-Segura E. Sustainable Business Model in the Product-Service System: Analysis of Global Research and Associated EU Legislation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph181910123. [PMID: 34639425 PMCID: PMC8508610 DOI: 10.3390/ijerph181910123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022]
Abstract
The business fabric is trying to resolve the many transformations that have occurred in recent decades. Companies are obliged to offer new ways to meet the needs of the market. This situation has led to the creation of new business models that combine both competitiveness and sustainability. Among the most consistent strategies, the product-service system (PSS) stands out. A bibliometric analysis was carried out on 1088 documents during the period 2000–2020, to synthesize the knowledge base on PSS in a global context and analyse future trends. The results obtained have made it possible to identify the evolution of scientific production, the main drivers of this issue, the lines of research developed and their link with EU legislation and reveal some critical gaps in knowledge. The main lines of research describe different aspects of PSS: servitisation, product design, manufacturing, life cycle, circular economy, and sustainable development. This study has identified how its analysis has developed to date and what terms allow us to glimpse new approaches; hence, it is a useful tool for PSS researchers and sponsors who provide financial resources that allow new directions in this research.
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Affiliation(s)
- Ana Batlles-delaFuente
- Department of Economy and Business, University of Almeria, 04120 Almeria, Spain; (A.B.-d.); (L.J.B.-U.); (J.A.P.-Ú.)
- Research Centre CIAMBITAL, University of Almeria, 04120 Almeria, Spain
| | - Luis Jesús Belmonte-Ureña
- Department of Economy and Business, University of Almeria, 04120 Almeria, Spain; (A.B.-d.); (L.J.B.-U.); (J.A.P.-Ú.)
- Research Centre CIAMBITAL, University of Almeria, 04120 Almeria, Spain
| | - José Antonio Plaza-Úbeda
- Department of Economy and Business, University of Almeria, 04120 Almeria, Spain; (A.B.-d.); (L.J.B.-U.); (J.A.P.-Ú.)
- Research Centre CIAMBITAL, University of Almeria, 04120 Almeria, Spain
| | - Emilio Abad-Segura
- Department of Economy and Business, University of Almeria, 04120 Almeria, Spain; (A.B.-d.); (L.J.B.-U.); (J.A.P.-Ú.)
- Research Centre CIAMBITAL, University of Almeria, 04120 Almeria, Spain
- Correspondence:
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16
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Hinsu A, Dumadiya A, Joshi A, Kotadiya R, Andharia K, Koringa P, Kothari R. To culture or not to culture: a snapshot of culture-dependent and culture-independent bacterial diversity from peanut rhizosphere. PeerJ 2021; 9:e12035. [PMID: 34557347 PMCID: PMC8418214 DOI: 10.7717/peerj.12035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/01/2021] [Indexed: 12/16/2022] Open
Abstract
Background Sequencing driven metagenomics studies have been instrumental in various aspects of microbiology including identification of newer taxa. While this culture-independent approach has its own merits and demerits, several studies have focussed on comparing it with traditional culture-dependent (CD) approach. However, most of these comparative studies rely on Sanger sequencing of complete 16S rRNA gene from pure culture colonies to determine the culturable bacterial diversity. This approach undercounts culturable diversity as only fewer isolates are selected, sequenced, and identified. Methods In this study, we have used an Illumina based partial 16S sequencing to identify all the microbes growing on the media and directly comparing with its culture-independent (CI) counterpart. Eight different media were used to target different organisms from soil. Diversity on these media were compared with their CI counterpart. The NGS data was analysed using DADA2 to provide more resolution to the data. Results In line with studies of similar nature, current study presented higher bacterial diversity in CI approach. However, the current study reflected that a greater number of sequence variants were missed out in CI approach as compared to number of sequence variants shared with CD approach. We observed around 322 (5.98%) ASVs (Amplicon Sequence Variants) exclusively present in CD samples while, 234 (4.35%) ASVs were shared between both approaches. Most of these 322 CD exclusive ASVs were classified as Enterobacteriaceae family and Bacillus genus, with several ASVs annotated at the species level as well, and these organisms are more commonly observed in soil and were also detected in CI approach. Furthermore, 22 genera were exclusively detected in CD samples, most of which were reported from soil and water.
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Affiliation(s)
- Ankit Hinsu
- Department of Biosciences, Saurashtra University, Rajkot, India.,Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Ashvin Dumadiya
- Department of Biosciences, Saurashtra University, Rajkot, India
| | - Anjali Joshi
- Department of Biosciences, Saurashtra University, Rajkot, India
| | | | - Kavan Andharia
- Department of Biosciences, Saurashtra University, Rajkot, India
| | - Prakash Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, India
| | - Ramesh Kothari
- Department of Biosciences, Saurashtra University, Rajkot, India
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17
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Belmok A, Rodrigues-Oliveira T, Lopes FAC, Krüger RH, Kyaw CM. The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR. BRAZ J BIOL 2021; 83:e247529. [PMID: 34550284 DOI: 10.1590/1519-6984.247529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/07/2021] [Indexed: 01/16/2023] Open
Abstract
Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.
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Affiliation(s)
- A Belmok
- Universidade de Brasília - UnB, Instituto de Ciências Biológicas, Departmento de Biologia Celular, Brasília, DF, Brasil
| | - T Rodrigues-Oliveira
- Universidade de Brasília - UnB, Instituto de Ciências Biológicas, Departmento de Biologia Celular, Brasília, DF, Brasil
| | - F A C Lopes
- Universidade Federal do Tocantins - UFT, Laboratório de Microbiologia, Porto Nacional, TO, Brasil
| | - R H Krüger
- Universidade de Brasília - UnB, Instituto de Ciências Biológicas, Departmento de Biologia Celular, Brasília, DF, Brasil
| | - C M Kyaw
- Universidade de Brasília - UnB, Instituto de Ciências Biológicas, Departmento de Biologia Celular, Brasília, DF, Brasil
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18
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Hadzega D, Minarik G, Karaba M, Kalavska K, Benca J, Ciernikova S, Sedlackova T, Nemcova P, Bohac M, Pindak D, Klucar L, Mego M. Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq. Int J Mol Sci 2021; 22:ijms22169058. [PMID: 34445764 PMCID: PMC8396677 DOI: 10.3390/ijms22169058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 01/04/2023] Open
Abstract
Recent research studies are showing breast tissues as a place where various species of microorganisms can thrive and cannot be considered sterile, as previously thought. We analysed the microbial composition of primary tumour tissue and normal breast tissue and found differences between them and between multiple breast cancer phenotypes. We sequenced the transcriptome of breast tumours and normal tissues (from cancer-free women) of 23 individuals from Slovakia and used bioinformatics tools to uncover differences in the microbial composition of tissues. To analyse our RNA-seq data (rRNA depleted), we used and tested Kraken2 and Metaphlan3 tools. Kraken2 has shown higher reliability for our data. Additionally, we analysed 91 samples obtained from SRA database, originated in China and submitted by Sichuan University. In breast tissue, the most enriched group were Proteobacteria, then Firmicutes and Actinobacteria for both datasets, in Slovak samples also Bacteroides, while in Chinese samples Cyanobacteria were more frequent. We have observed changes in the microbiome between cancerous and healthy tissues and also different phenotypes of diseases, based on the presence of circulating tumour cells and few other markers.
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Affiliation(s)
- Dominik Hadzega
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovakia;
| | - Gabriel Minarik
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 813 72 Bratislava, Slovakia; (G.M.); (M.M.)
| | - Marian Karaba
- Department of Oncosurgery, National Cancer Institute, 833 10 Bratislava, Slovakia; (M.K.); (J.B.); (M.B.); (D.P.)
| | - Katarina Kalavska
- Translational Research Unit, Faculty of Medicine, Comenius University and National Cancer Institute, 833 10 Bratislava, Slovakia;
| | - Juraj Benca
- Department of Oncosurgery, National Cancer Institute, 833 10 Bratislava, Slovakia; (M.K.); (J.B.); (M.B.); (D.P.)
- Department of Medicine, St. Elizabeth University, 810 00 Bratislava, Slovakia
| | - Sona Ciernikova
- Biomedical Research Center of the Slovak Academy of Sciences, Department of Genetics, Cancer Research Institute, 845 05 Bratislava, Slovakia;
| | - Tatiana Sedlackova
- Comenius University Science Park, Comenius University, 842 15 Bratislava, Slovakia;
| | | | - Martin Bohac
- Department of Oncosurgery, National Cancer Institute, 833 10 Bratislava, Slovakia; (M.K.); (J.B.); (M.B.); (D.P.)
- Translational Research Unit, Faculty of Medicine, Comenius University and National Cancer Institute, 833 10 Bratislava, Slovakia;
| | - Daniel Pindak
- Department of Oncosurgery, National Cancer Institute, 833 10 Bratislava, Slovakia; (M.K.); (J.B.); (M.B.); (D.P.)
| | - Lubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava, Slovakia;
- Correspondence:
| | - Michal Mego
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 813 72 Bratislava, Slovakia; (G.M.); (M.M.)
- 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, 833 10 Bratislava, Slovakia
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19
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Stevens BR, Roesch L, Thiago P, Russell JT, Pepine CJ, Holbert RC, Raizada MK, Triplett EW. Depression phenotype identified by using single nucleotide exact amplicon sequence variants of the human gut microbiome. Mol Psychiatry 2021; 26:4277-4287. [PMID: 31988436 DOI: 10.1038/s41380-020-0652-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/15/2022]
Abstract
Single nucleotide exact amplicon sequence variants (ASV) of the human gut microbiome were used to evaluate if individuals with a depression phenotype (DEPR) could be identified from healthy reference subjects (NODEP). Microbial DNA in stool samples obtained from 40 subjects were characterized using high throughput microbiome sequence data processed via DADA2 error correction combined with PIME machine-learning de-noising and taxa binning/parsing of prevalent ASVs at the single nucleotide level of resolution. Application of ALDEx2 differential abundance analysis with assessed effect sizes and stringent PICRUSt2 predicted metabolic pathways. This multivariate machine-learning approach significantly differentiated DEPR (n = 20) vs. NODEP (n = 20) (PERMANOVA P < 0.001) based on microbiome taxa clustering and neurocircuit-relevant metabolic pathway network analysis for GABA, butyrate, glutamate, monoamines, monosaturated fatty acids, and inflammasome components. Gut microbiome dysbiosis using ASV prevalence data may offer the diagnostic potential of using human metaorganism biomarkers to identify individuals with a depression phenotype.
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Affiliation(s)
- Bruce R Stevens
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, USA. .,Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL, USA. .,Division of Gastroenterology, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA.
| | - Luiz Roesch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.,Centro Interdisciplinar de Pesquisas em Biotecnologia-CIP-Biotec, Universidade Federal do Pampa, São Gabriel, Bagé, Brazil
| | - Priscila Thiago
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Jordan T Russell
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Carl J Pepine
- Division of Cardiovascular Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Richard C Holbert
- Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mohan K Raizada
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
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20
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El-Sayed A, Aleya L, Kamel M. Microbiota's role in health and diseases. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:36967-36983. [PMID: 34043164 PMCID: PMC8155182 DOI: 10.1007/s11356-021-14593-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/24/2021] [Indexed: 05/06/2023]
Abstract
The microbiome is a term that usually refers to the community of various microorganisms that inhabit/live inside human/animal bodies or on their skin. It forms a complex ecosystem that includes trillions of commensals, symbiotics, and even pathogenic microorganisms. The external environment, diet, and lifestyle are the major determinants influencing the microbiome's composition and vitality. Recent studies have indicated the tremendous influence of the microbiome on health and disease. Their number, constitution, variation, and viability are dynamic. All these elements are responsible for the induction, development, and treatment of many health disorders. Serious diseases such as cancer, metabolic disorders, cardiovascular diseases, and even psychological disorders such as schizophrenia are influenced directly or indirectly by microbiota. In addition, in the last few weeks, accumulating data about the link between COVID-19 and the microbiota were published. In the present work, the role of the microbiome in health and disease is discussed. A deep understanding of the exact role of microbiota in disease induction enables the prevention of diseases and the development of new therapeutic concepts for most diseases through the correction of diet and lifestyle. The present review brings together evidence from the most recent works and discusses suggested nutraceutical approaches for the management of COVID-19 pandemic.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Lotfi Aleya
- Chrono-Environnement Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, F-25030, Besançon Cedex, France
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
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21
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YAN H, ZHU L, WANG Y, ZHANG S, LIU P, DONG TTX, WU Q, DUAN JA. Comparative metagenomics analysis of the rhizosphere microbiota influence on Radix Angelica sinensis in different growth soil environments in China. FOOD SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1590/fst.65120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Hui YAN
- Nanjing University of Chinese Medicine, China
| | - Lei ZHU
- Nanjing University of Chinese Medicine, China
| | | | - Sen ZHANG
- Nanjing University of Chinese Medicine, China
| | - Pei LIU
- Nanjing University of Chinese Medicine, China
| | | | - Qinan WU
- Nanjing University of Chinese Medicine, China
| | - Jin-Ao DUAN
- Nanjing University of Chinese Medicine, China
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22
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Tonkovic P, Kalajdziski S, Zdravevski E, Lameski P, Corizzo R, Pires IM, Garcia NM, Loncar-Turukalo T, Trajkovik V. Literature on Applied Machine Learning in Metagenomic Classification: A Scoping Review. BIOLOGY 2020; 9:E453. [PMID: 33316921 PMCID: PMC7763105 DOI: 10.3390/biology9120453] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022]
Abstract
Applied machine learning in bioinformatics is growing as computer science slowly invades all research spheres. With the arrival of modern next-generation DNA sequencing algorithms, metagenomics is becoming an increasingly interesting research field as it finds countless practical applications exploiting the vast amounts of generated data. This study aims to scope the scientific literature in the field of metagenomic classification in the time interval 2008-2019 and provide an evolutionary timeline of data processing and machine learning in this field. This study follows the scoping review methodology and PRISMA guidelines to identify and process the available literature. Natural Language Processing (NLP) is deployed to ensure efficient and exhaustive search of the literary corpus of three large digital libraries: IEEE, PubMed, and Springer. The search is based on keywords and properties looked up using the digital libraries' search engines. The scoping review results reveal an increasing number of research papers related to metagenomic classification over the past decade. The research is mainly focused on metagenomic classifiers, identifying scope specific metrics for model evaluation, data set sanitization, and dimensionality reduction. Out of all of these subproblems, data preprocessing is the least researched with considerable potential for improvement.
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Affiliation(s)
- Petar Tonkovic
- Faculty of Computer Science and Engineering, Saints Cyril and Methodius University, 1000 Skopje, Macedonia; (S.K.); (E.Z.); (P.L.); (V.T.)
| | - Slobodan Kalajdziski
- Faculty of Computer Science and Engineering, Saints Cyril and Methodius University, 1000 Skopje, Macedonia; (S.K.); (E.Z.); (P.L.); (V.T.)
| | - Eftim Zdravevski
- Faculty of Computer Science and Engineering, Saints Cyril and Methodius University, 1000 Skopje, Macedonia; (S.K.); (E.Z.); (P.L.); (V.T.)
| | - Petre Lameski
- Faculty of Computer Science and Engineering, Saints Cyril and Methodius University, 1000 Skopje, Macedonia; (S.K.); (E.Z.); (P.L.); (V.T.)
| | - Roberto Corizzo
- Department of Computer Science, American University, Washington, DC 20016, USA;
| | - Ivan Miguel Pires
- Instituto de Telecomunicações, Universidade da Beira Interior, 6200-001 Covilhã, Portugal; (I.M.P.); (N.M.G.)
- Computer Science Department, Polytechnic Institute of Viseu, 3504-510 Viseu, Portugal
- Health Sciences Research Unit: Nursing, School of Health, Polytechnic Institute of Viseu, 3504-510 Viseu, Portugal
| | - Nuno M. Garcia
- Instituto de Telecomunicações, Universidade da Beira Interior, 6200-001 Covilhã, Portugal; (I.M.P.); (N.M.G.)
| | | | - Vladimir Trajkovik
- Faculty of Computer Science and Engineering, Saints Cyril and Methodius University, 1000 Skopje, Macedonia; (S.K.); (E.Z.); (P.L.); (V.T.)
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Metagenomic Analysis Exploring Taxonomic and Functional Diversity of Soil Microbial Communities in Sugarcane Fields Applied with Organic Fertilizer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9381506. [PMID: 33145361 PMCID: PMC7596465 DOI: 10.1155/2020/9381506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 12/14/2022]
Abstract
Organic fertilizers are critically important to soil fertility, microbial communities, and sustainable agricultural strategies. We compared the effect of two fertilizer groups (organic+chemical fertilizer: OM, chemical fertilizer: CK) on sugarcane growth, by observing the difference in microbial communities and functions, soil nutrient status, and agronomic characters of sugarcane. The results showed that the sugar content and yield of sugarcane increased significantly under organic fertilizer treatment. We believe that the increased soil nutrient status and soil microorganisms are the reasons for this phenomenon. In addition, redundancy analysis (RDA) shows that the soil nutrient condition has a major impact on the soil microbial community. In comparison with CK, the species richness of Acidobacteria, Proteobacteria, Chloroflexi, and Gemmatimonadetes as well as the functional abundance of nucleotide metabolism and energy metabolism increased significantly in the OM field. Moreover, compared with CK, genes related to the absorption and biosynthesis of sulfate were more prominent in OM. Therefore, consecutive organic fertilizer application could be an effective method in reference to sustainable production of sugarcane.
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Abstract
It is essential to address research into low-cost technologies, as those employed on a wide scale demand a great amount of resources. The main goal of this work was to analyze the research on low cost technologies worldwide by studying the scientific output recorded in the Scopus database. This analysis makes it possible to determine the evolution of research into low cost technologies. In particular, we analyzed the distribution of this research by the different scientific categories, the categories’ evolution over time, the types of publications, the geographical distribution throughout different countries, the main institutions in each scientific category, and the areas of research identified through the main keywords indexed in the publications. A remarkable finding of this work has been that the universities that are most active in low-cost technologies are those in the most technologically advanced countries. There is only one exception to the above statement and it is in the field of medicine, where the most technologically developed countries are not always the most interested in this field. Given the trends observed in recent years, there is a need for a major change and for low-cost technologies to become an area of interest in countries with emerging economies.
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Microbial Community Changes in the Rhizosphere Soil of Healthy and Rusty Panax ginseng and Discovery of Pivotal Fungal Genera Associated with Rusty Roots. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8018525. [PMID: 32016120 PMCID: PMC6985933 DOI: 10.1155/2020/8018525] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/18/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022]
Abstract
Panax ginseng Meyer, a valuable medicinal plant, is severely threatened by rusty root, a condition that greatly affects its yield and quality. Studies investigating the relationship between soil microbial community composition and rusty roots are vital for the production of high-quality ginseng. Here, high-throughput sequencing was employed to systematically characterize changes in the soil microbial community associated with rusty roots. Fungal diversity was lower in the soils of rusty root-affected P. ginseng than in those of healthy plants. Importantly, principal coordinate analysis separated the fungal communities in the rhizosphere soils of rusty root-affected ginseng from those of healthy plants. The dominant bacterial and fungal genera differed significantly between rhizosphere soils of healthy and rusty root-affected P. ginseng, and linear discriminant analysis effect size (LEfSe) further indicated a strong imbalance in the soil microbial community of diseased plants. Significantly enriched bacterial genera (including Rhodomicrobium, Knoellia, Nakamurella, Asticcacaulis, and Actinomadura) were mainly detected in the soil of rusty root-affected P. ginseng, whereas significantly enriched fungal genera (including Xenopolyscytalum, Arthrobotrys, Chalara, Cryptococcus, and Scutellinia) were primarily detected in the soil of healthy plants. Importantly, five fungal genera (Cylindrocarpon, Acrophialophora, Alternaria, Doratomyces, and Fusarium) were significantly enriched in the soil of rusty root-affected plants compared with that of healthy plants, suggesting that an increase in the relative abundance of these pathogenic fungi (Cylindrocarpon, Alternaria, and Fusarium) may be associated with ginseng rusty roots. Additionally, this study is the first to report that an increase in the relative abundances of Acrophialophora and Doratomyces in the rhizosphere of P. ginseng may be associated with the onset of rusty root symptoms in this plant. Our findings provide potentially useful information for developing biological control strategies against rusty root, as well as scope for future screening of fungal pathogens in rusty roots of P. ginseng.
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Lugli GA, Milani C, Mancabelli L, Turroni F, van Sinderen D, Ventura M. A microbiome reality check: limitations of in silico-based metagenomic approaches to study complex bacterial communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:840-847. [PMID: 31668006 DOI: 10.1111/1758-2229.12805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
In recent years, whole shotgun metagenomics (WSM) of complex microbial communities has become an established technology to perform compositional analyses of complex microbial communities, an approach that is heavily reliant on bioinformatic pipelines to process and interpret the generated raw sequencing data. However, the use of such in silico pipelines for the microbial taxonomic classification of short sequences may lead to significant errors in the compositional outputs deduced from such sequencing data. To investigate the ability of such in silico pipelines, we employed two commonly applied bioinformatic tools, i.e., MetaPhlAn2 and Kraken2 together with two metagenomic data sets originating from human and animal faecal samples. By using these bioinformatic programs that taxonomically classify WSM data based on marker genes, we observed a trend to depict a lower complexity of the microbial communities. Here, we assess the limitations of the most commonly employed bioinformatic pipelines, i.e., MetaPhlAn2 and Kraken2, and based on our findings, we propose that such analyses should ideally be combined with experimentally based microbiological validations.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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Saha S, Johnson J, Pal S, Weinstock GM, Rajasekaran S. MSC: a metagenomic sequence classification algorithm. Bioinformatics 2019; 35:2932-2940. [PMID: 30649204 DOI: 10.1093/bioinformatics/bty1071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/21/2018] [Accepted: 01/07/2019] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Metagenomics is the study of genetic materials directly sampled from natural habitats. It has the potential to reveal previously hidden diversity of microscopic life largely due to the existence of highly parallel and low-cost next-generation sequencing technology. Conventional approaches align metagenomic reads onto known reference genomes to identify microbes in the sample. Since such a collection of reference genomes is very large, the approach often needs high-end computing machines with large memory which is not often available to researchers. Alternative approaches follow an alignment-free methodology where the presence of a microbe is predicted using the information about the unique k-mers present in the microbial genomes. However, such approaches suffer from high false positives due to trading off the value of k with the computational resources. In this article, we propose a highly efficient metagenomic sequence classification (MSC) algorithm that is a hybrid of both approaches. Instead of aligning reads to the full genomes, MSC aligns reads onto a set of carefully chosen, shorter and highly discriminating model sequences built from the unique k-mers of each of the reference sequences. RESULTS Microbiome researchers are generally interested in two objectives of a taxonomic classifier: (i) to detect prevalence, i.e. the taxa present in a sample, and (ii) to estimate their relative abundances. MSC is primarily designed to detect prevalence and experimental results show that MSC is indeed a more effective and efficient algorithm compared to the other state-of-the-art algorithms in terms of accuracy, memory and runtime. Moreover, MSC outputs an approximate estimate of the abundances. AVAILABILITY AND IMPLEMENTATION The implementations are freely available for non-commercial purposes. They can be downloaded from https://drive.google.com/open?id=1XirkAamkQ3ltWvI1W1igYQFusp9DHtVl.
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Affiliation(s)
- Subrata Saha
- Healthcare and Life Sciences Division, IBM Thomas J. Watson Research Center, Yorktown Heights, NY, USA
| | - Jethro Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Soumitra Pal
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
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Casimiro-Soriguer CS, Loucera C, Perez Florido J, López-López D, Dopazo J. Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples. Biol Direct 2019; 14:15. [PMID: 31429791 PMCID: PMC6701120 DOI: 10.1186/s13062-019-0246-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 08/06/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles. RESULTS Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. These profiles are used as features for city classification in a machine learning algorithm that allows the extraction of the most relevant features for the classification. CONCLUSIONS We demonstrate here that the use of functional profiles not only predict accurately the most likely origin of a sample but also to provide an interesting functional point of view of the biogeography of the microbiota. Interestingly, we show how cities can be classified based on the observed profile of antibiotic resistances. REVIEWERS Open peer review: Reviewed by Jin Zhuang Dou, Jing Zhou, Torsten Semmler and Eran Elhaik.
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Affiliation(s)
- Carlos S. Casimiro-Soriguer
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Carlos Loucera
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Javier Perez Florido
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Daniel López-López
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Joaquin Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013 Sevilla, Spain
- Functional Genomics Node (INB), FPS, Hospital Virgen del Rocio, 41013 Sevilla, Spain
- Bioinformatics in Rare Diseases (BiER), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER). FPS, Hospital Virgen del Rocio, 41013 Sevilla, Spain
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29
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Fleiss A, Sarkisyan KS. A brief review of bioluminescent systems (2019). Curr Genet 2019; 65:877-882. [PMID: 30850867 PMCID: PMC6620254 DOI: 10.1007/s00294-019-00951-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022]
Abstract
Despite being widely used in reporter technologies, bioluminescent systems are largely understudied. Of at least forty different bioluminescent systems thought to exist in nature, molecular components of only seven light-emitting reactions are known, and the full biochemical pathway leading to light emission is only understood for two of them. Here, we provide a succinct overview of currently known bioluminescent systems highlighting available tools for research and discussing future applications.
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Affiliation(s)
- Aubin Fleiss
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Karen S Sarkisyan
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London, UK. .,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK. .,Planta LLC, Bolshoi Boulevard, 42 Str 1, Office 335, Moscow, 121205, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya, 16/10, Moscow, 117997, Russia.
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30
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Saleem F, Mustafa A, Kori JA, Hussain MS, Kamran Azim M. Metagenomic Characterization of Bacterial Communities in Drinking Water Supply System of a Mega City. MICROBIAL ECOLOGY 2018; 76:899-910. [PMID: 29691611 DOI: 10.1007/s00248-018-1192-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/11/2018] [Indexed: 06/08/2023]
Abstract
Supplying safe water to consumers is vital for protection of public health. With population of > 15 million, Karachi is the main economical hub of Pakistan. Lake Keenjhar serves as the main source of fresh water while Hub dam is the secondary water reservoir for Karachi. In this study, bacterial community of the drinking water supply system (DWSS) of Karachi was studied from source to tap using metagenomics approach. For this purpose, we collected 41 water samples from different areas of the city (n = 38) and water reservoirs (n = 3). 16S rDNA metagenomic sequencing of water samples revealed that 88% sequences were associated with Proteobacteria (52%), Planctomycetes (15%), Becteroidetes (12%), and Verrucomicrobia (6%). On the class level, α-proteobacteria (6-56%) were found to be the most abundant followed by β- (8-41%) and γ-proteobacteria (6-52%). On the genus level, substantial diversity was observed among the samples. Bacterial communities in water from Hub dam was found to be distantly related while among the residential towns, Lyari was highly distant from the others. Twenty-four bacterial genera were found to be exclusively present in residential area samples in comparison to the source waters which is suggestive of their resistance against treatment procedures and/or contamination. Metagenomic analysis revealed abundance of Pseudomonas, Legionella, Neisseria, Acinetobacter, Bosea, and Microcystis genera in residential areas water samples. The present metagenomic analysis of DWSS of Karachi has allowed the evaluation of bacterial communities in source water and the water being supplied to the city. Moreover, measurement of heavy metals in water samples from Karachi revealed arsenic concentration according to WHO standards which is in contrast of recent study which reported extensive arsenic contamination in aquifers in the Indus valley plain. To the best of our knowledge, this is the first metagenomic study of DWSS of Karachi.
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Affiliation(s)
- Faizan Saleem
- Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Atif Mustafa
- Department of Environmental Engineering, N.E.D. University of Engineering and Technology, Karachi, Pakistan
| | - Junaid Ahmed Kori
- Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Muhammad Saad Hussain
- Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - M Kamran Azim
- Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
- Department of Biosciences, Mohammad Ali Jinnah University, Karachi, Pakistan.
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32
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Cremonesi P, Ceccarani C, Curone G, Severgnini M, Pollera C, Bronzo V, Riva F, Addis MF, Filipe J, Amadori M, Trevisi E, Vigo D, Moroni P, Castiglioni B. Milk microbiome diversity and bacterial group prevalence in a comparison between healthy Holstein Friesian and Rendena cows. PLoS One 2018; 13:e0205054. [PMID: 30356246 PMCID: PMC6200206 DOI: 10.1371/journal.pone.0205054] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023] Open
Abstract
Dry and early lactation periods represent the most critical phases for udder health in cattle, especially in highly productive breeds, such as the Holstein Friesian (HF). On the other hand, some autochthonous cattle breeds, such as the Rendena (REN), have a lower prevalence of mastitis and other transition-related diseases. In this study, milk microbiota of 6 HF and 3 REN cows, all raised on the same farm under the same conditions, was compared. A special focus was placed on the transition period to define bacterial groups’ prevalence with a plausible effect on mammary gland health. Four time points (dry-off, 1 d, 7–10 d and 30 d after calving) were considered. Through 16S rRNA sequencing, we characterized the microbiota composition for 117 out of the 144 milk samples initially collected, keeping only the healthy quarters, in order to focus on physiological microbiome changes and avoid shifts due to suspected diseases. Microbial populations were very different in the two breeds along all the time points, with REN milk showing a significantly lower microbial biodiversity. The taxonomic profiles of both cosmopolitan and local breeds were dominated by Firmicutes, mostly represented by the Streptococcus genus, although in very different proportions (HF 27.5%, REN 68.6%). Large differences in HF and REN cows were, also, evident from the metabolic predictive analysis from microbiome data. Finally, only HF milk displayed significant changes in the microbial composition along the transition period, while REN maintained a more stable microbiota. In conclusion, in addition to the influence on the final characteristics of dairy products obtained from milk of the two breeds, differences in the milk microbiome might, also, have an impact on their mammary gland health.
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Affiliation(s)
- Paola Cremonesi
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Lodi, Italy
- * E-mail:
| | - Camilla Ceccarani
- Institute of Biomedical Technologies, National Research Council, (CNR), Segrate, Milan, Italy
- Dipartimento di Scienze della Salute, San Paolo Hospital Medical School, Università degli Studi di Milano, Milan, Italy
| | - Giulio Curone
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council, (CNR), Segrate, Milan, Italy
| | - Claudia Pollera
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Valerio Bronzo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Federica Riva
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Maria Filippa Addis
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Joel Filipe
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Massimo Amadori
- Laboratory of Cellular Immunology, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | - Erminio Trevisi
- Department of Animal Sciences, Food and Nutrition (DIANA), Facoltà di Scienze Agrarie, Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Daniele Vigo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Paolo Moroni
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
- Quality Milk Production Services, Animal Health Diagnostic Center, Cornell University, Ithaca, NY, United States of America
| | - Bianca Castiglioni
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Lodi, Italy
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Abstract
The bicycle has gone from being an old-fashioned recreational product to a less polluting means of transport and a compact, ultra-light personal mobility tool. This is how electrical bicycles will be used as the pillar that could support individual public transport in large cities worldwide. The objective of this manuscript is to detect how worldwide research on the electric bicycle is being developed, and, especially, around which scientific domains is it clustered, to finally identify the main trends in the field. This study has been carried out based on the Scopus database, where all the publications related to the topic of the electric bicycle have been analyzed up to the year 2017. ¨Therefore, research on the global research trends of this topic was conducted. Its evolution over time shows that since 2008 the growth of publications is much higher than in the previous period. The main countries are China and the USA, and it can be inferred that there are two major trend countries with high environmental awareness, which also have a large population and that the electric bicycle is a suitable and sustainable form of transport. Among the main scientific fields, engineering leads in research. The keyword analysis shows that the central theme is electric, then battery and motor stand out. A community detection was applied to detect the six main clusters of this research, largely dedicated to the following topics: Transportation–Environment, Electrical Engineering, Safety, Batteries, Sporting Goods–Urban Planning, and Mechanical Engineering. This manuscript shows that global research trends about the electric bicycle are increasing, and that it should be considered a means of sustainable urban transport and will therefore contribute to energy saving and sustainable energy.
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Mining Waste and Its Sustainable Management: Advances in Worldwide Research. MINERALS 2018. [DOI: 10.3390/min8070284] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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35
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Borthong J, Omori R, Sugimoto C, Suthienkul O, Nakao R, Ito K. Comparison of Database Search Methods for the Detection of Legionella pneumophila in Water Samples Using Metagenomic Analysis. Front Microbiol 2018; 9:1272. [PMID: 29971047 PMCID: PMC6018159 DOI: 10.3389/fmicb.2018.01272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 05/24/2018] [Indexed: 12/12/2022] Open
Abstract
Metagenomic analysis has become a powerful tool to analyze bacterial communities in environmental samples. However, the detection of a specific bacterial species using metagenomic analysis remains difficult due to false positive detections of sequences shared between different bacterial species. In this study, 16S rRNA amplicon and shotgun metagenomic analyses were conducted on samples collected along a stream and ponds in the campus of Hokkaido University. We compared different database search methods for bacterial detection by focusing on Legionella pneumophila. In this study, we used L. pneumophila-specific nested PCR as a gold standard to evaluate the results of the metagenomic analysis. Comparison with the results from L. pneumophila-specific nested PCR indicated that a blastn search of shotgun reads against the NCBI-NT database led to false positive results and had problems with specificity. We also found that a blastn search of shotgun reads against a database of the catalase-peroxidase (katB) gene detected L. pneumophila with the highest area under the receiver operating characteristic curve among the tested search methods; indicating that a blastn search against the katB gene database had better diagnostic ability than searches against other databases. Our results suggest that sequence searches targeting long genes specifically associated with the bacterial species of interest is a prerequisite to detecting the bacterial species in environmental samples using metagenomic analyses.
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Affiliation(s)
- Jednipit Borthong
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryosuke Omori
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Chihiro Sugimoto
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Global Institute for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Orasa Suthienkul
- Faculty of Public Health, Thammasat University, Rangsit Campus, Pathumthani, Thailand
| | - Ryo Nakao
- Laboratory of Parasitology, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Global Institute for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.,Faculty of Public Health, Thammasat University, Rangsit Campus, Pathumthani, Thailand
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36
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Tetz G, Tetz V. Bacteriophages as New Human Viral Pathogens. Microorganisms 2018; 6:E54. [PMID: 29914145 PMCID: PMC6027513 DOI: 10.3390/microorganisms6020054] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 12/12/2022] Open
Abstract
The pathogenesis of numerous human multifaceted devastating diseases, including a variety of neurodegenerative and autoimmune diseases, is associated with alterations in the gut microbiota; however, the underlying mechanisms are not completely understood. Our recent human metagenome and phagobiota proteome analyses and studies in relevant animal models suggested that bacterial viruses might be implicated in the progression and maintenance of at least some pathologies, including those associated with protein misfolding. Here, for the first time, we propose the concept of bacteriophages as human pathogens. We suggest that bacterial viruses have different ways to directly and indirectly interact with eukaryotic cells and proteins, leading to human diseases. Furthermore, we suggest different causes of bacteriophages infection on the basis of the unique ways of interplay of phages, microbiota, and the human host. This concept opens a discussion of the role of bacteriophages as previously overlooked pathogenic factors and suggests that bacterial viruses have to be further explored as a diagnostic and treatment target for therapeutic intervention.
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Affiliation(s)
- George Tetz
- Human Microbiology Institute, 101 6th Street, New York, NY 10013, USA.
| | - Victor Tetz
- Human Microbiology Institute, 101 6th Street, New York, NY 10013, USA.
- Tetz Laboratories, 423W 127th Street, New York, NY 10027, USA.
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Abstract
Water use efficiency in agriculture (WUEA) has become a priority given increasing limitations on hydric resources. As a result, this area of research has increased in importance, becoming one of the most prolific lines of study. The main aim of this study was to present a review of worldwide WUEA research over the last 30 years. A bibliometric analysis was developed based on the Scopus database. The sample included 6063 articles. The variables analyzed were: articles per year, category, journal, country, institution, author, and keyword. The results indicate that a remarkable growth in the number of articles published per year is occurring. The main category is environmental science and the main journal Agricultural Water Management. The countries with the highest number of articles were China, the United States of America, and India. The institution that published the most articles was the Chinese Academy of Sciences and the authors from China also were the most productive. The most frequently used keywords were irrigation, crop yield, water supply, and crops. The findings of this study can assist researchers in this field by providing an overview of worldwide research.
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Garrido-Cardenas JA, Mesa-Valle C, Manzano-Agugliaro F. Trends in plant research using molecular markers. PLANTA 2018; 247:543-557. [PMID: 29243155 DOI: 10.1007/s00425-017-2829-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/08/2017] [Indexed: 05/21/2023]
Abstract
A deep bibliometric analysis has been carried out, obtaining valuable parameters that facilitate the understanding around the research in plant using molecular markers. The evolution of the improvement in the field of agronomy is fundamental for its adaptation to the new exigencies that the current world context raises. In addition, within these improvements, this article focuses on those related to the biotechnology sector. More specifically, the use of DNA markers that allow the researcher to know the set of genes associated with a particular quantitative trait or QTL. The use of molecular markers is widely extended, including: restriction fragment length polymorphism, random-amplified polymorphic DNA, amplified fragment length polymorphism, microsatellites, and single-nucleotide polymorphisms. In addition to classical methodology, new approaches based on the next generation sequencing are proving to be fundamental. In this article, a historical review of the molecular markers traditionally used in plants, since its birth and how the new molecular tools facilitate the work of plant breeders is carried out. The evolution of the most studied cultures from the point of view of molecular markers is also reviewed and other parameters whose prior knowledge can facilitate the approach of researchers to this field of research are analyzed. The bibliometric analysis of molecular markers in plants shows that top five countries in this research are: US, China, India, France, and Germany, and from 2013, this research is led by China. On the other hand, the basic research using Arabidopsis is deeper in France and Germany, while other countries focused its efforts in their main crops as the US for wheat or maize, while China and India for wheat and rice.
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Worldwide Research on Plant Defense against Biotic Stresses as Improvement for Sustainable Agriculture. SUSTAINABILITY 2018. [DOI: 10.3390/su10020391] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Dielectric and Bioimpedance Research Studies: A Scientometric Approach Using the Scopus Database. PUBLICATIONS 2018. [DOI: 10.3390/publications6010006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Abstract
In this article, the trends in human parasitology have been studied through the analysis of the number of publications in this area. The parameters studied were: number of articles, language, countries and institutions with the highest number of publications, and keywords with greater presence in the articles of human parasitology. The results of the analysis confirm the growing interest in this area, observing an exponential growth in the number of publications in the last decades. We also verified that the main country in terms of scientific production is the USA, although among the most important institutions, we find non-US centres such as the Oswaldo Cruz Foundation and the London School of Hygiene and Tropical Medicine. For observing the relative importance of the journals that publish articles in this specific topic, an index has been created based on the h-index of the journal with publications related to human parasitology and divided by every 100 items. This rank is led fist by 'Journal of Medical Entomology' closely followed by 'Parasitology'. The analysis of the keywords allows to draw conclusions about the great importance of malaria in the current world research. A change in analytical methodology is also observed, and molecular techniques are now being imposed. These techniques, in the near future, have to influence in an improvement in the treatments and prevention of the diseases caused by parasites. Finally, it can be seen that diseases traditionally studied as helminthiasis and amebiasis are currently as well studied as others such as toxoplasmosis or leishmaniasis.
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Gimenez E, Manzano-Agugliaro F. DNA Damage Repair System in Plants: A Worldwide Research Update. Genes (Basel) 2017; 8:genes8110299. [PMID: 29084140 PMCID: PMC5704212 DOI: 10.3390/genes8110299] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 12/14/2022] Open
Abstract
Living organisms are usually exposed to various DNA damaging agents so the mechanisms to detect and repair diverse DNA lesions have developed in all organisms with the result of maintaining genome integrity. Defects in DNA repair machinery contribute to cancer, certain diseases, and aging. Therefore, conserving the genomic sequence in organisms is key for the perpetuation of life. The machinery of DNA damage repair (DDR) in prokaryotes and eukaryotes is similar. Plants also share mechanisms for DNA repair with animals, although they differ in other important details. Plants have, surprisingly, been less investigated than other living organisms in this context, despite the fact that numerous lethal mutations in animals are viable in plants. In this manuscript, a worldwide bibliometric analysis of DDR systems and DDR research in plants was made. A comparison between both subjects was accomplished. The bibliometric analyses prove that the first study about DDR systems in plants (1987) was published thirteen years later than that for other living organisms (1975). Despite the increase in the number of papers about DDR mechanisms in plants in recent decades, nowadays the number of articles published each year about DDR systems in plants only represents 10% of the total number of articles about DDR. The DDR research field was done by 74 countries while the number of countries involved in the DDR & Plant field is 44. This indicates the great influence that DDR research in the plant field currently has, worldwide. As expected, the percentage of studies published about DDR systems in plants has increased in the subject area of agricultural and biological sciences and has diminished in medicine with respect to DDR studies in other living organisms. In short, bibliometric results highlight the current interest in DDR research in plants among DDR studies and can open new perspectives in the research field of DNA damage repair.
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Affiliation(s)
- Estela Gimenez
- Central Research Services, University of Almería, C/ Sacramento s/n, Almería 04120, Spain.
| | - Francisco Manzano-Agugliaro
- Central Research Services, University of Almería, C/ Sacramento s/n, Almería 04120, Spain.
- Engineering Department, University of Almería, C/ Sacramento s/n., Almería 04120, Spain.
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Advanced microbial analysis for wastewater quality monitoring: metagenomics trend. Appl Microbiol Biotechnol 2017; 101:7445-7458. [DOI: 10.1007/s00253-017-8490-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 08/19/2017] [Indexed: 12/20/2022]
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