1
|
Alanzi AR. Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods. J Microbiol Biotechnol 2024; 35:e2407064. [PMID: 39639495 PMCID: PMC11813339 DOI: 10.4014/jmb.2407.07064] [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: 08/14/2024] [Revised: 10/22/2024] [Accepted: 10/30/2024] [Indexed: 12/07/2024]
Abstract
The objective of this review is to investigate microbial dark matter (MDM) with a focus on its potential for discovering novel natural products (NPs). This first part will examine the characteristics and abundance of these previously unexplored microbial communities, as well as the challenges faced in identifying and harnessing their unique biochemical properties and novel methods in this field. MDMs are thought to hold great potential for the discovery of novel NPs, which could have significant applications in medicine, agriculture, and industry. In recent years, there has been a growing interest in exploring MDM to unlock its potential. In fact, developments in genome-sequencing technologies and sophisticated phylogenetic procedures and metagenomic techniques have contributed to drastically make important changes in our sights on the diversity of microbial life, including the very outline of the tree of life. This has led to the development of novel technologies and methodologies for studying these elusive microorganisms, such as single-cell genomics, metagenomics, and culturomics. These approaches enable researchers to isolate and analyze individual microbial cells, as well as entire communities, providing insights into their genetic and metabolic potential. By delving into the MDM, scientists hope to uncover new compounds and biotechnological advancements that could have far-reaching impacts on various fields.
Collapse
Affiliation(s)
- Abdullah R Alanzi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
2
|
Wang J, Ou Y, Li R, Tao C, Liu H, Li R, Shen Z, Shen Q. The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 283:116982. [PMID: 39217893 DOI: 10.1016/j.ecoenv.2024.116982] [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: 05/30/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
The spread of antibiotic resistance genes (ARGs) and subsequent soil-borne disease outbreaks are major threats to soil health and sustainable crop production. However, the relationship between occurrences of soil-borne diseases and the transmission of soil ARGs remains unclear. Here, soil ARGs, mobile genetic elements and microbial communities from co-located disease suppressive and conducive banana orchards were deciphered using metagenomics and metatranscriptomics approaches. In total, 23 ARG types, with 399 subtypes, were detected using a metagenomics approach, whereas 23 ARG types, with 452 subtypes, were discovered using a metatranscriptomics method. Furthermore, the metagenomics analysis revealed that the ARG total abundance levels were greater in rhizospheres (0.45 ARGs/16S rRNA on average) compared with bulk (0.32 ARGs/16S rRNA on average) soils. Interestingly, metatranscriptomics revealed that the total ARG abundances were greater in disease-conducive (8.85 ARGs/16S rRNA on average) soils than disease suppressive (1.45 ARGs/16S rRNA on average) soils. Mobile genetic elements showed the same trends as ARGs. Network and binning analyses indicated that Mycobacterium, Streptomyces, and Blastomonas are the main potential hosts of ARGs. Furthermore, Bacillus was significantly and negatively correlated with Fusarium (P < 0.05, r = -0.84) and hosts of ARGs (i.e., Mycobacterium, Streptomyces, and Blastomonas). By comparing metagenomic and metatranscriptomic analyses,this study demonstrated that metatranscriptomics may be more sensitive in indicating ARGs activities in soil. Our findings enable the more accurate assessment of the transmission risk of ARGs. The data provide a new perspective for recognizing soil health, in which soil-borne disease outbreaks appear to be associated with ARG spread, whereas beneficial microbe enrichment may mitigate wilt disease and ARG transmission.
Collapse
Affiliation(s)
- Jiabao Wang
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yannan Ou
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Ruochen Li
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chengyuan Tao
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Hongjun Liu
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Rong Li
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zongzhuan Shen
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
| | - Qirong Shen
- The Sanya Institute of the Nanjing Agricultural University, Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| |
Collapse
|
3
|
Wen L, Yang L, Chen C, Li J, Fu J, Liu G, Kan Q, Ho CT, Huang Q, Lan Y, Cao Y. Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods. Crit Rev Food Sci Nutr 2023; 64:8367-8383. [PMID: 37068005 DOI: 10.1080/10408398.2023.2199425] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fermented foods are important components of the human diet. There is increasing awareness of abundant nutritional and functional properties present in fermented foods that arise from the transformation of substrates by microbial communities. Thus, it is significant to unravel the microbial communities and mechanisms of characteristic flavor formation occurring during fermentation. There has been rapid development of high-throughput and other omics technologies, such as metaproteomics and metabolomics, and as a result, there is growing recognition of the importance of integrating these approaches. The successful applications of multi-omics approaches and bioinformatics analyses have provided a solid foundation for exploring the fermentation process. Compared with single-omics, multi-omics analyses more accurately delineate microbial and molecular features, thus they are more apt to reveal the mechanisms of fermentation. This review introduces fermented foods and an overview of single-omics technologies - including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. We also discuss integrated multi-omics and bioinformatic analyses and their role in recent research progress related to fermented foods, as well as summarize the main potential pathways involved in certain fermented foods. In the future, multilayered analyses of multi-omics data should be conducted to enable better understanding of flavor formation mechanisms in fermented foods.
Collapse
Affiliation(s)
- Linfeng Wen
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Lixin Yang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Cong Chen
- Guangdong Eco-engineering Polytechnic, Guangzhou, China
| | - Jun Li
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Meiweixian Flavoring Foods Co., Ltd, Zhongshan, China
| | - Jiangyan Fu
- Guangdong Meiweixian Flavoring Foods Co., Ltd, Zhongshan, China
| | - Guo Liu
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Qixin Kan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Qingrong Huang
- Department of Food Science, Rutgers University, New Brunswick, New Jersey, USA
| | - Yaqi Lan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| |
Collapse
|
4
|
Kuraji R, Shiba T, Dong TS, Numabe Y, Kapila YL. Periodontal treatment and microbiome-targeted therapy in management of periodontitis-related nonalcoholic fatty liver disease with oral and gut dysbiosis. World J Gastroenterol 2023; 29:967-996. [PMID: 36844143 PMCID: PMC9950865 DOI: 10.3748/wjg.v29.i6.967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
A growing body of evidence from multiple areas proposes that periodontal disease, accompanied by oral inflammation and pathological changes in the microbiome, induces gut dysbiosis and is involved in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). A subgroup of NAFLD patients have a severely progressive form, namely nonalcoholic steatohepatitis (NASH), which is characterized by histological findings that include inflammatory cell infiltration and fibrosis. NASH has a high risk of further progression to cirrhosis and hepatocellular carcinoma. The oral microbiota may serve as an endogenous reservoir for gut microbiota, and transport of oral bacteria through the gastro-intestinal tract can set up a gut microbiome dysbiosis. Gut dysbiosis increases the production of potential hepatotoxins, including lipopolysaccharide, ethanol, and other volatile organic compounds such as acetone, phenol and cyclopentane. Moreover, gut dysbiosis increases intestinal permeability by disrupting tight junctions in the intestinal wall, leading to enhanced translocation of these hepatotoxins and enteric bacteria into the liver through the portal circulation. In particular, many animal studies support that oral administration of Porphyromonas gingivalis, a typical periodontopathic bacterium, induces disturbances in glycolipid metabolism and inflammation in the liver with gut dysbiosis. NAFLD, also known as the hepatic phenotype of metabolic syndrome, is strongly associated with metabolic complications, such as obesity and diabetes. Periodontal disease also has a bidirectional relationship with metabolic syndrome, and both diseases may induce oral and gut microbiome dysbiosis with insulin resistance and systemic chronic inflammation cooperatively. In this review, we will describe the link between periodontal disease and NAFLD with a focus on basic, epidemiological, and clinical studies, and discuss potential mechanisms linking the two diseases and possible therapeutic approaches focused on the microbiome. In conclusion, it is presumed that the pathogenesis of NAFLD involves a complex crosstalk between periodontal disease, gut microbiota, and metabolic syndrome. Thus, the conventional periodontal treatment and novel microbiome-targeted therapies that include probiotics, prebiotics and bacteriocins would hold great promise for preventing the onset and progression of NAFLD and subsequent complications in patients with periodontal disease.
Collapse
Affiliation(s)
- Ryutaro Kuraji
- Department of Periodontology, The Nippon Dental University School of Life Dentistry at Tokyo, Tokyo 102-0071, Japan
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA 94143, United States
| | - Takahiko Shiba
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, United States
- Department of Periodontology, Tokyo Medical and Dental University, Tokyo 113-8549, Japan
| | - Tien S Dong
- The Vatche and Tamar Manoukian Division of Digestive Diseases, University of California Los Angeles, Department of Medicine, University of California David Geffen School of Medicine, Los Angeles, CA 90095, United States
| | - Yukihiro Numabe
- Department of Periodontology, The Nippon Dental University School of Life Dentistry at Tokyo, Tokyo 102-8159, Japan
| | - Yvonne L Kapila
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA 94143, United States
- Sections of Biosystems and Function and Periodontics, Professor and Associate Dean of Research, Felix and Mildred Yip Endowed Chair in Dentistry, University of California Los Angeles, Los Angeles, CA 90095, United States
| |
Collapse
|
5
|
Chaudhari HG, Prajapati S, Wardah ZH, Raol G, Prajapati V, Patel R, Shati AA, Alfaifi MY, Elbehairi SEI, Sayyed RZ. Decoding the microbial universe with metagenomics: a brief insight. Front Genet 2023; 14:1119740. [PMID: 37197021 PMCID: PMC10183756 DOI: 10.3389/fgene.2023.1119740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
A major part of any biological system on earth involves microorganisms, of which the majority are yet to be cultured. The conventional methods of culturing microbes have given fruitful outcomes yet have limitations. The curiosity for better understanding has led to the development of culture-independent molecular methods that help push aside the roadblocks of earlier methods. Metagenomics unifies the scientific community in search of a better understanding of the functioning of the ecosystem and its component organisms. This approach has opened a new paradigm in advanced research. It has brought to light the vast diversity and novelty among microbial communities and their genomes. This review focuses on the development of this field over time, the techniques and analysis of data generated through sequencing platforms, and its prominent interpretation and representation.
Collapse
Affiliation(s)
- Hiral G. Chaudhari
- Shri Alpesh N. Patel PG Institute of Science and Research, Sardar Patel University, Anand, Gujarat, India
| | - Shobha Prajapati
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Zuhour Hussein Wardah
- Shri Alpesh N. Patel PG Institute of Science and Research, Sardar Patel University, Anand, Gujarat, India
| | - Gopal Raol
- Shri R. P. Arts, Shri K.B. Commerce, and Smt. BCJ Science College, Khambhat, Gujarat, India
| | - Vimalkumar Prajapati
- Division of Microbial and Environmental Biotechnology, Aspee Shakilam Biotechnology Institute, Navsari Agricultural University, Surat, Gujarat, India
- *Correspondence: Vimalkumar Prajapati,
| | - Rajesh Patel
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | | | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandal's S I Patil Arts, G B Patel Science and STKV Sangh Commerce College, Shahada, India
| |
Collapse
|
6
|
Zhao B, van Bodegom PM, Trimbos KB. Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA. Mol Ecol Resour 2023; 23:81-91. [PMID: 35899418 PMCID: PMC10087510 DOI: 10.1111/1755-0998.13691] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 07/12/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Environmental DNA (eDNA) approaches contributing to species identifications are quickly becoming the new norm in biomonitoring and ecosystem assessments. Yet, information such as age and health state of the population, which is vital to species biomonitoring, has not been accessible from eDNA. DNA methylation has the potential to provide such information on the state of a population. Here, we measured the methylation of eDNA along with tissue DNA (tDNA) of Lymnaea stagnalis at four life stages. We demonstrate that eDNA methylation varies with age and allows distinguishing among age classes. Moreover, eDNA was globally hypermethylated in comparison to tDNA. This difference was age-specific and connected to a limited number of eDNA sites. This differential methylation pattern suggests that eDNA release with age is partially regulated through DNA methylation. Our findings help to understand mechanisms involved in eDNA release and shows the potential of eDNA methylation analysis to assess age classes. Such age class assessments will encourage future eDNA studies to assess fundamental processes of population dynamics and functioning in ecology, biodiversity conservation and impact assessments.
Collapse
Affiliation(s)
- Beilun Zhao
- Department of Environmental BiologyInstitute of Environmental Sciences, Leiden UniversityLeidenThe Netherlands
| | - Peter M. van Bodegom
- Department of Environmental BiologyInstitute of Environmental Sciences, Leiden UniversityLeidenThe Netherlands
| | - Krijn B. Trimbos
- Department of Environmental BiologyInstitute of Environmental Sciences, Leiden UniversityLeidenThe Netherlands
| |
Collapse
|
7
|
Ko KKK, Chng KR, Nagarajan N. Metagenomics-enabled microbial surveillance. Nat Microbiol 2022; 7:486-496. [PMID: 35365786 DOI: 10.1038/s41564-022-01089-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
Lessons learnt from the COVID-19 pandemic include increased awareness of the potential for zoonoses and emerging infectious diseases that can adversely affect human health. Although emergent viruses are currently in the spotlight, we must not forget the ongoing toll of morbidity and mortality owing to antimicrobial resistance in bacterial pathogens and to vector-borne, foodborne and waterborne diseases. Population growth, planetary change, international travel and medical tourism all contribute to the increasing frequency of infectious disease outbreaks. Surveillance is therefore of crucial importance, but the diversity of microbial pathogens, coupled with resource-intensive methods, compromises our ability to scale-up such efforts. Innovative technologies that are both easy to use and able to simultaneously identify diverse microorganisms (viral, bacterial or fungal) with precision are necessary to enable informed public health decisions. Metagenomics-enabled surveillance methods offer the opportunity to improve detection of both known and yet-to-emerge pathogens.
Collapse
Affiliation(s)
- Karrie K K Ko
- Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore, Singapore.,Department of Microbiology, Singapore General Hospital, Singapore, Singapore.,Department of Molecular Pathology, Singapore General Hospital, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Yong Loo Lin School of Medicine, National Univerisity of Singapore, Singapore, Singapore
| | - Kern Rei Chng
- Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore, Singapore.,National Centre for Food Science, Singapore Food Agency, Singapore, Singapore
| | - Niranjan Nagarajan
- Laboratory of Metagenomic Technologies and Microbial Systems, Genome Institute of Singapore, Singapore, Singapore. .,Yong Loo Lin School of Medicine, National Univerisity of Singapore, Singapore, Singapore.
| |
Collapse
|
8
|
Biotechnological approaches in agriculture and environmental management - bacterium Kocuria rhizophila 14ASP as heavy metal and salt- tolerant plant growth- promoting strain. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00826-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
9
|
Liu Z, Ma A, Mathé E, Merling M, Ma Q, Liu B. Network analyses in microbiome based on high-throughput multi-omics data. Brief Bioinform 2021; 22:1639-1655. [PMID: 32047891 PMCID: PMC7986608 DOI: 10.1093/bib/bbaa005] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Together with various hosts and environments, ubiquitous microbes interact closely with each other forming an intertwined system or community. Of interest, shifts of the relationships between microbes and their hosts or environments are associated with critical diseases and ecological changes. While advances in high-throughput Omics technologies offer a great opportunity for understanding the structures and functions of microbiome, it is still challenging to analyse and interpret the omics data. Specifically, the heterogeneity and diversity of microbial communities, compounded with the large size of the datasets, impose a tremendous challenge to mechanistically elucidate the complex communities. Fortunately, network analyses provide an efficient way to tackle this problem, and several network approaches have been proposed to improve this understanding recently. Here, we systemically illustrate these network theories that have been used in biological and biomedical research. Then, we review existing network modelling methods of microbial studies at multiple layers from metagenomics to metabolomics and further to multi-omics. Lastly, we discuss the limitations of present studies and provide a perspective for further directions in support of the understanding of microbial communities.
Collapse
Affiliation(s)
- Zhaoqian Liu
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Ewy Mathé
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Marlena Merling
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| | - Bingqiang Liu
- Department of Biomedical Informatics, College of Medicine, the Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
10
|
Mehta S, Kumar P, Crane M, Johnson JE, Sajulga R, Nguyen DDA, McGowan T, Arntzen MØ, Griffin TJ, Jagtap PD. Updates on metaQuantome Software for Quantitative Metaproteomics. J Proteome Res 2021; 20:2130-2137. [PMID: 33683127 DOI: 10.1021/acs.jproteome.0c00960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
metaQuantome is a software suite that enables the quantitative analysis, statistical evaluation. and visualization of mass-spectrometry-based metaproteomics data. In the latest update of this software, we have provided several extensions, including a step-by-step training guide, the ability to perform statistical analysis on samples from multiple conditions, and a comparative analysis of metatranscriptomics data. The training module, accessed via the Galaxy Training Network, will help users to use the suite effectively both for functional as well as for taxonomic analysis. We extend the ability of metaQuantome to now perform multi-data-point quantitative and statistical analyses so that studies with measurements across multiple conditions, such as time-course studies, can be analyzed. With an eye on the multiomics analysis of microbial communities, we have also initiated the use of metaQuantome statistical and visualization tools on outputs from metatranscriptomics data, which complements the metagenomic and metaproteomic analyses already available. For this, we have developed a tool named MT2MQ ("metatranscriptomics to metaQuantome"), which takes in outputs from the ASaiM metatranscriptomics workflow and transforms them so that the data can be used as an input for comparative statistical analysis and visualization via metaQuantome. We believe that these improvements to metaQuantome will facilitate the use of the software for quantitative metaproteomics and metatranscriptomics and will enable multipoint data analysis. These improvements will take us a step toward integrative multiomic microbiome analysis so as to understand dynamic taxonomic and functional responses of these complex systems in a variety of biological contexts. The updated metaQuantome and MT2MQ are open-source software and are available via the Galaxy Toolshed and GitHub.
Collapse
Affiliation(s)
- Subina Mehta
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Praveen Kumar
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Marie Crane
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Ray Sajulga
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Dinh Duy An Nguyen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Thomas McGowan
- Minnesota Supercomputing Institute, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
11
|
Imchen M, Moopantakath J, Kumavath R, Barh D, Tiwari S, Ghosh P, Azevedo V. Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance. Front Genet 2020; 11:563975. [PMID: 33240317 PMCID: PMC7677515 DOI: 10.3389/fgene.2020.563975] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022] Open
Abstract
A multitude of factors, such as drug misuse, lack of strong regulatory measures, improper sewage disposal, and low-quality medicine and medications, have been attributed to the emergence of drug resistant microbes. The emergence and outbreaks of multidrug resistance to last-line antibiotics has become quite common. This is further fueled by the slow rate of drug development and the lack of effective resistome surveillance systems. In this review, we provide insights into the recent advances made in computational approaches for the surveillance of antibiotic resistomes, as well as experimental formulation of combinatorial drugs. We explore the multiple roles of antibiotics in nature and the current status of combinatorial and adjuvant-based antibiotic treatments with nanoparticles, phytochemical, and other non-antibiotics based on synergetic effects. Furthermore, advancements in machine learning algorithms could also be applied to combat the spread of antibiotic resistance. Development of resistance to new antibiotics is quite rapid. Hence, we review the recent literature on discoveries of novel antibiotic resistant genes though shotgun and expression-based metagenomics. To decelerate the spread of antibiotic resistant genes, surveillance of the resistome is of utmost importance. Therefore, we discuss integrative applications of whole-genome sequencing and metagenomics together with machine learning models as a means for state-of-the-art surveillance of the antibiotic resistome. We further explore the interactions and negative effects between antibiotics and microbiomes upon drug administration.
Collapse
Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
12
|
Prayogo FA, Budiharjo A, Kusumaningrum HP, Wijanarka W, Suprihadi A, Nurhayati N. Metagenomic applications in exploration and development of novel enzymes from nature: a review. J Genet Eng Biotechnol 2020; 18:39. [PMID: 32749574 PMCID: PMC7403272 DOI: 10.1186/s43141-020-00043-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Microbial community has an essential role in various fields, especially the industrial sector. Microbes produce metabolites in the form of enzymes, which are one of the essential compounds for industrial processes. Unfortunately, there are still numerous microbes that cannot be identified and cultivated because of the limitations of the culture-based method. The metagenomic approach is a solution for researchers to overcome these problems. Metagenomics is a strategy used to analyze the genomes of microbial communities in the environment directly. Metagenomics application used to explore novel enzymes is essential because it allows researchers to obtain data on microbial diversity, reaching of 99% and various types of genes encoding an enzyme that has not yet been identified. Basic methods in metagenomics have been developed and are commonly used in various studies. A basic understanding of metagenomics for researchers is needed, especially young researchers to support the success of the research. SHORT CONCLUSION Therefore, this review was done in order to provide a deep understanding of metagenomics. It also discussed the application and basic methods of metagenomics in the exploration of novel enzymes, especially in the latest research. Several types of enzymes, such as cellulases, proteases, and lipases, which have been explored using metagenomics, were reviewed in this article.
Collapse
Affiliation(s)
- Fitra Adi Prayogo
- Department of Biology, Faculty of Science and Mathematics, Diponegoro University, Semarang City, 50275 Indonesia
| | - Anto Budiharjo
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
- Molecular and Applied Microbiology Laboratory, Center Central Laboratory of Research and Service - Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| | | | - Wijanarka Wijanarka
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| | - Agung Suprihadi
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| | - Nurhayati Nurhayati
- Biotechnology Study Program, Faculty of Science and Mathematics, Diponegoro University, Jl. Prof. Sudharto SH, Semarang, 50275 Indonesia
| |
Collapse
|
13
|
Utro F, Haiminen N, Siragusa E, Gardiner LJ, Seabolt E, Krishna R, Kaufman JH, Parida L. Hierarchically Labeled Database Indexing Allows Scalable Characterization of Microbiomes. iScience 2020; 23:100988. [PMID: 32248063 PMCID: PMC7125348 DOI: 10.1016/j.isci.2020.100988] [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: 01/20/2020] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 12/14/2022] Open
Abstract
Increasingly available microbial reference data allow interpreting the composition and function of previously uncharacterized microbial communities in detail, via high-throughput sequencing analysis. However, efficient methods for read classification are required when the best database matches for short sequence reads are often shared among multiple reference sequences. Here, we take advantage of the fact that microbial sequences can be annotated relative to established tree structures, and we develop a highly scalable read classifier, PRROMenade, by enhancing the generalized Burrows-Wheeler transform with a labeling step to directly assign reads to the corresponding lowest taxonomic unit in an annotation tree. PRROMenade solves the multi-matching problem while allowing fast variable-size sequence classification for phylogenetic or functional annotation. Our simulations with 5% added differences from reference indicated only 1.5% error rate for PRROMenade functional classification. On metatranscriptomic data PRROMenade highlighted biologically relevant functional pathways related to diet-induced changes in the human gut microbiome.
Collapse
Affiliation(s)
- Filippo Utro
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Niina Haiminen
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Enrico Siragusa
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | | | - Ed Seabolt
- IBM Research, Almaden Research Center, San Jose, CA 95120, USA
| | - Ritesh Krishna
- IBM Research, The Hartree Centre, Warrington, WA4 4AD, UK
| | - James H Kaufman
- IBM Research, Almaden Research Center, San Jose, CA 95120, USA.
| | - Laxmi Parida
- IBM Research, T.J. Watson Research Center, Yorktown Heights, NY 10598, USA.
| |
Collapse
|
14
|
Jo J, Oh J, Park C. Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists. J Microbiol 2020; 58:176-192. [PMID: 32108314 DOI: 10.1007/s12275-020-9525-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022]
Abstract
Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted ("shotgun") sequencing of all ("meta") microbial genomes ("genomic") present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.
Collapse
Affiliation(s)
- Jihoon Jo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jooseong Oh
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
| |
Collapse
|
15
|
Breitwieser FP, Lu J, Salzberg SL. A review of methods and databases for metagenomic classification and assembly. Brief Bioinform 2019; 20:1125-1136. [PMID: 29028872 PMCID: PMC6781581 DOI: 10.1093/bib/bbx120] [Citation(s) in RCA: 297] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Microbiome research has grown rapidly over the past decade, with a proliferation of new methods that seek to make sense of large, complex data sets. Here, we survey two of the primary types of methods for analyzing microbiome data: read classification and metagenomic assembly, and we review some of the challenges facing these methods. All of the methods rely on public genome databases, and we also discuss the content of these databases and how their quality has a direct impact on our ability to interpret a microbiome sample.
Collapse
Affiliation(s)
| | | | - Steven L Salzberg
- Corresponding author: Steven L. Salzberg, Center for Computational Biology, Johns Hopkins University, 1900 E. Monument St., Baltimore, MD, 21205, USA. E-mail:
| |
Collapse
|
16
|
Niu SY, Liu B, Ma Q, Chou WC. rSeqTU-A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units. Front Genet 2019; 10:374. [PMID: 31156694 PMCID: PMC6529933 DOI: 10.3389/fgene.2019.00374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/09/2019] [Indexed: 11/13/2022] Open
Abstract
A transcription unit (TU) is composed of one or multiple adjacent genes on the same strand that are co-transcribed in mostly prokaryotes. Accurate identification of TUs is a crucial first step to delineate the transcriptional regulatory networks and elucidate the dynamic regulatory mechanisms encoded in various prokaryotic genomes. Many genomic features, for example, gene intergenic distance, and transcriptomic features including continuous and stable RNA-seq reads count signals, have been collected from a large amount of experimental data and integrated into classification techniques to computationally predict genome-wide TUs. Although some tools and web servers are able to predict TUs based on bacterial RNA-seq data and genome sequences, there is a need to have an improved machine learning prediction approach and a better comprehensive pipeline handling QC, TU prediction, and TU visualization. To enable users to efficiently perform TU identification on their local computers or high-performance clusters and provide a more accurate prediction, we develop an R package, named rSeqTU. rSeqTU uses a random forest algorithm to select essential features describing TUs and then uses support vector machine (SVM) to build TU prediction models. rSeqTU (available at https://s18692001.github.io/rSeqTU/) has six computational functionalities including read quality control, read mapping, training set generation, random forest-based feature selection, TU prediction, and TU visualization.
Collapse
Affiliation(s)
- Sheng-Yong Niu
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
| | - Binqiang Liu
- School of Mathematics, Shandong University, Jinan, China
| | - Qin Ma
- Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Wen-Chi Chou
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| |
Collapse
|