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Matys J, Kensy J, Gedrange T, Zawiślak I, Grzech-Leśniak K, Dobrzyński M. A Molecular Approach for Detecting Bacteria and Fungi in Healthcare Environment Aerosols: A Systematic Review. Int J Mol Sci 2024; 25:4154. [PMID: 38673740 PMCID: PMC11050369 DOI: 10.3390/ijms25084154] [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: 02/25/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information.
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Affiliation(s)
- Jacek Matys
- Oral Surgery Department, Medical University of Wroclaw, 50-425 Wroclaw, Poland; (T.G.); (K.G.-L.)
| | - Julia Kensy
- Faculty of Dentistry, Medical University of Wroclaw, 50-425 Wroclaw, Poland;
| | - Tomasz Gedrange
- Oral Surgery Department, Medical University of Wroclaw, 50-425 Wroclaw, Poland; (T.G.); (K.G.-L.)
| | - Ireneusz Zawiślak
- Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, 37 Chełmońskiego Str., 51-630 Wrocław, Poland;
| | - Kinga Grzech-Leśniak
- Oral Surgery Department, Medical University of Wroclaw, 50-425 Wroclaw, Poland; (T.G.); (K.G.-L.)
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Maciej Dobrzyński
- Department of Pediatric Dentistry and Preclinical Dentistry, Wroclaw Medical University, Krakowska 26, 50-425 Wrocław, Poland;
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Parida D, Katare K, Ganguly A, Chakraborty D, Konar O, Nogueira R, Bala K. Molecular docking and metagenomics assisted mitigation of microplastic pollution. CHEMOSPHERE 2024; 351:141271. [PMID: 38262490 DOI: 10.1016/j.chemosphere.2024.141271] [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: 09/29/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.
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Affiliation(s)
- Dinesh Parida
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
| | - Konica Katare
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
| | - Atmaadeep Ganguly
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, West Bengal State University, Kolkata, 700118, India.
| | - Disha Chakraborty
- Department of Botany, Shri Shikshayatan College, University of Calcutta, Lord Sinha Road, Kolkata, 700071, India.
| | - Oisi Konar
- Department of Botany, Shri Shikshayatan College, University of Calcutta, Lord Sinha Road, Kolkata, 700071, India.
| | - Regina Nogueira
- Institute of Sanitary Engineering and Waste Management, Leibniz Universität, Hannover, Germany.
| | - Kiran Bala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, 453552, India.
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Holstein T, Muth T. Bioinformatic Workflows for Metaproteomics. Methods Mol Biol 2024; 2820:187-213. [PMID: 38941024 DOI: 10.1007/978-1-0716-3910-8_16] [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] [Indexed: 06/29/2024]
Abstract
The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.
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Affiliation(s)
- Tanja Holstein
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
- VIB-UGent Center for Medical Biotechnology, VIB and Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Data Competence Center, Robert Koch Institute, Berlin, Deutschland
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany.
- Data Competence Center, Robert Koch Institute, Berlin, Deutschland.
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Song M, Han C, Liu L, Li Q, Fan Y, Gao H, Zhang D, Ren Y, Qin F, Yang M. MIST: A microbial identification and source tracking system for next-generation sequencing data. IMETA 2023; 2:e146. [PMID: 38868214 PMCID: PMC10989743 DOI: 10.1002/imt2.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 06/14/2024]
Abstract
The Professional Committee of Microbiology of the National Pharmacopoeia Commission organized the drafting of the Technical Guidelines for Microbial Whole Genome Sequencing (WGS), aiming to standardize the method process and technical indicators of microbial WGS and ensure the accuracy of sequencing and identification. On the basis of the Guidelines, we developed an integrated microbial identification and source tracking (MIST) system, which could meet the needs of microbial identification and contamination investigation in food and drug quality control. MIST integrates three analysis pipelines: 16S/18S/internal transcribed spacer amplicon-based microbial identification, WGS-based microbial identification, and single-nucleotide polymorphism-based microbial source tracking. MIST can analyze sequence data in a variety of formats, such as Fasta, base call file, and FASTQ. It can be connected to a high-throughput sequencing instrument to acquire sequencing data directly. We also developed a publicly accessible web server for MIST (http://syj.i-sanger.cn).
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Affiliation(s)
- Minghui Song
- Shanghai Institute for Food and Drug ControlNMPA Key Laboratory for Testing Technology of Pharmaceutical MicrobiologyShanghai
| | - Chang Han
- Shanghai Majorbio Bio‐Pharm Technology Co., Ltd.ShanghaiChina
| | - Linmeng Liu
- Shanghai Majorbio Bio‐Pharm Technology Co., Ltd.ShanghaiChina
| | - Qiongqiong Li
- Shanghai Institute for Food and Drug ControlNMPA Key Laboratory for Testing Technology of Pharmaceutical MicrobiologyShanghai
| | - Yiling Fan
- Shanghai Institute for Food and Drug ControlNMPA Key Laboratory for Testing Technology of Pharmaceutical MicrobiologyShanghai
| | - Hao Gao
- Shanghai Majorbio Bio‐Pharm Technology Co., Ltd.ShanghaiChina
| | - Dan Zhang
- Shanghai Majorbio Bio‐Pharm Technology Co., Ltd.ShanghaiChina
| | - Yi Ren
- Shanghai Majorbio Bio‐Pharm Technology Co., Ltd.ShanghaiChina
| | - Feng Qin
- Shanghai Institute for Food and Drug ControlNMPA Key Laboratory for Testing Technology of Pharmaceutical MicrobiologyShanghai
| | - Meicheng Yang
- Shanghai Institute for Food and Drug ControlNMPA Key Laboratory for Testing Technology of Pharmaceutical MicrobiologyShanghai
- Shanghai food and drug packaging material control centerShanghaiChina
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Arikawa K, Hosokawa M. Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics. Comput Struct Biotechnol J 2023; 21:4508-4518. [PMID: 37771751 PMCID: PMC10523443 DOI: 10.1016/j.csbj.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 09/30/2023] Open
Abstract
Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.
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Affiliation(s)
- Koji Arikawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- bitBiome, Inc., 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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Vasina M, Kovar D, Damborsky J, Ding Y, Yang T, deMello A, Mazurenko S, Stavrakis S, Prokop Z. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnol Adv 2023; 66:108171. [PMID: 37150331 DOI: 10.1016/j.biotechadv.2023.108171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.
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Affiliation(s)
- Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - David Kovar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic
| | - Yun Ding
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Tianjin Yang
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland; Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital, 656 91 Brno, Czech Republic.
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7
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A Taxonomy-Agnostic Approach to Targeted Microbiome Therapeutics-Leveraging Principles of Systems Biology. Pathogens 2023; 12:pathogens12020238. [PMID: 36839510 PMCID: PMC9959781 DOI: 10.3390/pathogens12020238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The study of human microbiomes has yielded insights into basic science, and applied therapeutics are emerging. However, conflicting definitions of what microbiomes are and how they affect the health of the "host" are less understood. A major impediment towards systematic design, discovery, and implementation of targeted microbiome therapeutics is the continued reliance on taxonomic indicators to define microbiomes in health and disease. Such reliance often confounds analyses, potentially suggesting associations where there are none, and conversely failing to identify significant, causal relationships. This review article discusses recent discoveries pointing towards a molecular understanding of microbiome "dysbiosis" and away from a purely taxonomic approach. We highlight the growing role of systems biological principles in the complex interrelationships between the gut microbiome and host cells, and review current approaches commonly used in targeted microbiome therapeutics, including fecal microbial transplant, bacteriophage therapies, and the use of metabolic toxins to selectively eliminate specific taxa from dysbiotic microbiomes. These approaches, however, remain wholly or partially dependent on the bacterial taxa involved in dysbiosis, and therefore may not capitalize fully on many therapeutic opportunities presented at the bioactive molecular level. New technologies capable of addressing microbiome-associated diseases as molecular problems, if solved, will open possibilities of new classes and categories of targeted microbiome therapeutics aimed, in principle, at all dysbiosis-driven disorders.
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Bambaradeniya YTB, Magni PA, Dadour IR. Traumatic sheep myiasis: A review of the current understanding. Vet Parasitol 2023; 314:109853. [PMID: 36577285 DOI: 10.1016/j.vetpar.2022.109853] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Myiasis, or the infestation of live humans and vertebrate animals by dipterous larvae, is a health issue worldwide. The economic impact and potential threat to animal health and wellbeing of this disease under the animal husbandry sector is considerable. Sheep are a highly vulnerable livestock category exposed to myiasis (sheep strike), due to several unique predisposing factors that attract flies. The successful mitigation of this disease relies on a thorough understanding of fly population dynamics associated with the change in weather patterns and the evaluation of this disease through different branches of science such as chemistry, molecular biology, and microbiology. The present review provides a summary of the existing knowledge of strike in sheep, discussed in relation to the application of volatile organic compounds, metagenomics, and molecular biology, and their use regarding implementing fly control strategies such as traps, and to increase the resilience of sheep to this disease through improving their health and wellbeing.
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Affiliation(s)
- Y T B Bambaradeniya
- Discipline of Medical, Molecular & Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia.
| | - P A Magni
- Discipline of Medical, Molecular & Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia; Murdoch University Singapore, King's Centre, Singapore.
| | - I R Dadour
- Discipline of Medical, Molecular & Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia; Source Certain, PO Box 1570, Wangara DC, Western Australia 6947, Australia.
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Kibegwa FM, Bett RC, Gachuiri CK, Machuka E, Stomeo F, Mujibi FD. Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle. PLoS One 2023; 18:e0274371. [PMID: 36638091 PMCID: PMC9838872 DOI: 10.1371/journal.pone.0274371] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/29/2022] [Indexed: 01/14/2023] Open
Abstract
The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.
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Affiliation(s)
- Felix M. Kibegwa
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
- * E-mail:
| | - Rawlynce C. Bett
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Charles K. Gachuiri
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi, Kenya
| | - Eunice Machuka
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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Koner S, Tsai HC, Chen JS, Hussain B, Rajendran SK, Hsu BM. Exploration of pristine plate-tectonic plains and mining exposure areas for indigenous microbial communities and its impact on the mineral-microbial geochemical weathering process in ultramafic setting. ENVIRONMENTAL RESEARCH 2022; 214:113802. [PMID: 35810813 DOI: 10.1016/j.envres.2022.113802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Heavy metal release from harsh ultramafic settings influences microbial diversity and function in soil ecology. This study aimed to determine how serpentine mineralosphere bacterial assemblies and their functions differed in two different plate-tectonic plains and mining exposure sites under heavy metal release conditions. The results showed that the Proteobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Chloroflexi were the most abundant bacterial groups among all the sites. The log10-based LDA scores highlighted that some specific groups of bacterial assemblies were enriched in plate-tectonic plains and mining activity areas of the serpentine mineralosphere. Functional prediction revealed that the abundance of heavy metal (Cr and Ni) resistance and biogeochemical cycles involving functional KEGG orthology varied in samples from plate-tectonic plains and mining activity sites. The bipartite plot showed that the enrichment of the biogeochemical cycle and heavy metal resistance functional genes correlated with the abundance of serpentine mineralosphere bacterial groups at a 0.005% confidence level. The co-occurrence network plot revealed that the interconnection pattern of the indigenous bacterial assemblies changed in different plate-tectonic plains and mining exposure areas. Finally, this study concluded that due to heavy metal release, the variation in bacterial assemblies, their functioning, and intercommunity co-occurrence patterns were clarified the synergetic effect of mineral-microbial geochemical weathering process in serpentine mining areas.
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Affiliation(s)
- Suprokash Koner
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Psychiatry, Tzu Chi General Hospital, Hualien, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Senthil Kumar Rajendran
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi County, Taiwan; Center for Innovative on Aging Society, National Chung Cheng University, Chiayi County, Taiwan.
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11
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Carratto TMT, Moraes VMS, Recalde TSF, Oliveira MLGD, Teixeira Mendes-Junior C. Applications of massively parallel sequencing in forensic genetics. Genet Mol Biol 2022; 45:e20220077. [PMID: 36121926 PMCID: PMC9514793 DOI: 10.1590/1678-4685-gmb-2022-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | - Vitor Matheus Soares Moraes
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | | | | | - Celso Teixeira Mendes-Junior
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
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12
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Effects of Land Use Conversion on the Soil Microbial Community Composition and Functionality in the Urban Wetlands of North-Eastern China. FORESTS 2022. [DOI: 10.3390/f13071148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Urban wetlands are undergoing intensive conversion from natural wetlands to farmlands, woodlands, and even alkaline land. This study aimed to determine the effects of land conversion on soil microbial communities of urban wetlands in the hinterland of Songnen Plain, Northeastern China. Soil samples were collected from various sites of Longfeng wetland, including swamp wetland (SW), meadow wetland (MW), woodland (WL), farmland (FL), and alkaline land (AL). High-throughput sequencing followed by bioinformatic analysis was conducted to evaluate the structure, composition, and function of soil bacterial and fungal communities. The most dominant bacterial and fungal phylum among the land-use types were Proteobacteria and Ascomycota, respectively. In addition, the bacterial diversity and functions varied significantly across different land-use types. However, no remarkable differences in fungal communities were observed under various land-use types. Edaphic parameters, including exchange sodium percent (ESP) and total nitrogen (TN), remarkably influenced the abundance and diversity of soil microbial communities. These results show that land-use type shapes various aspects of soil microbial communities, including soil physicochemical properties, microbial taxa structure, potential functional genes, and correlation with environmental factors. This study provides reliable data to guide land use management and supervision by decision-makers in this region.
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Nan L, Guo Q, Cao S, Zhan Z. Diversity of bacterium communities in saline-alkali soil in arid regions of Northwest China. BMC Microbiol 2022; 22:11. [PMID: 34991470 PMCID: PMC8734156 DOI: 10.1186/s12866-021-02424-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The saline-alkali soil area accounts for over 1/4-1/5 of the land area in Gansu Province of China, which are mainly distributed in the north of Hexi corridor and Jingtai basin. The unique ecological environment contains unique and diverse microbial resources. The investigation of microbial diversity in saline environment is vital to comprehend the biological mechanisms of saline adaption, develop and utilize microbial resources. RESULTS The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. The results from this study show that Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Gemmatimonadetes were the dominant bacterial groups in 13 saline soil. Proteobacteria had the greatest abundance in sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks, sulfate-chloride-type, chloride-sulfate-type, and sulfate-type dry solonchaks. Halobacteria was the dominant bacterial class in soil samples except for sulfate-type meadow solonchaks and orthic solonchaks, chloride-type orthic solonchaks and bog solonchaks. The richness estimators of Ace and Chao 1 and the diversity indices of Shannon and Simpson revealed the least diversity in bacterial community in sulfate-chloride-type orthic solonchaks. CONCLUSIONS The sulfate anion was the most important driving force for bacterial composition (17.7%), and the second most influencing factor was pH value (11.7%).
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Affiliation(s)
- Lili Nan
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
| | - Quanen Guo
- Institute of Soil, Fertilizer and Water-saving, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, China
| | - Shiyu Cao
- Institute of Soil, Fertilizer and Water-saving, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, China
| | - Zongbing Zhan
- Institute of Soil, Fertilizer and Water-saving, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, China
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Akan OD, Udofia GE, Okeke ES, Mgbechidinma CL, Okoye CO, Zoclanclounon YAB, Atakpa EO, Adebanjo OO. Plastic waste: Status, degradation and microbial management options for Africa. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 292:112758. [PMID: 34030015 DOI: 10.1016/j.jenvman.2021.112758] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/25/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
This paper presents a review of synthetic polymer (notably plastic) wastes profiles in Africa, their current management status, and better options. Data revealed that of the approximated 86.14 million metric tonnes and 31.5 million metric tonnes of primary polymers and plastics, respectively, and an estimated 230 million metric tonnes of plastic components imported between 1990 and 2017, about 17 million metric tonnes are mismanaged. Leading African nations on the plastic wastes generator table in increasing order are Tunisia (6.9%), Morocco (9.6%), Algeria (11.2%), South Africa (11.6%), Nigeria (16.9%), and the chief is Egypt (18.4%). The volume of plastic wastes generated in Africa directly correlates with her increasing population status, however, the current treatment options have major drawbacks (high energy and technological input, high demand for space, and creation of obnoxious by-products). Ineffective regulations, poor monitoring, and slow adoption of veritable practices by governments are responsible for the steady increase in plastic volume in the African landscapes and environments. In Nigeria, only about 9% and 12% of the total generated wastes are recycled and incinerated. The remainder bulk is either discarded into waste dumps (and a few available landfills) or natural environments. There is a paucity of standard plastic biodegradative work by African scientists, and only a few works show detection of competent synthetic plastic degrading microbes globally. Asides from the ills of possible omission of core degraders, there is a need for researchers to follow standard degradation procedures to arrive at efficient, reproducible, and generally accepted outcomes utilizable on a larger scale. Thus, metagenomic search on the vast African urban and rural plastisphere is the best isolation option.
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Affiliation(s)
- Otobong Donald Akan
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, 41004, China; Microbiology Department, Faculty of Biological Science, Akwa-Ibom State University, Ikot Akpaden, Mkpat Enin LGA, Uyo P.M.B., 1167, Akwa-Ibom State, Nigeria.
| | - Godwin Evans Udofia
- Department of Microbiology, Faculty of Science, University of Uyo, Uyo PMB, 1017, Nigeria
| | - Emmanuel Sunday Okeke
- Environmental Chemistry and Toxicology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies University of Nigeria, Nsukka, 410001, Nigeria.
| | - Chiamaka Linda Mgbechidinma
- Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China; Department of Microbiology, University of Ibadan, Ibadan, Oyo State, 200243, Nigeria
| | - Charles Obinwanne Okoye
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Department of Zoology and Environmental Biology, University of Nigeria, Nsukka, 410001, Nigeria
| | - Yedomon Ange Bovys Zoclanclounon
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, 54896, South Korea; Department of Management of Environment, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01 POB 2009, Cotonou, Benin
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Current Status of Mining, Modification, and Application of Cellulases in Bioactive Substance Extraction. Curr Issues Mol Biol 2021; 43:687-703. [PMID: 34287263 PMCID: PMC8929041 DOI: 10.3390/cimb43020050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
Cellulases have been used to extract bioactive ingredients from medical plants; however, the poor enzymatic properties of current cellulases significantly limit their application. Two strategies are expected to address this concern: (1) new cellulase gene mining strategies have been promoted, optimized, and integrated, thanks to the improvement of gene sequencing, genomic data, and algorithm optimization, and (2) known cellulases are being modified, thanks to the development of protein engineering, crystal structure data, and computing power. Here, we focus on mining strategies and provide a systemic overview of two approaches based on sequencing and function. Strategies based on protein structure modification, such as introducing disulfide bonds, proline, salt bridges, N-glycosylation modification, and truncation of loop structures, have already been summarized. This review discusses four aspects of cellulase-assisted extraction. Initially, cellulase alone was used to extract bioactive substances, and later, mixed enzyme systems were developed. Physical methods such as ultrasound, microwave, and high hydrostatic pressure have assisted in improving extraction efficiency. Cellulase changes the structure of biomolecules during the extraction process to convert them into effective ingredients with better activity and bioavailability. The combination of cellulase with other enzymes and physical technologies is a promising strategy for future extraction applications.
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Conchouso D, Al-Ma'abadi A, Behzad H, Alarawi M, Hosokawa M, Nishikawa Y, Takeyama H, Mineta K, Gojobori T. Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:504-518. [PMID: 34952209 PMCID: PMC8864243 DOI: 10.1016/j.gpb.2021.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 02/09/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022]
Abstract
Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput. However, their adoption in laboratories studying “-omics” sciences is still irrelevant due to the complex and multidisciplinary nature of the field. To facilitate their use, here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput. First, a device encapsulating single cells in droplets at a rate of ∼250 Hz is described considering droplet size and cell growth. Then, we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers (i.e., 405, 488, 561, and 637 nm) in a single platform to make it compatible with different fluorescence-emitting biosensors. For this sorter, both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz. Then, a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz. Finally, we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools. Because of the overall integration and the technical details presented here, our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability (>50,000 cells/day) for mining and bioprospecting metagenomic data
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Affiliation(s)
- David Conchouso
- Department of Industrial and Mechanical Engineering, Universidad de las Américas Puebla, Puebla 72810, Mexico; Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Amani Al-Ma'abadi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Hayedeh Behzad
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mohammed Alarawi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo 169-0072, Japan
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo 169-0072, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Computer, Electrical, and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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Tolani P, Gupta S, Yadav K, Aggarwal S, Yadav AK. Big data, integrative omics and network biology. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:127-160. [PMID: 34340766 DOI: 10.1016/bs.apcsb.2021.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A cell integrates various signals through a network of biomolecules that crosstalk to synergistically regulate the replication, transcription, translation and other metabolic activities of a cell. These networks regulate signal perception and processing that drives biological functions. The biological complexity cannot be fully captured by a single -omics discipline. The holistic study of an organism-in health, perturbation, exposure to environment and disease, is studied under systems biology. The bottom-up molecular approaches (genes, mRNA, protein, metabolite, etc.) have laid the foundation of current biological knowledge covering the horizon from viruses, bacteria, fungi, plants and animals. Yet, these techniques provide a rather myopic view of biology at the molecular level. To understand how the interconnected molecular components are formed and rewired in disease or exposure to environmental stimuli is the holy grail of modern biology. The omics era was heralded by the genomics revolution but advanced sequencing techniques are now also ubiquitous in transcriptomics, proteomics, metabolomics and lipidomics. Multi-omics data analysis and integration techniques are driving the quest for deeper insights into how the different layers of biomolecules talk to each other in diverse contexts.
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Affiliation(s)
- Priya Tolani
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Srishti Gupta
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India; School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Kirti Yadav
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India; Department of Pharmaceutical Biotechnology, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Suruchi Aggarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India; Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam, India
| | - Amit Kumar Yadav
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India.
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Brumfield KD, Huq A, Colwell RR, Olds JL, Leddy MB. Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data. PLoS One 2020; 15:e0228899. [PMID: 32053657 PMCID: PMC7018008 DOI: 10.1371/journal.pone.0228899] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/24/2020] [Indexed: 01/01/2023] Open
Abstract
Microorganisms are ubiquitous in the biosphere, playing a crucial role in both biogeochemistry of the planet and human health. However, identifying these microorganisms and defining their function are challenging. Widely used approaches in comparative metagenomics, 16S amplicon sequencing and whole genome shotgun sequencing (WGS), have provided access to DNA sequencing analysis to identify microorganisms and evaluate diversity and abundance in various environments. However, advances in parallel high-throughput DNA sequencing in the past decade have introduced major hurdles, namely standardization of methods, data storage, reproducible interoperability of results, and data sharing. The National Ecological Observatory Network (NEON), established by the National Science Foundation, enables all researchers to address queries on a regional to continental scale around a variety of environmental challenges and provide high-quality, integrated, and standardized data from field sites across the U.S. As the amount of metagenomic data continues to grow, standardized procedures that allow results across projects to be assessed and compared is becoming increasingly important in the field of metagenomics. We demonstrate the feasibility of using publicly available NEON soil metagenomic sequencing datasets in combination with open access Metagenomics Rapid Annotation using the Subsystem Technology (MG-RAST) server to illustrate advantages of WGS compared to 16S amplicon sequencing. Four WGS and four 16S amplicon sequence datasets, from surface soil samples prepared by NEON investigators, were selected for comparison, using standardized protocols collected at the same locations in Colorado between April-July 2014. The dominant bacterial phyla detected across samples agreed between sequencing methodologies. However, WGS yielded greater microbial resolution, increased accuracy, and allowed identification of more genera of bacteria, archaea, viruses, and eukaryota, and putative functional genes that would have gone undetected using 16S amplicon sequencing. NEON open data will be useful for future studies characterizing and quantifying complex ecological processes associated with changing aquatic and terrestrial ecosystems.
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Affiliation(s)
- Kyle D. Brumfield
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, College Park, Maryland, United States of America
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, United States of America
- CosmosID Inc., Rockville, MD, United States of America
| | - James L. Olds
- Schar School, George Mason University, Arlington, Virginia, United States of America
| | - Menu B. Leddy
- Essential Environmental and Engineering Systems, Huntington Beach, California, United States of America
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Abstract
The marine environment encompasses a huge biological diversity and can be considered as an underexplored location for prospecting bioactive molecules. In this review, the current state of art about antimicrobial molecules from marine bacteria has been summarized considering the main phylum and sources evolved in a marine environment. Considering the last two decades, we have found as most studied group of bacteria producers of substances with antimicrobial activity is the Firmicutes phylum, in particular strains of the Bacillus genus. The reason for that can be attributed to the difficult cultivation of typical Actinobacteria from a marine sediment, whose members are the major producers of antimicrobial substances in land environments. However, a reversed trend has been observed in recent years with an increasing number of reports settling on Actinobacteria. Great diversity of chemical structures have been identified, such as fijimicyns and lynamicyns from Actinomycetes and macrolactins produced by Bacillus.
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Affiliation(s)
- Paolo Stincone
- Laboratório de Bioquímica e Microbiologia Aplicada, Departamento de Ciência de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriano Brandelli
- Laboratório de Bioquímica e Microbiologia Aplicada, Departamento de Ciência de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Wang S, Sun L, Ling N, Zhu C, Chi F, Li W, Hao X, Zhang W, Bian J, Chen L, Wei D. Exploring Soil Factors Determining Composition and Structure of the Bacterial Communities in Saline-Alkali Soils of Songnen Plain. Front Microbiol 2020; 10:2902. [PMID: 32010065 PMCID: PMC6972583 DOI: 10.3389/fmicb.2019.02902] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022] Open
Abstract
Songnen Plain is originally one of the three major glasslands in China and has now become one of the three most concentrated distribution areas of sodic-saline soil worldwide. The soil is continuously degraded by natural and anthropogenic processes, which has a negative impact on agricultural production. The investigation of microbial diversity in this degraded ecosystem is fundamental for comprehending biological and ecological processes and harnessing the potential of microbial resources. The Illumina MiSeq sequencing method was practiced to investigate the bacterial diversity and composition in saline-alkali soil. The results from this study show that the change in pH under alkaline conditions was not the major contributor in shaping bacterial community in Songnen Plain. The electrical conductivity (EC) content of soil was the most important driving force for bacterial composition (20.83%), and the second most influencing factor was Na+ content (14.17%). Bacterial communities were clearly separated in accordance with the EC. The dominant bacterial groups were Planctomycetes, Proteobacteria, and Bacteroidetes among the different salinity soil. As the salt concentration increased, the indicators changed from Planctomycetes and Bacteroidetes to Proteobacteria and Firmicutes. Our results suggest that Proteobacteria and Firmicutes were the main indicator species reflecting changes of the main microbial groups and the EC as a key factor drives the composition of the bacterial community under alkaline conditions in saline-alkali soil of Songnen Plain.
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Affiliation(s)
- Shuang Wang
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lei Sun
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chen Zhu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Fengqin Chi
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Weiqun Li
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xiaoyu Hao
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Wu Zhang
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, China
| | - Jingyang Bian
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Lei Chen
- Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province, Heilongjiang Fertilizer Engineering Research Center, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Dan Wei
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Bioprospection of Enzymes and Microorganisms in Insects to Improve Second-Generation Ethanol Production. Ind Biotechnol (New Rochelle N Y) 2019. [DOI: 10.1089/ind.2019.0019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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22
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Tian M, Chen M, Bao Y, Xu C, Qin Q, Zhang W, He Y, Shao Q. Microbial contributions to bronchial asthma occurrence in children: A metagenomic study. J Cell Biochem 2019; 120:13853-13860. [PMID: 30957268 DOI: 10.1002/jcb.28658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/21/2018] [Accepted: 02/21/2019] [Indexed: 12/31/2022]
Abstract
Bronchial asthma, a common chronic respiratory disease in children, is traditionally regarded as a noninfectious disease. Current hypotheses, however, argue that asthma can be caused by microbial infection. We, therefore, hypothesize that a variety of microbes are more commonly found in the sputum of children with asthma, and these microbes may contribute to the occurrence and development of asthma. The present study proposes to use metagenomic approach to explore microbial diversity and to identify the microbial community characteristics of sputum from children with asthma. We found that microbial communities in the sputum of children differed significantly between asthmatics and controls. Kruskal-Wallis testing showed that 16 phyla, 104 genera, and 159 species were significantly downregulated, whereas two phyla including Platyhelminthes phylum and Chordata phylum, two genera including Spirometra genus and Homo sapiens, and the Spirometra erinaceieuropaei species were significantly upregulated in asthma patients compared with controls (P < 0.05). Among them, H. sapiens and S. erinaceieuropaei exhibited 2.3- and 2.0-fold overabundance in asthmatics vs controls, respectively. Meanwhile, metastats assay demonstrated that 31 phyla, 400 genera, and 813 species were significantly downregulated, whereas two phyla, 10 genera, and 16 species were significantly upregulated in asthma patients compared with controls (P < 0.05). Among them, Tetrahymena thermophila and Candidatus Zinderia insecticola exhibited 4.7-fold overabundance in asthmatics vs controls. Our study establishes a link between microbial infection and the mechanisms leading to asthma development, which will be useful for developing novel diagnostic biomarkers and aiding in the prevention and control of asthma.
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Affiliation(s)
- Man Tian
- Department of Respiratory Medicine, Affiliated Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Meng Chen
- Department of Respiratory Medicine, Affiliated Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Yuling Bao
- Department of Respiratory Medicine, Affiliated Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Changdi Xu
- Department of Respiratory Medicine, Affiliated Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Qiaozhi Qin
- Department of Respiratory Medicine, Affiliated Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Wenxin Zhang
- Department of Respiratory Medicine, Affiliated Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Yuting He
- Department of Respiratory Medicine, Affiliated Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
| | - Qi Shao
- Department of Respiratory Medicine, Affiliated Nanjing Children's Hospital, Nanjing Medical University, Nanjing, China
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Calderon D, Peña L, Suarez A, Villamil C, Ramirez-Rojas A, Anzola JM, García-Betancur JC, Cepeda ML, Uribe D, Del Portillo P, Mongui A. Recovery and functional validation of hidden soil enzymes in metagenomic libraries. Microbiologyopen 2019; 8:e00572. [PMID: 30851083 PMCID: PMC6460280 DOI: 10.1002/mbo3.572] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/01/2017] [Accepted: 11/09/2017] [Indexed: 11/10/2022] Open
Abstract
The vast microbial diversity on the planet represents an invaluable source for identifying novel activities with potential industrial and therapeutic application. In this regard, metagenomics has emerged as a group of strategies that have significantly facilitated the analysis of DNA from multiple environments and has expanded the limits of known microbial diversity. However, the functional characterization of enzymes, metabolites, and products encoded by diverse microbial genomes is limited by the inefficient heterologous expression of foreign genes. We have implemented a pipeline that combines NGS and Sanger sequencing as a way to identify fosmids within metagenomic libraries. This strategy facilitated the identification of putative proteins, subcloning of targeted genes and preliminary characterization of selected proteins. Overall, the in silico approach followed by the experimental validation allowed us to efficiently recover the activity of previously hidden enzymes derived from agricultural soil samples. Therefore, the methodology workflow described herein can be applied to recover activities encoded by environmental DNA from multiple sources.
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Affiliation(s)
- Dayana Calderon
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Luis Peña
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Friedrich-Schiller Universität, Jena, Germany
| | - Angélica Suarez
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Carolina Villamil
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Adan Ramirez-Rojas
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Juan M Anzola
- Computational Biology, Corporación CorpoGen, Bogotá, Colombia
| | | | - Martha L Cepeda
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia
| | - Daniel Uribe
- Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Alvaro Mongui
- Molecular Biotechnology Research Group, Corporación CorpoGen, Bogotá, Colombia.,Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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Ngara TR, Zhang H. Recent Advances in Function-based Metagenomic Screening. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:405-415. [PMID: 30597257 PMCID: PMC6411959 DOI: 10.1016/j.gpb.2018.01.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/01/2022]
Abstract
Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.
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Affiliation(s)
- Tanyaradzwa Rodgers Ngara
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China.
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25
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Alves LDF, Westmann CA, Lovate GL, de Siqueira GMV, Borelli TC, Guazzaroni ME. Metagenomic Approaches for Understanding New Concepts in Microbial Science. Int J Genomics 2018; 2018:2312987. [PMID: 30211213 PMCID: PMC6126073 DOI: 10.1155/2018/2312987] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/21/2018] [Accepted: 07/29/2018] [Indexed: 12/15/2022] Open
Abstract
Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such as disease susceptibility, immunological response, and social and nutritional behaviors. In this context, metagenomics has established a powerful framework for understanding the intricate connections between human societies and microbial communities, ultimately allowing for the optimization of both human health and productivity. Thus, we have shifted from the old concept of microbes as harmful organisms to a broader panorama, in which the signal of the relationship between humans and microbes is flexible and directly dependent on our own decisions and practices. In parallel, metagenomics has also been playing a major role in the prospection of "hidden" genetic features and the development of biotechnological applications, through the discovery of novel genes, enzymes, pathways, and bioactive molecules with completely new or improved biochemical functions. Therefore, this review highlights the major milestones over the last three decades of metagenomics, providing insights into both its potentialities and current challenges.
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Affiliation(s)
- Luana de Fátima Alves
- Department of Biochemistry, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Cauã Antunes Westmann
- Department of Cell Biology, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Gabriel Lencioni Lovate
- Department of Biochemistry, Faculdade de Medicina de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Tiago Cabral Borelli
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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26
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Shamim K, Sharma J, Mutnale M, Dubey SK, Mujawar S. Characterization of a metagenomic serine metalloprotease and molecular docking studies. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.05.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Sola-Oladokun B, Culligan EP, Sleator RD. Engineered Probiotics: Applications and Biological Containment. Annu Rev Food Sci Technol 2017; 8:353-370. [PMID: 28125354 DOI: 10.1146/annurev-food-030216-030256] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bioengineered probiotics represent the next generation of whole cell-mediated biotherapeutics. Advances in synthetic biology, genome engineering, and DNA sequencing and synthesis have enabled scientists to design and develop probiotics with increased stress tolerance and the ability to target specific pathogens and their associated toxins, as well as to mediate targeted delivery of vaccines, drugs, and immunomodulators directly to host cells. Herein, we review the most significant advances in the development of this field. We discuss the critical issue of biological containment and consider the role of synthetic biology in the design and construction of the probiotics of the future.
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Affiliation(s)
- Babasola Sola-Oladokun
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland; , ,
| | - Eamonn P Culligan
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland; , ,
| | - Roy D Sleator
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland; , , .,APC Microbiome Institute, University College Cork, Cork, Ireland
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28
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Sedlar K, Kupkova K, Provaznik I. Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics. Comput Struct Biotechnol J 2016; 15:48-55. [PMID: 27980708 PMCID: PMC5148923 DOI: 10.1016/j.csbj.2016.11.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/24/2016] [Accepted: 11/26/2016] [Indexed: 12/11/2022] Open
Abstract
One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments. On the other hand, the output of whole metagenomic shotgun sequencing is mixture of short DNA fragments belonging to various genomes, therefore this approach requires more sophisticated computational algorithms for clustering of related sequences, commonly referred to as sequence binning. There are currently two types of binning methods: taxonomy dependent and taxonomy independent. The first type classifies the DNA fragments by performing a standard homology inference against a reference database, while the latter performs the reference-free binning by applying clustering techniques on features extracted from the sequences. In this review, we describe the strategies within the second approach. Although these strategies do not require prior knowledge, they have higher demands on the length of sequences. Besides their basic principle, an overview of particular methods and tools is provided. Furthermore, the review covers the utilization of the methods in context with the length of sequences and discusses the needs for metagenomic data preprocessing in form of initial assembly prior to binning.
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Affiliation(s)
- Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, Brno, Czech Republic
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Hobbs ET, Pereira T, O’Neill PK, Erill I. A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. Algorithms Mol Biol 2016; 11:19. [PMID: 27398089 PMCID: PMC4938975 DOI: 10.1186/s13015-016-0082-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/30/2016] [Indexed: 11/13/2022] Open
Abstract
Background Metagenomics enables the analysis of bacterial population composition and the study of emergent population features, such as shared metabolic pathways. Recently, we have shown that metagenomics datasets can be leveraged to characterize population-wide transcriptional regulatory networks, or meta-regulons, providing insights into how bacterial populations respond collectively to specific triggers. Here we formalize a Bayesian inference framework to analyze the composition of transcriptional regulatory networks in metagenomes by determining the probability of regulation of orthologous gene sequences. We assess the performance of this approach on synthetic datasets and we validate it by analyzing the copper-homeostasis network of Firmicutes species in the human gut microbiome. Results Assessment on synthetic datasets shows that our method provides a robust and interpretable metric for assessing putative regulation by a transcription factor on sets of promoter sequences mapping to an orthologous gene cluster. The inference framework integrates the regulatory contribution of secondary sites and can discern false positives arising from multiple instances of a clonal sequence. Posterior probabilities for orthologous gene clusters decline sharply when less than 20 % of mapped promoters have binding sites, but we introduce a sensitivity adjustment procedure to speed up computation that enhances regulation assessment in heterogeneous ortholog clusters. Analysis of the copper-homeostasis regulon governed by CsoR in the human gut microbiome Firmicutes reveals that CsoR controls itself and copper-translocating P-type ATPases, but not CopZ-type copper chaperones. Our analysis also indicates that CsoR frequently targets promoters with dual CsoR-binding sites, suggesting that it exploits higher-order binding conformations to fine-tune its activity. Conclusions We introduce and validate a method for the analysis of transcriptional regulatory networks from metagenomic data that enables inference of meta-regulons in a systematic and interpretable way. Validation of this method on the CsoR meta-regulon of gut microbiome Firmicutes illustrates the usefulness of the approach, revealing novel properties of the copper-homeostasis network in poorly characterized bacterial species and putting forward evidence of new mechanisms of DNA binding for this transcriptional regulator. Our approach will enable the comparative analysis of regulatory networks across metagenomes, yielding novel insights into the evolution of transcriptional regulatory networks. Electronic supplementary material The online version of this article (doi:10.1186/s13015-016-0082-8) contains supplementary material, which is available to authorized users.
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30
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Sleator RD. Synthetic biology: from mainstream to counterculture. Arch Microbiol 2016; 198:711-3. [DOI: 10.1007/s00203-016-1257-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/01/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
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Perlejewski K, Bukowska-Ośko I, Nakamura S, Motooka D, Stokowy T, Płoski R, Rydzanicz M, Zakrzewska-Pniewska B, Podlecka-Piętowska A, Nojszewska M, Gogol A, Caraballo Cortés K, Demkow U, Stępień A, Laskus T, Radkowski M. Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 935:89-98. [PMID: 27311319 DOI: 10.1007/5584_2016_25] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of central nervous system of unknown etiology. However, some infectious agents have been suggested to play a significant role in its pathogenesis. Next-generation sequencing (NGS) and metagenomics can be employed to characterize microbiome of MS patients and to identify potential causative pathogens. In this study, 12 patients with idiopathic inflammatory demyelinating disorders (IIDD) of the central nervous system were studied: one patient had clinically isolated syndrome, one patient had recurrent optic neuritis, and ten patients had multiple sclerosis (MS). In addition, there was one patient with other non-inflammatory neurological disease. Cerebrospinal fluid (CSF) was sampled from all patients. RNA was extracted from CSF and subjected to a single-primer isothermal amplification followed by NGS and comprehensive data analysis. Altogether 441,608,474 reads were obtained and mapped using blastn. In a CSF sample from the patient with clinically isolated syndrome, 11 varicella-zoster virus reads were found. Other than that similar bacterial, fungal, parasitic, and protozoan reads were identified in all samples, indicating a common presence of contamination in metagenomics. In conclusion, we identified varicella zoster virus sequences in one out of the 12 patients with IIDD, which suggests that this virus could be occasionally related to the MS pathogenesis. A widespread bacterial contamination seems inherent to NGS and complicates the interpretation of results.
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Affiliation(s)
- Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | - Iwona Bukowska-Ośko
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland.
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Osaka, Japan
| | - Tomasz Stokowy
- Department of Clinical Science, University of Bergen, Bergen, 5021, Norway
| | - Rafał Płoski
- Department of the Medical Genetics, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | - Małgorzata Rydzanicz
- Department of the Medical Genetics, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | | | | | - Monika Nojszewska
- Department of Neurology, Warsaw Medical University, 1A Banacha, Warsaw, 02-097, Poland
| | - Anna Gogol
- Department of Neurology, Warsaw Medical University, 1A Banacha, Warsaw, 02-097, Poland
| | - Kamila Caraballo Cortés
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | - Urszula Demkow
- Department of Laboratory Medicine and Clinical Immunology of Developmental Age, Medical University of Warsaw, 24 Marszałkowska Street, Warsaw, 00-576, Poland
| | - Adam Stępień
- Department of Neurology, Military Institute of Medicine, 128 Szaserów Street, Warsaw, 04-141, Poland
| | - Tomasz Laskus
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
| | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, 3C Pawińskiego Street, Warsaw, 02-106, Poland
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Abstract
The review centers on the human gastrointestinal tract; focusing first on the bacterial stress responses needed to overcome the physiochemical defenses of the host, specifically how these stress survival strategies can be used as targets for alternative infection control strategies. The concluding section focuses on recent developments in molecular diagnostics; centring on the shifting paradigm from culture to molecular based diagnostics.
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Affiliation(s)
- Roy D Sleator
- a Department of Biological Sciences ; Cork Institute of Technology ; Bishopstown , Cork , Ireland
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33
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Sleator RD. Designer probiotics: Development and applications in gastrointestinal health. World J Gastrointest Pathophysiol 2015; 6:73-78. [PMID: 26301121 PMCID: PMC4540709 DOI: 10.4291/wjgp.v6.i3.73] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/23/2015] [Accepted: 07/14/2015] [Indexed: 02/06/2023] Open
Abstract
Given the increasing commercial and clinical relevance of probiotics, improving their stress tolerance profile and ability to overcome the physiochemical defences of the host is an important biological goal. Herein, I review the current state of the art in the design of engineered probiotic cultures, with a specific focus on their utility as therapeutics for the developing world; from the treatment of chronic and acute enteric infections, and their associated diarrhoeal complexes, to targeting HIV and application as novel mucosal vaccine delivery vehicles.
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Abstract
This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.
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Affiliation(s)
- Rimantas Kodzius
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
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35
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Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria. Inflamm Bowel Dis 2015; 21:1419-27. [PMID: 25939040 PMCID: PMC4450971 DOI: 10.1097/mib.0000000000000344] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inflammatory bowel diseases (IBD), Crohn's disease and ulcerative colitis, are poorly understood disorders affecting the intestinal tract. The current model for disease suggests that genetically susceptible patients develop intolerance to gut microflora, and chronic inflammation develops as a result of environmental insults. Although interest has mainly focused on studying genetic variants and gut bacterial flora, little is known about the potential of viral infection to contribute to disease. Accordingly, we conducted a metagenomic analysis to document the baseline virome in colonic biopsy samples from patients with IBD in order to assess the contribution of viral infection to IBD. Libraries were generated from colon RNA to create approximately 2 GB sequence data per library. Using a bioinformatic pipeline designed to detect viral sequences, more than 1000 viral reads were derived directly from tissue without any coculture or isolation procedure. Herein, we describe the complexity and abundance of viruses, bacteria/bacteriophage, and human endogenous retroviral sequences from 10 patients with IBD and 5 healthy subjects undergoing surveillance colonoscopy. Differences in gut microflora and the abundance of mammalian viruses and human endogenous retroviruses were readily detected in the metagenomic analyses. Specifically, patients with herpesviridae sequences in their colon demonstrated increased expression of human endogenous viral sequences and differences in the diversity of their microbiome. This study provides a promising metagenomic approach to describe the colonic microbiome that can be used to better understand virus-host and phage-bacteria interactions in IBD.
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36
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Tuning the Brain-Gut Axis in Health and Disease. CURRENT STEM CELL REPORTS 2015. [DOI: 10.1007/s40778-014-0004-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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37
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HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool. J Biomed Inform 2015; 54:58-64. [PMID: 25625550 DOI: 10.1016/j.jbi.2015.01.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 12/08/2014] [Accepted: 01/19/2015] [Indexed: 12/29/2022]
Abstract
The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples.
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Abstract
Biothreats are a high priority concern for public safety and national security. The field of microbial forensics was developed to analyze evidence associated with biological crimes in which microbes or their toxins are used as weapons. Microbial forensics is the scientific discipline dedicated to analyzing evidence from a bioterrorism act, biocrime, hoax, or inadvertent microorganism/toxin release for attribution purposes. Microbial forensics combines the practices of epidemiology with the characterization of microbial and microbial-related evidence to assist in determining the specific source of the sample, as individualizing as possible, and/or the methods, means, processes and locations involved to determine the identity of the perpetrator(s) of an attack.
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39
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Sharma S, Vakhlu J. Metagenomics as advanced screening methods for novel microbial metabolites. Microb Biotechnol 2014. [DOI: 10.1201/b17587-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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40
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de Castro AP, Fernandes GDR, Franco OL. Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes. Front Microbiol 2014; 5:489. [PMID: 25278933 PMCID: PMC4166954 DOI: 10.3389/fmicb.2014.00489] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/01/2014] [Indexed: 11/13/2022] Open
Abstract
In recent years a major worldwide problem has arisen with regard to infectious diseases caused by resistant bacteria. Resistant pathogens are related to high mortality and also to enormous healthcare costs. In this field, cultured microorganisms have been commonly focused in attempts to isolate antibiotic resistance genes or to identify antimicrobial compounds. Although this strategy has been successful in many cases, most of the microbial diversity and related antimicrobial molecules have been completely lost. As an alternative, metagenomics has been used as a reliable approach to reveal the prospective reservoir of antimicrobial compounds and antibiotic resistance genes in the uncultured microbial community that inhabits a number of environments. In this context, this review will focus on resistance genes as well as on novel antibiotics revealed by a metagenomics approach from the soil environment. Biotechnology prospects are also discussed, opening new frontiers for antibiotic development.
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Affiliation(s)
- Alinne P de Castro
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Laboratórios Inova, Campo Grande, Brazil
| | - Gabriel da R Fernandes
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Analises Proteomicas e Bioquimicas, Universidade Católica de Brasília Brasilia, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Laboratórios Inova, Campo Grande, Brazil ; Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Centro de Analises Proteomicas e Bioquimicas, Universidade Católica de Brasília Brasilia, Brazil
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41
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Guazzaroni ME, Silva-Rocha R, Ward RJ. Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. Microb Biotechnol 2014; 8:52-64. [PMID: 25123225 PMCID: PMC4321373 DOI: 10.1111/1751-7915.12146] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/22/2014] [Accepted: 06/28/2014] [Indexed: 11/28/2022] Open
Abstract
There is a growing demand for enzymes with improved catalytic performance or tolerance to process-specific parameters, and biotechnology plays a crucial role in the development of biocatalysts for use in industry, agriculture, medicine and energy generation. Metagenomics takes advantage of the wealth of genetic and biochemical diversity present in the genomes of microorganisms found in environmental samples, and provides a set of new technologies directed towards screening for new catalytic activities from environmental samples with potential biotechnology applications. However, biased and low level of expression of heterologous proteins in Escherichia coli together with the use of non-optimal cloning vectors for the construction of metagenomic libraries generally results in an extremely low success rate for enzyme identification. The bottleneck arising from inefficient screening of enzymatic activities has been addressed from several perspectives; however, the limitations related to biased expression in heterologous hosts cannot be overcome by using a single approach, but rather requires the synergetic implementation of multiple methodologies. Here, we review some of the principal constraints regarding the discovery of new enzymes in metagenomic libraries and discuss how these might be resolved by using synthetic biology methods.
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42
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Martin M, Biver S, Steels S, Barbeyron T, Jam M, Portetelle D, Michel G, Vandenbol M. Identification and characterization of a halotolerant, cold-active marine endo-β-1,4-glucanase by using functional metagenomics of seaweed-associated microbiota. Appl Environ Microbiol 2014; 80:4958-67. [PMID: 24907332 PMCID: PMC4135742 DOI: 10.1128/aem.01194-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/29/2014] [Indexed: 11/20/2022] Open
Abstract
A metagenomic library was constructed from microorganisms associated with the brown alga Ascophyllum nodosum. Functional screening of this library revealed 13 novel putative esterase loci and two glycoside hydrolase loci. Sequence and gene cluster analysis showed the wide diversity of the identified enzymes and gave an idea of the microbial populations present during the sample collection period. Lastly, an endo-β-1,4-glucanase having less than 50% identity to sequences of known cellulases was purified and partially characterized, showing activity at low temperature and after prolonged incubation in concentrated salt solutions.
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Affiliation(s)
- Marjolaine Martin
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
| | - Sophie Biver
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
| | - Sébastien Steels
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
| | - Tristan Barbeyron
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France
| | - Murielle Jam
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France
| | - Daniel Portetelle
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, Bretagne, France
| | - Micheline Vandenbol
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomics and novel gene discovery: promise and potential for novel therapeutics. Virulence 2014; 5:399-412. [PMID: 24317337 PMCID: PMC3979868 DOI: 10.4161/viru.27208] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/21/2013] [Accepted: 11/14/2013] [Indexed: 02/06/2023] Open
Abstract
Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics.
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Affiliation(s)
- Eamonn P Culligan
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- School of Microbiology; University College Cork; Cork, Ireland
| | - Roy D Sleator
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- Department of Biological Sciences; Cork Institute of Technology; Bishopstown, Cork, Ireland
| | - Julian R Marchesi
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- Cardiff School of Biosciences; Cardiff University; Cardiff, UK
- Department of Hepatology and Gastroenterology; Imperial College London; London, UK
| | - Colin Hill
- Alimentary Pharmabiotic Centre; University College Cork; Cork, Ireland
- School of Microbiology; University College Cork; Cork, Ireland
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Abstract
Herein, I track the evolution of synthetic biology from its earliest incarnations more than 50 years ago, through the DIYbio revolution, to the next 50 years.
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Affiliation(s)
- Roy D Sleator
- Department of Biological Sciences; Cork Institute of Technology; Cork, Ireland
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Peng Q, Wang X, Shang M, Huang J, Guan G, Li Y, Shi B. Isolation of a novel alkaline-stable lipase from a metagenomic library and its specific application for milkfat flavor production. Microb Cell Fact 2014; 13:1. [PMID: 24387764 PMCID: PMC3880967 DOI: 10.1186/1475-2859-13-1] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 12/29/2013] [Indexed: 12/01/2022] Open
Abstract
Background Lipolytic enzymes are commonly used to produce desired flavors in lipolyzed milkfat (LMF) manufacturing processes. However, the choice of enzyme is critical because it determines the final profile of fatty acids released and the consequent flavor of the product. We previously constructed a metagenomic library from marine sediments, to explore the novel enzymes which have unique properties useful in flavor-enhancing LMF. Results A novel lipase Est_p6 was isolated from a metagenomic library and was expressed highly in E.coli. Bioinformatic analysis indicated that Est_p6 belongs to lipolytic enzyme family IV, the molecular weight of purified Est_p6 was estimated at 36 kDa by SDS-PAGE. The hydrolytic activity of the enzyme was stable under alkaline condition and the optimal temperature was 50°C. It had a high specific activity (2500 U/mg) toward pNP butyrate (pNP-C4), with Km and Vmax values of 1.148 mM and 3497 μmol∙min-1∙mg-1, respectively. The enzyme activity was enhanced by DTT and was not significantly inhibited by PMSF, EDTA or SDS. This enzyme also showed high hydrolysis specificity for myristate (C14) and palmitate (C16). It seems that Est_p6 has safety for commercial LMF flavor production and food manufacturing processes. Conclusions The ocean is a vast and largely unexplored resource for enzymes. According the outstanding alkaline-stability of Est_p6 and it produced myristic acid and palmitic acid more efficiently than other free fatty acids in lipolyzed milkfat. This novel lipase may be used to impart a distinctive and desirable flavor and odor in milkfat flavor production.
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Affiliation(s)
| | | | | | | | | | - Ying Li
- State Key Laboratories for Agro-biotechnology and College of Biological Sciences, China Agricultural University, Beijing 100193, P, R, China.
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome. PLoS One 2013; 8:e82985. [PMID: 24349412 PMCID: PMC3861447 DOI: 10.1371/journal.pone.0082985] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/29/2013] [Indexed: 12/27/2022] Open
Abstract
Functional environmental screening of metagenomic libraries is a powerful means to identify and assign function to novel genes and their encoded proteins without any prior sequence knowledge. In the current study we describe the identification and subsequent analysis of a salt-tolerant clone from a human gut metagenomic library. Following transposon mutagenesis we identified an unknown gene (stlA, for “salt tolerance locus A”) with no current known homologues in the databases. Subsequent cloning and expression in Escherichia coli MKH13 revealed that stlA confers a salt tolerance phenotype in its surrogate host. Furthermore, a detailed in silico analysis was also conducted to gain additional information on the properties of the encoded StlA protein. The stlA gene is rare when searched against human metagenome datasets such as MetaHit and the Human Microbiome Project and represents a novel and unique salt tolerance determinant which appears to be found exclusively in the human gut environment.
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Affiliation(s)
- Eamonn P. Culligan
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Roy D. Sleator
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
- * E-mail: (RS); (JM); (CH)
| | - Julian R. Marchesi
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- Department of Hepatology and Gastroenterology, Imperial College London, London, United Kingdom
- * E-mail: (RS); (JM); (CH)
| | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- * E-mail: (RS); (JM); (CH)
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Walsh P, Carroll J, Sleator RD. Accelerating in silico research with workflows: a lesson in Simplicity. Comput Biol Med 2013; 43:2028-35. [PMID: 24290918 DOI: 10.1016/j.compbiomed.2013.09.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 09/09/2013] [Accepted: 09/12/2013] [Indexed: 10/26/2022]
Abstract
Bioinformatics is the application of computer science and related disciplines to the field of molecular biology. While there are currently several web based and desktop tools available for biologists to perform routine bioinformatics tasks, these tools often require users to manually and repeatedly co-ordinate multiple applications before reaching a result. In an effort to reduce time and error, workflow tools have been developed to automate these tasks. However, many of these tools require expert knowledge of the techniques and supporting databases which more often than not lies outside the scope of most biologists. Herein, we describe the development of sequence information management platform (Simplicity), a workflow-based bioinformatics management tool, which allows non-bioinformaticians to rapidly annotate large amounts of DNA and protein sequence data.
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Affiliation(s)
- Paul Walsh
- nSilico LifeSciences, Ltd., Melbourne Building, Bishopstown, Cork, Ireland
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O'Driscoll A, Daugelaite J, Sleator RD. 'Big data', Hadoop and cloud computing in genomics. J Biomed Inform 2013; 46:774-81. [PMID: 23872175 DOI: 10.1016/j.jbi.2013.07.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 06/17/2013] [Accepted: 07/08/2013] [Indexed: 12/18/2022]
Abstract
Since the completion of the Human Genome project at the turn of the Century, there has been an unprecedented proliferation of genomic sequence data. A consequence of this is that the medical discoveries of the future will largely depend on our ability to process and analyse large genomic data sets, which continue to expand as the cost of sequencing decreases. Herein, we provide an overview of cloud computing and big data technologies, and discuss how such expertise can be used to deal with biology's big data sets. In particular, big data technologies such as the Apache Hadoop project, which provides distributed and parallelised data processing and analysis of petabyte (PB) scale data sets will be discussed, together with an overview of the current usage of Hadoop within the bioinformatics community.
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Affiliation(s)
- Aisling O'Driscoll
- Department of Computing, Cork Institute of Technology, Rossa Avenue, Bishopstown, Cork, Ireland
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Alteration of bacterial communities and organic matter in microbial fuel cells (MFCs) supplied with soil and organic fertilizer. Appl Microbiol Biotechnol 2013; 97:1299-315. [PMID: 22290652 DOI: 10.1007/s00253-012-3906-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/12/2012] [Accepted: 01/16/2012] [Indexed: 10/14/2022]
Abstract
The alteration of the organic matter (OM) and the composition of bacterial community in microbial fuel cells (MFCs) supplied with soil (S) and a composted organic fertilizer (A) was examined at the beginning and at the end of 3 weeks of incubation under current-producing as well as no-current-producing conditions. Denaturing gradient gel electrophoresis revealed a significant alteration of the microbial community structure in MFCs generating electricity as compared with no-current-producing MFCs. The genetic diversity of cultivable bacterial communities was assessed by random amplified polymorphic DNA (RAPD) analysis of 106 bacterial isolates obtained by using both generic and elective media. Sequencing of the 16S rRNA genes of the more representative RAPD groups indicated that over 50.4% of the isolates from MFCs fed with S were Proteobacteria, 25.1% Firmicutes, and 24.5% Actinobacteria, whereas in MFCs supplied with A 100% of the dominant species belonged to γ-Proteobacteria. The chemical analysis performed by fractioning the OM and using thermal analysis showed that the amount of total organic carbon contained in the soluble phase of the electrochemically active chambers significantly decreased as compared to the no-current-producing systems, whereas the OM of the solid phase became more humified and aromatic along with electricity generation, suggesting a significant stimulation of a humification process of the OM. These findings demonstrated that electroactive bacteria are commonly present in aerobic organic substrates such as soil or a fertilizer and that MFCs could represent a powerful tool for exploring the mineralization and humification processes of the soil OM.
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Sleator RD. A beginner's guide to phylogenetics. MICROBIAL ECOLOGY 2013; 66:1-4. [PMID: 23624570 DOI: 10.1007/s00248-013-0236-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 04/17/2013] [Indexed: 06/02/2023]
Abstract
Metagenomics and the development of high throughput next generation sequencing capabilities have forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet's inhabitants. Herein, I review the major tree-building strategies, challenges and opportunities which exist in this rapidly expanding field of evolutionary biology.
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