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Hou S, Tang T, Cheng S, Liu Y, Xia T, Chen T, Fuhrman J, Sun F. DeepMicroClass sorts metagenomic contigs into prokaryotes, eukaryotes and viruses. NAR Genom Bioinform 2024; 6:lqae044. [PMID: 38711860 PMCID: PMC11071121 DOI: 10.1093/nargab/lqae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/18/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Sequence classification facilitates a fundamental understanding of the structure of microbial communities. Binary metagenomic sequence classifiers are insufficient because environmental metagenomes are typically derived from multiple sequence sources. Here we introduce a deep-learning based sequence classifier, DeepMicroClass, that classifies metagenomic contigs into five sequence classes, i.e. viruses infecting prokaryotic or eukaryotic hosts, eukaryotic or prokaryotic chromosomes, and prokaryotic plasmids. DeepMicroClass achieved high performance for all sequence classes at various tested sequence lengths ranging from 500 bp to 100 kbps. By benchmarking on a synthetic dataset with variable sequence class composition, we showed that DeepMicroClass obtained better performance for eukaryotic, plasmid and viral contig classification than other state-of-the-art predictors. DeepMicroClass achieved comparable performance on viral sequence classification with geNomad and VirSorter2 when benchmarked on the CAMI II marine dataset. Using a coastal daily time-series metagenomic dataset as a case study, we showed that microbial eukaryotes and prokaryotic viruses are integral to microbial communities. By analyzing monthly metagenomes collected at HOT and BATS, we found relatively higher viral read proportions in the subsurface layer in late summer, consistent with the seasonal viral infection patterns prevalent in these areas. We expect DeepMicroClass will promote metagenomic studies of under-appreciated sequence types.
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Affiliation(s)
- Shengwei Hou
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Tianqi Tang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Siliangyu Cheng
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Yuanhao Liu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Tian Xia
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ting Chen
- Department of Computer Science and Technology, Institute of Artificial Intelligence & BNRist, Tsinghua University, Beijing 100084, China
| | - Jed A Fuhrman
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Fengzhu Sun
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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2
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Chuzel L, Sinha A, Cunningham CV, Taron CH. High-throughput nanopore DNA sequencing of large insert fosmid clones directly from bacterial colonies. Appl Environ Microbiol 2024:e0024324. [PMID: 38767355 DOI: 10.1128/aem.00243-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/21/2024] [Indexed: 05/22/2024] Open
Abstract
Fosmids and cosmids are vectors frequently used in functional metagenomic studies. With a large insert capacity (around 30 kb) they can encode dozens of cloned genes or in some cases, entire biochemical pathways. Fosmids with cloned inserts can be transferred to heterologous hosts and propagated to enable screening for new enzymes and metabolites. After screening, fosmids from clones with an activity of interest must be de novo sequenced, a critical step toward the identification of the gene(s) of interest. In this work, we present a new approach for rapid and high-throughput fosmid sequencing directly from Escherichia coli colonies without liquid culturing or fosmid purification. Our sample preparation involves fosmid amplification with phi29 polymerase and then direct nanopore sequencing using the Oxford Nanopore Technologies system. We also present a bioinformatics pipeline termed "phiXXer" that facilitates both de novo read assembly and vector trimming to generate a linear sequence of the fosmid insert. Finally, we demonstrate the accurate sequencing of 96 fosmids in a single run and validate the method using two fosmid libraries that contain cloned large insert (~30-40 kb) genomic or metagenomic DNA.IMPORTANCELarge-insert clone (fosmids or cosmids) sequencing is challenging and arguably the most limiting step of functional metagenomic screening workflows. Our study establishes a new method for high-throughput nanopore sequencing of fosmid clones directly from lysed Escherichia coli cells. It also describes a companion bioinformatic pipeline that enables de novo assembly of fosmid DNA insert sequences. The devised method widens the potential of functional metagenomic screening by providing a simple, high-throughput approach to fosmid clone sequencing that dramatically speeds the pace of discovery.
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Affiliation(s)
- Léa Chuzel
- New England Biolabs, Ipswich, Massachusetts, USA
| | - Amit Sinha
- New England Biolabs, Ipswich, Massachusetts, USA
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Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy SF. Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. Nucleic Acids Res 2024:gkae332. [PMID: 38709890 DOI: 10.1093/nar/gkae332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/23/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.
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Affiliation(s)
- Weiyi Li
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Darach Miller
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Xianan Liu
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Lamia Chkaiban
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Han Mei
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Po-Hsiang Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
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Sun X, Guo N, Gao J, Xiao N. Using eDNA to survey amphibians: Methods, applications, and challenges. Biotechnol Bioeng 2024; 121:456-471. [PMID: 37986625 DOI: 10.1002/bit.28592] [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: 08/16/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023]
Abstract
In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.
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Affiliation(s)
- Xiaoxuan Sun
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Ningning Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jianan Gao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
- Collage of Forestry, Shanxi Agricultural University, Jinzhong, China
| | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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5
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Shen Y, Liu N, Wang Z. Recent advances in the culture-independent discovery of natural products using metagenomic approaches. Chin J Nat Med 2024; 22:100-111. [PMID: 38342563 DOI: 10.1016/s1875-5364(24)60585-6] [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: 08/24/2023] [Indexed: 02/13/2024]
Abstract
Natural products derived from bacterial sources have long been pivotal in the discovery of drug leads. However, the cultivation of only about 1% of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured bacteria. Advances in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent methods. This approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening, sequence tag-based homology screening, and bioinformatic-assisted chemical synthesis. Through this process, numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic territories. This paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries.
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Affiliation(s)
- Yiping Shen
- Laboratory of Microbial Drug Discovery, China Pharmaceutical University, Nanjing 211198, China
| | - Nan Liu
- Laboratory of Microbial Drug Discovery, China Pharmaceutical University, Nanjing 211198, China
| | - Zongqiang Wang
- Laboratory of Microbial Drug Discovery, China Pharmaceutical University, Nanjing 211198, China.
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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7
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Allan EA, Kelly RP, D'Agnese ER, Garber-Yonts MN, Shaffer MR, Gold ZJ, Shelton AO. Quantifying impacts of an environmental intervention using environmental DNA. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2914. [PMID: 37641194 DOI: 10.1002/eap.2914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/12/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023]
Abstract
Environmental laws around the world require some version of an environmental-impact assessment surrounding construction projects and other discrete instances of human development. Information requirements for these assessments vary by jurisdiction, but nearly all require an analysis of the biological elements of ecosystems. Amplicon-sequencing-also called metabarcoding-of environmental DNA (eDNA) has made it possible to sample and amplify the genetic material of many species present in those environments, providing a tractable, powerful, and increasingly common way of doing environmental-impact analysis for development projects. Here, we analyze an 18-month time series of water samples taken before, during, and after two culvert removals in a salmonid-bearing freshwater stream. We also sampled multiple control streams to develop a robust background expectation against which to evaluate the impact of this discrete environmental intervention in the treatment stream. We generate calibrated, quantitative metabarcoding data from amplifying the 12s MiFish mtDNA locus and complementary species-specific quantitative PCR data to yield multispecies estimates of absolute eDNA concentrations across time, creeks, and sampling stations. We then use a linear mixed effects model to reveal patterns of eDNA concentrations over time, and to estimate the effects of the culvert removal on salmonids in the treatment creek. We focus our analysis on four common salmonid species: cutthroat trout (Oncorhynchus clarkii), coho salmon (Oncorhynchus kisutch), rainbow trout (Oncorhynchus mykiss), and sockeye salmon (Oncorhynchus nerka). We find that one culvert in the treatment creek seemed to have no impact while the second culvert had a large impact on fish passage. The construction itself seemed to have only transient effects on salmonid species during the two construction events. In the context of billions of dollars of court-mandated road culvert replacements taking place in Washington State, USA, our results suggest that culvert replacement can be conducted with only minimal impact of construction to key species of management concern. Furthermore, eDNA methods can be an effective and efficient approach for monitoring hundreds of culverts to prioritize culverts that are required to be replaced. More broadly, we demonstrate a rigorous, quantitative method for environmental-impact reporting using eDNA that is widely applicable in environments worldwide.
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Affiliation(s)
| | - Ryan P Kelly
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA
| | - Erin R D'Agnese
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA
| | - Maya N Garber-Yonts
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA
| | - Megan R Shaffer
- University of Washington, School of Marine and Environmental Affairs, Seattle, Washington, USA
| | - Zachary J Gold
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | - Andrew O Shelton
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
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Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy SF. Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562064. [PMID: 37873145 PMCID: PMC10592806 DOI: 10.1101/2023.10.13.562064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45,000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.
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Affiliation(s)
- Weiyi Li
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Darach Miller
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Xianan Liu
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Lamia Chkaiban
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Han Mei
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Po-Hsiang Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
- Present Address: BacStitch DNA, Los Altos, CA, USA
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E Z, Luo P, Ren C, Cheng C, Pan W, Jiang X, Jiang F, Ma B, Yu S, Zhang X, Chen T, Hu C. Applications of Environmental DNA (eDNA) in Monitoring the Endangered Status and Evaluating the Stock Enhancement Effect of Tropical Sea Cucumber Holothuria Scabra. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:778-789. [PMID: 37658250 DOI: 10.1007/s10126-023-10239-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
The tropical sea cucumber Holothuria scabra is naturally found in the Indo-West Pacific. However, due to their commercial value, natural H. scabra populations have declined significantly in recent years, resulting in its status as an endangered species. Surveys of H. scabra resource pose a challenge due to its specific characteristics, such as sand-burrowing behavior. To overcome this problem, our study established a convenient and feasible method for assessing H. scabra resources using environmental DNA (eDNA) monitoring technology. First, H. scabra-specific TaqMan primers and probe were designed based on its cox1 gene, followed by the development of an eDNA monitoring method for H. scabra in two separate sea areas (Xuwen and Daya Bay). The method was subsequently employed to investigate the distribution of H. scabra and assess the effects of aquaculture stock enhancement through juvenile releasing in the Weizhou Island sea area. The H. scabra eDNA monitoring approach was found to be more appropriate and credible than traditional methods, and a positive impact of stocking on H. scabra populations was observed. In summary, this is the first report to quantify eDNA concentration in a Holothuroidea species, and it provides a convenient and accurate method for surveying H. scabra resources. This study introduces novel concepts for eDNA-based detection of endangered marine benthic animals and monitoring their population distribution and abundance.
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Affiliation(s)
- Zixuan E
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China
| | - Chuhang Cheng
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Wenjie Pan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiao Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China
| | - Fajun Jiang
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Bo Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Suzhong Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xin Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China
| | - Ting Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, People's Republic of China.
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, People's Republic of China.
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China.
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Li B, Yan T. Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment. ADVANCES IN APPLIED MICROBIOLOGY 2023; 123:41-89. [PMID: 37400174 DOI: 10.1016/bs.aambs.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.
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Affiliation(s)
- Bo Li
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Tao Yan
- Department of Civil and Environmental Engineering, University of Hawaii at Manoa, Honolulu, HI, United States.
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Thermophilic Carboxylesterases from Hydrothermal Vents of the Volcanic Island of Ischia Active on Synthetic and Biobased Polymers and Mycotoxins. Appl Environ Microbiol 2023; 89:e0170422. [PMID: 36719236 PMCID: PMC9972953 DOI: 10.1128/aem.01704-22] [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] [Indexed: 02/01/2023] Open
Abstract
Hydrothermal vents are geographically widespread and host microorganisms with robust enzymes useful in various industrial applications. We examined microbial communities and carboxylesterases of two terrestrial hydrothermal vents of the volcanic island of Ischia (Italy) predominantly composed of Firmicutes, Proteobacteria, and Bacteroidota. High-temperature enrichment cultures with the polyester plastics polyhydroxybutyrate and polylactic acid (PLA) resulted in an increase of Thermus and Geobacillus species and to some extent Fontimonas and Schleiferia species. The screening at 37 to 70°C of metagenomic fosmid libraries from above enrichment cultures identified three hydrolases (IS10, IS11, and IS12), all derived from yet-uncultured Chloroflexota and showing low sequence identity (33 to 56%) to characterized enzymes. Enzymes expressed in Escherichia coli exhibited maximal esterase activity at 70 to 90°C, with IS11 showing the highest thermostability (90% activity after 20-min incubation at 80°C). IS10 and IS12 were highly substrate promiscuous and hydrolyzed all 51 monoester substrates tested. Enzymes were active with PLA, polyethylene terephthalate model substrate, and mycotoxin T-2 (IS12). IS10 and IS12 had a classical α/β-hydrolase core domain with a serine hydrolase catalytic triad (Ser155, His280, and Asp250) in their hydrophobic active sites. The crystal structure of IS11 resolved at 2.92 Å revealed the presence of a N-terminal β-lactamase-like domain and C-terminal lipocalin domain. The catalytic cleft of IS11 included catalytic Ser68, Lys71, Tyr160, and Asn162, whereas the lipocalin domain enclosed the catalytic cleft like a lid and contributed to substrate binding. Our study identified novel thermotolerant carboxylesterases with a broad substrate range, including polyesters and mycotoxins, for potential applications in biotechnology. IMPORTANCE High-temperature-active microbial enzymes are important biocatalysts for many industrial applications, including recycling of synthetic and biobased polyesters increasingly used in textiles, fibers, coatings and adhesives. Here, we identified three novel thermotolerant carboxylesterases (IS10, IS11, and IS12) from high-temperature enrichment cultures from Ischia hydrothermal vents and incubated with biobased polymers. The identified metagenomic enzymes originated from uncultured Chloroflexota and showed low sequence similarity to known carboxylesterases. Active sites of IS10 and IS12 had the largest effective volumes among the characterized prokaryotic carboxylesterases and exhibited high substrate promiscuity, including hydrolysis of polyesters and mycotoxin T-2 (IS12). Though less promiscuous than IS10 and IS12, IS11 had a higher thermostability with a high temperature optimum (80 to 90°C) for activity and hydrolyzed polyesters, and its crystal structure revealed an unusual lipocalin domain likely involved in substrate binding. The polyesterase activity of these enzymes makes them attractive candidates for further optimization and potential application in plastics recycling.
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Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome. Microorganisms 2023; 11:microorganisms11010224. [PMID: 36677516 PMCID: PMC9867489 DOI: 10.3390/microorganisms11010224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers' point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.
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Rebets Y, Kormanec J, Lutzhetskyy A, Bernaerts K, Anné J. Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Its Subsequent Fermentation for Optimized Production. Methods Mol Biol 2023; 2555:213-260. [PMID: 36306090 DOI: 10.1007/978-1-0716-2795-2_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: 06/16/2023]
Abstract
The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the Gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40% of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60%, alternative cloning hosts such as Streptomyces spp. have been used. Streptomycetes are high-GC Gram-positive bacteria belonging to the Actinomycetales and they have been studied extensively for more than 25 years as an alternative expression system. They are extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content. Furthermore, due to its high innate, extracellular secretion capacity, Streptomyces can be a better system than E. coli for the production of many extracellular proteins. In this article, an overview is given about the materials and methods for growth and successful expression and secretion of heterologous proteins from diverse origin using Streptomyces lividans as a host. More in detail, an overview is given about the protocols of transformation, type of plasmids used and of vectors useful for integration of DNA into the host chromosome, and accompanying cloning strategies. In addition, various control elements for gene expression including synthetic promoters are discussed, and methods to compare their strength are described. Stable and efficient marker-less integration of the gene of interest under the control of the promoter of choice into S. lividans chromosome via homologous recombination using pAMR23A-based system will be explained. Finally, a basic protocol for bench-top bioreactor experiments which can form the start in the production process optimization and up-scaling will be provided.
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Affiliation(s)
| | - Jan Kormanec
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andriy Lutzhetskyy
- Department of Pharmaceutical Biotechnology, University of Saarland, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), University of Saarland, Saarbrücken, Germany
| | - Kristel Bernaerts
- Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety Division, KU Leuven, Leuven, Belgium
| | - Jozef Anné
- Department of Microbiology, Immunology and Transplantation, lab. Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.
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Reineke W, Schlömann M. Microbial Communities: Structural and Functional Analyses with Molecular Biological Approach. Environ Microbiol 2023. [DOI: 10.1007/978-3-662-66547-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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Santana-Pereira ALR. Identification of PKS Gene Clusters from Metagenomic Libraries Using a Next-Generation Sequencing Approach. Methods Mol Biol 2023; 2555:73-90. [PMID: 36306079 DOI: 10.1007/978-1-0716-2795-2_5] [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: 06/16/2023]
Abstract
Microbial secondary metabolites have been an important source of bioactive compounds with diverse applications from medicine to agriculture, noticeably those encoded by polyketide synthase (PKS) clusters due to their astounding chemical diversity. While most discovered compounds originate from culturable microorganisms, yet-to-be cultured microbes represent a reservoir of previously inaccessible compounds. The advent and development of metagenomics have allowed not only the characterization of these microorganisms but also their metabolic potential, making viable the prospection of environmental PKS for natural product discovery.Study of environmental PKSs often relies on the construction of metagenomic libraries and their mining, with clones containing PKS clusters identified via amplification of conserved domains and then screened for an activity of interest. Compounds produced by clones exhibiting the desired bioactivity can be isolated and characterized. However, these approaches can be less sensitive and biased against more divergent clusters, in addition to precluding the use of bioinformatics for cluster characterization prior to expression. While direct shotgun sequencing of metagenomes has identified and profiled a great number of PKSs from different environments and yet-to-be cultured microorganisms, it does not lend itself well to heterologous expression, the cruxes of natural product discovery.Here, we describe a strategy for sequencing entire metagenomic libraries while maintaining correspondence between sequence and clone, allowing the full characterization and annotation of all clusters present in a library using bioinformatic tools and then seamlessly passing clones of interest for activity screening through heterologous expression. Once a library is sequenced, the methods herein can be adapted for the mining of any biosynthetic gene cluster of interest within a metagenomic library.
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Yan F, Xia L, Xu L, Deng L, Jin G. A comparative study to determine the association of gut microbiome with schizophrenia in Zhejiang, China. BMC Psychiatry 2022; 22:731. [PMID: 36424595 PMCID: PMC9694861 DOI: 10.1186/s12888-022-04328-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND With the rapid progress of high-throughput sequencing technology, characterization of schizophrenia (SZ) with underlying probing of the gut microbiome can explore pathogenic mechanisms, estimate disease risk, and allow customization of therapeutic and prophylactic modalities. In this study, we compared the differences in gut microbial diversity and composition between 50 SZ subjects and 50 healthy matched subjects in Zhejiang, China via targeted next-generation sequencing (16S rRNA amplicon). RESULTS Accordingly, the alpha diversity indices (observed species index, Shannon index, and Simpson index) of the gut microbiome in the healthy control group were higher than those in the SZ group. Additionally, principal coordinate analysis and non-metric multidimensional scaling of beta diversity revealed that patients with SZ clustered more tightly than healthy controls. At the phylum level, we found that the abundance of Bacteroidetes and Proteobacteria in the SZ group was significantly increased. At the genus level, the relative abundances of Prevotella, Parabacteroides, and Sutterella were significantly higher, whereas the abundances of Faecalibacterium, Blautia, Lachnospira, Clostridium, Ruminococcus, and Coprococcus were lower than those in the healthy control group. Further analyses revealed that Succinivibrio, Megasphaera, and Nesterenkonia may serve as potential biomarkers for distinguishing patients with SZ from those in the control cohort. CONCLUSIONS This study profiled differences in gut microbiome diversity, taxonomic composition, and function between SZ and healthy cohorts, and the insights from this research could be used to develop targeted next-generation sequencing-based diagnoses for SZ.
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Affiliation(s)
- Fuyang Yan
- The Second People’s Hospital of Lishui, Lishui, 323000 China
| | - Lehong Xia
- The Second People’s Hospital of Lishui, Lishui, 323000 China
| | - Li Xu
- The Second People’s Hospital of Lishui, Lishui, 323000 China
| | - Liyun Deng
- The Second People’s Hospital of Lishui, Lishui, 323000 China
| | - Guolin Jin
- The Second People's Hospital of Lishui, Lishui, 323000, China.
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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Singh R, Pal DB, Alkhanani MF, Almalki AH, Areeshi MY, Haque S, Srivastava N. Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155966. [PMID: 35584752 DOI: 10.1016/j.scitotenv.2022.155966] [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: 02/14/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.
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Affiliation(s)
- Rajeev Singh
- Department of Environmental Studies, Satyawati College, University of Delhi, Delhi, 110052, India
| | - Dan Bahadur Pal
- Department of Chemical Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Mustfa F Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; Addiction and Neuroscience Research Unit, College of Pharmacy, Taif University, Al-Hawiah, Taif 21944, Saudi Arabia
| | - Mohammed Yahya Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia; Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Bursa Uludağ University, Faculty of Medicine, Görükle Campus, 16059 Nilüfer, Bursa, Turkey
| | - Neha Srivastava
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, India.
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20
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Banerjee P, Stewart KA, Dey G, Antognazza CM, Sharma RK, Maity JP, Saha S, Doi H, de Vere N, Chan MWY, Lin PY, Chao HC, Chen CY. Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AOB PLANTS 2022; 14:plac031. [PMID: 35990516 PMCID: PMC9389569 DOI: 10.1093/aobpla/plac031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Kathryn A Stewart
- Institute of Environmental Science, Leiden University, 2333 CC Leiden, The Netherlands
| | - Gobinda Dey
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Caterina M Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Jyoti Prakash Maity
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Santanu Saha
- Post Graduate Department of Botany, Bidhannagar College, Salt Lake City, Kolkata 700064, India
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K
| | - Michael W Y Chan
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Pin-Yun Lin
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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Chandrasiri S, Perera T, Dilhara A, Perera I, Mallawaarachchi V. CH-Bin: A Convex Hull Based Approach for Binning Metagenomic Contigs. Comput Biol Chem 2022; 100:107734. [DOI: 10.1016/j.compbiolchem.2022.107734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 07/12/2022] [Indexed: 11/30/2022]
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22
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Multidrug resistance from a one health perspective in Ethiopia: A systematic review and meta-analysis of literature (2015–2020). One Health 2022; 14:100390. [PMID: 35686143 PMCID: PMC9171526 DOI: 10.1016/j.onehlt.2022.100390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 11/22/2022] Open
Abstract
Purpose The emergence of antimicrobial resistance is a major global health challenge and becoming an urgent priority for policymakers. There is a paucity of scientific studies presenting the multidrug resistance pattern from one health perspective in Ethiopia. Therefore, a systematic review and meta-analysis aimed to determine the pooled prevalence of multidrug resistance in bacteria from human, animal, food, and environmental sources. Methods In this systematic review and meta-analysis, an electronic search was made in PubMed & Google scholar using different keywords. The studies conducted in all areas of Ethiopia, published from 2015 to 2020 in peer-reviewed journals, English full-length papers were included. The meta-analysis was done on STATA version 14. The pooled prevalence of multidrug resistance for each bacterium was analysed using the random-effects model; Cochran Q statistics and the I2 statistic was used to analyse heterogeneity and considered significant at p < 0.01. Results 81 studies were included in the systematic review and meta-analysis; 53 human studies, eight animal studies, and 16 environments/food studies. The meta-analysis included six species from gram-positive bacteria and 13 from gram-negative bacteria. S. aureus 53% (95%CI: 42–64%), Coagulase negative Staphylococci 68%(95%CI:53–82), Pseudomonas spp. 73%(95%CI:48–93%), E. coli 70% (95%CI:61–78%), Citrobacter spp. 71%(95%CI:54–87%), Klebsiella spp. 68% (54–80%), Enterobacter spp. 67% (48–83%) and Salmonella spp. 65% (95%CI:48–81%) were the common multidrug-resistant species of bacteria from two or more sources. Conclusion In Ethiopia, the pooled prevalence of MDR is high in most bacterial species from humans, animals, food, and environmental sources. Staphylococcus, most members of the Enterobacteriaceae and Pseudomonas, are the standard MDR bacterial population involving all sources. Therefore, integrated policy and intervention measures should be implemented to reduce the emergence and spread of MDR bacteria for better animal and human health outcomes.
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23
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Parihar J, Parihar SP, Suravajhala P, Bagaria A. Spatial Metagenomic Analysis in Understanding the Microbial Diversity of Thar Desert. BIOLOGY 2022; 11:biology11030461. [PMID: 35336834 PMCID: PMC8945486 DOI: 10.3390/biology11030461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary We present a systematic investigation of the distribution of microbial communities in arid and semi-arid regions of Thar Desert Rajasthan, India. Their responses in multiple environmental stresses, including surface soil, surface water and underground water were evaluated. We further assess the biotechnological potential of native microorganisms and discover functional species with results providing a detailed understanding of the abundance of microbial communities in these regions, associated with various stress-related biogeochemical and biotechnological processes. We hope our work will facilitate the development of effective future strategies for the use of extremophiles in complex environments. Abstract The arid and semi-arid regions of Rajasthan are one of the most extreme biomes of India, possessing diverse microbial communities that exhibit immense biotechnological potential for industries. Herein, we sampled study sites from arid and semi-arid regions of Thar Desert, Rajasthan, India and subjected them to chemical, physical and metagenomics analysis. The microbial diversity was studied using V3–V4 amplicon sequencing of 16S rRNA gene by Illumina MiSeq. Our metagenomic analyses revealed that the sampled sites consist mainly of Proteobacteria (19–31%) followed by unclassified bacteria (5–21%), Actinobacteria (3–25%), Planctomycetes (5–13%), Chloroflexi (2–14%), Bacteroidetes (3–12%), Firmicutes (3–7%), Acidobacteria (1–4%) and Patescibacteria (1–4%). We have found Proteobacteria in abundance which is associated with a range of activities involved in biogeochemical cycles such as carbon, nitrogen, and sulphur. Our study is perhaps the first of its kind to explore soil bacteria from arid and semi-arid regions of Rajasthan, India. We believe that the new microbial candidates found can be further explored for various industrial and biotechnological applications.
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Affiliation(s)
- Jagdish Parihar
- Department of Physics, Manipal University Jaipur, Jaipur 303007, India
| | - Suraj P Parihar
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town 7701, South Africa
| | - Prashanth Suravajhala
- Bioclues.org, Vivekananda Nagar, Kukatpally, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwavidyapeetham, Amritapuri Campus, Clappana P.O., Kollam 690525, India
| | - Ashima Bagaria
- Department of Physics, Manipal University Jaipur, Jaipur 303007, India
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Sarma H, Joshi SJ. Metagenomics Combined with Stable Isotope Probe (SIP) for the Discovery of Novel Dehalogenases Producing Bacteria. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 108:478-484. [PMID: 32978646 DOI: 10.1007/s00128-020-03004-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Halogenated compounds are one of the largest groups of environmental-hazardous chemicals. The removal of the halogen atom from the substrate is possible by the catalytic activity of a type of enzyme called dehalogenase. Hydrolytic dehalogenases are suggested to be a good biodegradation catalyst for halogenated compounds with potential bioremediation applications. Therefore, the identification of possible bacterial strains that produce dehalogenase is of great importance. Soil microorganisms that are regularly exposed to halogenated pesticides are a major source of hydrolytic dehalogenase. Their proper identification may be useful in the production of high-quality dehalogenase. DNA stable isotope probing (DNA-SIP) is quite a useful technique for the identification of active microorganisms that assimilate specific carbon substrates and nutrients. Metagenomics combined with a stable isotope probe (SIP) technique could therefore be used to detect bacterial dehalogenases in pesticides exposed agricultural soil.
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Affiliation(s)
- Hemen Sarma
- Department of Botany, N. N. Saikia College, Titabar, Assam, 785630, India.
| | - Sanket J Joshi
- Oil & Gas Research Center, Central Analytical and Applied Research Unit, Sultan Qaboos University, Muscat, Oman.
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25
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Understanding Interaction Patterns within Deep-Sea Microbial Communities and Their Potential Applications. Mar Drugs 2022; 20:md20020108. [PMID: 35200637 PMCID: PMC8874374 DOI: 10.3390/md20020108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022] Open
Abstract
Environmental microbes living in communities engage in complex interspecies interactions that are challenging to decipher. Nevertheless, the interactions provide the basis for shaping community structure and functioning, which is crucial for ecosystem service. In addition, microbial interactions facilitate specific adaptation and ecological evolution processes particularly essential for microbial communities dwelling in resource-limiting habitats, such as the deep oceans. Recent technological and knowledge advancements provide an opportunity for the study of interactions within complex microbial communities, such as those inhabiting deep-sea waters and sediments. The microbial interaction studies provide insights into developing new strategies for biotechnical applications. For example, cooperative microbial interactions drive the degradation of complex organic matter such as chitins and celluloses. Such microbiologically-driven biogeochemical processes stimulate creative designs in many applied sciences. Understanding the interaction processes and mechanisms provides the basis for the development of synthetic communities and consequently the achievement of specific community functions. Microbial community engineering has many application potentials, including the production of novel antibiotics, biofuels, and other valuable chemicals and biomaterials. It can also be developed into biotechniques for waste processing and environmental contaminant bioremediation. This review summarizes our current understanding of the microbial interaction mechanisms and emerging techniques for inferring interactions in deep-sea microbial communities, aiding in future biotechnological and therapeutic applications.
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Rodriguez-Valera F, Pushkarev A, Rosselli R, Béjà O. Searching Metagenomes for New Rhodopsins. Methods Mol Biol 2022; 2501:101-108. [PMID: 35857224 DOI: 10.1007/978-1-0716-2329-9_4] [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: 06/15/2023]
Abstract
Most microbial groups have not been cultivated yet, and the only way to approach the enormous diversity of rhodopsins that they contain in a sensible timeframe is through the analysis of their genomes. High-throughput sequencing technologies have allowed the release of community genomics (metagenomics) of many habitats in the photic zones of the ocean and lakes. Already the harvest is impressive and included from the first bacterial rhodopsin (proteorhodopsin) to the recent discovery of heliorhodopsin by functional metagenomics. However, the search continues using bioinformatic or biochemical routes.
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Affiliation(s)
- Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Alina Pushkarev
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Riccardo Rosselli
- Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
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27
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Fish Diversity Monitored by Environmental DNA in the Yangtze River Mainstream. FISHES 2021. [DOI: 10.3390/fishes7010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Surveys and assessments based on environmental DNA are not only efficient and time-saving, but also cause less harm to monitoring targets. Environmental DNA has become a common tool for the assessment and monitoring of aquatic organisms. In this study, we investigated fish resources in the Yangtze River mainstream using environmental DNA, and the variations in fish during two seasons (spring and autumn) were compared. The results showed that 13 species were identified in spring, and nine species of fish were identified in autumn. The fish with higher eDNA detection were Sinibotia superciliaris, Tachysurus fulvidraco, Cyprinus carpio, Ctenopharyngodon Idella, Monopterus albus, Acanthogobius hasta, Saurogobio dabryi, Oncorhynchus mykiss, Mugil cephalus, Odontamblyopus rubicundus. Seasonal variation between spring and autumn was not significant, and the environmental factors had different effects on fish assemblages during the two seasons. Our study used the eDNA technique to monitor the composition of fish in the spring and autumn in the Yangtze River mainstream, providing a new technology for the long-term management and protection of fishery resources in the region. Of course, problems such as pollution and insufficient databases are the current shortcomings of environmental DNA, which will be the focus of our future research and study.
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Chevrette MG, Handelsman J. Needles in haystacks: reevaluating old paradigms for the discovery of bacterial secondary metabolites. Nat Prod Rep 2021; 38:2083-2099. [PMID: 34693961 DOI: 10.1039/d1np00044f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Natural products research is in the midst of a renaissance ushered in by a modern understanding of microbiology and the technological explosions of genomics and metabolomics. As the exploration of uncharted chemical space expands into high-throughput discovery campaigns, it has become increasingly clear how design elements influence success: (bio)geography, habitat, community dynamics, culturing/induction methods, screening methods, dereplication, and more. We explore critical considerations and assumptions in natural products discovery. We revisit previous estimates of chemical rediscovery and discuss their relatedness to study design and producer taxonomy. Through frequency analyses of biosynthetic gene clusters in publicly available genomic data, we highlight phylogenetic biases that influence rediscovery rates. Through selected examples of how study design at each level determines discovery outcomes, we discuss the challenges and opportunities for the future of high-throughput natural product discovery.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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Mining of a novel esterase (est3S) gene from a cow rumen metagenomic library with organosphosphorus insecticides degrading capability: Catalytic insights by site directed mutations, docking, and molecular dynamic simulations. Int J Biol Macromol 2021; 190:441-455. [PMID: 34506858 DOI: 10.1016/j.ijbiomac.2021.08.224] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 11/22/2022]
Abstract
A novel esterase (est3S) gene, 1026 bp in size, was cloned from a metagenomic library made of uncultured microorganisms from the contents of cow rumen. The esterolytic enzyme (Est3S) is composed of 342 amino acids and shows the highest identity with EstGK1 (71.7%) and EstZ3 (63.78%) esterases from the uncultured bacterium. The Est3S did not cluster in any up-to-date classes (I to XVIII) of esterase and lipase. Est3S protein molecular weight was determined to be 38 kDa by gel electrophoresis and showed optimum activity at pH 7.0 and 40 °C and is partially resistant to organic solvents. Est3S activity was enhanced by K+, Na+, Mg2+, and Ca2+ and its highest activity was observed toward the short-chain p-nitrophenyl esters. Additionally, Est3S can degrade chlorpyrifos (CP) and methyl parathion (70% to 80%) in an hour. A mutated Est3S (Ser132-Ala132) did not show any activity toward CP and ester substrates. Notably, the GHS132QG motif is superimposed with the homolog esterase and cutinase-like esterase. Therefore, Ser132 is the critical amino acid like other esterases. The Est3S is relatively stable with ester compounds, and the methyl parathion complex was confirmed by molecular dynamics simulation. NOVELTY STATEMENT: A novel esterase gene (est3S) expressing esters and organophosphorus insecticide degradation traits was isolated from the uncultured bacterium in the contents of cow rumen. The Est3S protein did not cluster in any up-to-date classes (I to XVIII) of esterase/lipase proteins. Est3S was stable with the ligands up to 100 ns during the molecular dynamic simulations.
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McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021; 205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.
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Affiliation(s)
- Elizabeth A McDaniel
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.
| | | | - Shun'ichi Ishii
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Yokosuka 237-0061, Japan
| | - Ameet Pinto
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, USA
| | - Ryan Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, BC, Canada
| | | | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA; Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Republic of Singapore.
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31
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Galanie S, Entwistle D, Lalonde J. Engineering biosynthetic enzymes for industrial natural product synthesis. Nat Prod Rep 2021; 37:1122-1143. [PMID: 32364202 DOI: 10.1039/c9np00071b] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2000 to 2020 Natural products and their derivatives are commercially important medicines, agrochemicals, flavors, fragrances, and food ingredients. Industrial strategies to produce these structurally complex molecules encompass varied combinations of chemical synthesis, biocatalysis, and extraction from natural sources. Interest in engineering natural product biosynthesis began with the advent of genetic tools for pathway discovery. Genes and strains can now readily be synthesized, mutated, recombined, and sequenced. Enzyme engineering has succeeded commercially due to the development of genetic methods, analytical technologies, and machine learning algorithms. Today, engineered biosynthetic enzymes from organisms spanning the tree of life are used industrially to produce diverse molecules. These biocatalytic processes include single enzymatic steps, multienzyme cascades, and engineered native and heterologous microbial strains. This review will describe how biosynthetic enzymes have been engineered to enable commercial and near-commercial syntheses of natural products and their analogs.
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Affiliation(s)
- Stephanie Galanie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
| | - David Entwistle
- Process Chemistry, Codexis, Inc., Redwood City, California, USA
| | - James Lalonde
- Microbial Digital Genome Engineering, Inscripta, Inc., Pleasanton, California, USA
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32
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Thiele-Bruhn S. The role of soils in provision of genetic, medicinal and biochemical resources. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200183. [PMID: 34365823 DOI: 10.1098/rstb.2020.0183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Intact, 'healthy' soils provide indispensable ecosystem services that largely depend on the biotic activity. Soil health is connected with human health, yet, knowledge of the underlying soil functioning remains incomplete. This review highlights selected services, i.e. (i) soil as a genetic resource and hotspot of biodiversity, forming the basis for providing (ii) biochemical resources and (iii) medicinal services and goods. Soils harbour an unrivalled biodiversity of organisms, especially microorganisms. Some of the abilities of autochthonous microorganisms and their relevant enzymes serve (i) to improve natural soil functions and in particular plant growth, e.g. through beneficial plant growth-promoting, symbiotic and mycorrhizal microorganisms, (ii) to act as biopesticides, (iii) to facilitate biodegradation of pollutants for soil bioremediation and (iv) to yield enzymes or chemicals for industrial use. Soils also exert direct effects on human health. Contact with soil enriches the human microbiome, affords protection against allergies and promotes emotional well-being. Medicinally relevant are soil substrates such as loams, clays and various minerals with curative effects as well as pharmaceutically active organic chemicals like antibiotics that are formed by soil microorganisms. By contrast, irritating minerals, soil dust inhalation and misguided soil ingestion may adversely affect humans. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People.
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Affiliation(s)
- Sören Thiele-Bruhn
- Soil Science, University of Trier, Behringstrasse 21, D-54286 Trier, Germany
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Park JE, Jeong GS, Lee HW, Kim H. Molecular Characterization of Novel Family IV and VIII Esterases from a Compost Metagenomic Library. Microorganisms 2021; 9:microorganisms9081614. [PMID: 34442693 PMCID: PMC8399190 DOI: 10.3390/microorganisms9081614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
Two novel esterase genes, est8L and est13L, were isolated and identified from a compost metagenomic library. The encoded Est8L and Est13L had molecular masses of 33,181 and 44,913 Da consisting of 314 and 411 amino acids, respectively, without signal peptides. Est8L showed the highest identity (32.9%) to a hyper-thermophilic carboxylesterase AFEST from Archaeoglobus fulgidus compared to other esterases reported and was classified to be a novel member of family IV esterases with conserved regions such as HGGG, DY, GXSXG, DPL, and GXIH. Est13L showed the highest identity (98.5%) to the family VIII esterase Est7K from the metagenome library. Est8L and Est13L had the highest activities for p-nitrophenyl butyrate (C4) and p-nitrophenyl caproate (C6), respectively, and Est13L showed a broad substrate specificity for p-nitrophenyl substrates. Est8L and Est13L effectively hydrolyzed glyceryl tributyrate. The optimum temperatures for activities of Est8L and Est13L were identical (40 °C), and the optimum pH values were 9.0 and 10.0, respectively. Est13L showed higher thermostability than Est8L. Sephacryl S-200 HR chromatography showed that the native form of Est8L was a dimer. Interestingly, Est13L was found to be a tetramer, contrary to other family VIII esterases reported. Est8L was inhibited by 30% isopropanol, methanol, and acetonitrile; however, Est13L was activated to 182.9% and 356.1%, respectively, by 30% isopropanol and methanol. Est8L showed enantioselectivity for the S-form, but Est13L showed no enantioselectivity. These results show that intracellular Est8L and/or Est13L are oligomeric in terms of native forms and can be used for pharmaceutical and industrial applications with organic solvents under alkaline conditions.
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Affiliation(s)
| | | | | | - Hoon Kim
- Correspondence: ; Tel.: +82-617503751
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34
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Crofts TS, McFarland AG, Hartmann EM. Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries. mSystems 2021; 6:e0052421. [PMID: 34184912 PMCID: PMC8269240 DOI: 10.1128/msystems.00524-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Functional metagenomic libraries, physical bacterial libraries which allow the high-throughput capture and expression of microbiome genes, have been instrumental in the sequence-naive and cultivation-independent exploration of metagenomes. However, preparation of these libraries is often limited by their high DNA input requirement and their low cloning efficiency. Here, we describe a new method, mosaic ends tagmentation (METa) assembly, for highly efficient functional metagenomic library preparation. We applied tagmentation to metagenomic DNA from soil and gut microbiomes to prepare DNA inserts for high-throughput cloning into functional metagenomic libraries. The presence of mosaic end sequences in the resulting DNA fragments synergized with homology-based assembly cloning to result in a 300-fold increase in cloning efficiency compared to traditional blunt-cloning-based protocols. We show that compared to published libraries prepared by state-of-the-art protocols, METa assembly is on average ca. 20- to 200-fold more efficient and can prepare gigabase-sized libraries with as little as 200 ng of input DNA. We show the usefulness of METa assembly first by using a normative 5-μg mass of soil metagenomic DNA to prepare a 700-Gb library that allowed us to discover novel nourseothricin resistance genes and a potentially new mode of resistance to this antibiotic and second by using only 300 ng of goose fecal metagenomic DNA to prepare a 27-Gb library that captured numerous tetracycline and colistin resistance genes. METa assembly provides a streamlined, flexible, and efficient method for preparing functional metagenomic libraries, enabling new avenues of genetic and biochemical research into low-biomass or scarce microbiomes. IMPORTANCE Medically and industrially important genes can be recovered from microbial communities by high-throughput sequencing, but precise annotation is often limited to characterized genes and their relatives. Cloning a metagenome en masse into an expression host to produce a functional metagenomic library, directly connecting genes to functions, is a sequence-naive and cultivation-independent method to discover novel genes. The process of preparing these libraries is DNA greedy and inefficient, however. Here, we describe a library preparation method that is an order of magnitude more efficient and less DNA greedy. This method is consistently efficient across libraries prepared from cultures, a soil microbiome, and a goose fecal microbiome and allowed us to discover new antibiotic resistance genes and mechanisms. This library preparation method will potentially allow the functional metagenomic exploration of microbiomes that were previously off limits due to their rarity or low microbial biomass, such as biomedical swabs or exotic samples.
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Affiliation(s)
- Terence S. Crofts
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
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35
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Characterization of a Novel Family IV Esterase Containing a Predicted CzcO Domain and a Family V Esterase with Broad Substrate Specificity from an Oil-Polluted Mud Flat Metagenomic Library. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11135905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two novel esterase genes, est2L and est4L, were identified from a previously constructed metagenomic library derived from an oil-polluted mud flat sample. The encoded Est2L and Est4L were composed of 839 and 267 amino acids, respectively, without signal peptides. Est2L was a unique fusion type of protein composed of two domains: a domain of the CzcO superfamily, associated with a cationic diffusion promoter with CzcD, and a domain of the acetylesterase superfamily, belonging to family IV with conserved motifs, such as HGG, GXSAG, and GXPP. Est2L was the first fused esterase with a CzcO domain. Est4L belonged to family V with GXS, GXSMGG, and PTL motifs. Native Est2L and Est4L were found to be in dimeric and tetrameric forms, respectively. Est2L and Est4L showed the highest activities at 60 °C and 50 °C, respectively, and at a pH of 10.0. Est2L preferred short length substrates, especially p-nitrophenyl (pNP)-acetate, with moderate butyrylcholinesterase activity, whereas Est4L showed the highest activity with pNP-decanoate and had broad specificity. Significant effects were not observed in Est2L from Co2+ and Zn2+, although Est2L contains the domain CzcD. Est2L and Est4L showed high stabilities in 30% methanol and 1% Triton X-100. These enzymes could be used for a variety of applications, such as detergent and mining processing under alkaline conditions.
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36
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Sander D, Yu Y, Sukul P, Schäkermann S, Bandow JE, Mukherjee T, Mukhopadhyay SK, Leichert LI. Metaproteomic Discovery and Characterization of a Novel Lipolytic Enzyme From an Indian Hot Spring. Front Microbiol 2021; 12:672727. [PMID: 34149658 PMCID: PMC8212958 DOI: 10.3389/fmicb.2021.672727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/19/2021] [Indexed: 11/18/2022] Open
Abstract
Lipolytic enzymes are produced by animals, plants and microorganisms. With their chemo-, regio-, and enantio-specific characteristics, lipolytic enzymes are important biocatalysts useful in several industrial applications. They are widely used in the processing of fats and oils, detergents, food processing, paper and cosmetics production. In this work, we used a new functional metaproteomics approach to screen sediment samples of the Indian Bakreshwar hot spring for novel thermo- and solvent-stable lipolytic enzymes. We were able to identify an enzyme showing favorable characteristics. DS-007 showed high hydrolytic activity with substrates with shorter chain length (<C8) with the maximum activity observed against p-nitrophenyl butyrate (C4). For substrates with a chain length >C10, significantly less hydrolytic activity was observed. A preference for short chain acyl groups is characteristic for esterases, suggesting that DS-007 is an esterase. Consistent with the high temperature at its site of isolation, DS-007 showed a temperature optimum at 55°C and retained 80% activity even after prolonged exposure to temperatures as high as 60°C. The enzyme showed optimum activity at pH 9.5, with more than 50% of its optimum activity between pH 8.0 and pH 9.5. DS-007 also exhibited tolerance toward organic solvents at a concentration of 1% (v/v). One percent of methanol increased the activity of DS-007 by 40% in comparison to the optimum conditions without solvent. In the presence of 10% methanol, DMSO or isopropanol DS-007 still showed around 50% activity. This data indicates that DS-007 is a temperature- and solvent-stable thermophilic enzyme with reasonable activity even at lower temperatures as well as a catalyst that can be used at a broad range of pH values with an optimum in the alkaline range, showing the adaptation to the habitat’s temperature and alkaline pH.
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Affiliation(s)
- Dennis Sander
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Yanfei Yu
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Premankur Sukul
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Trinetra Mukherjee
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany.,Department of Microbiology, The University of Burdwan, Burdwan, India
| | | | - Lars I Leichert
- Department of Microbial Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
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37
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Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
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Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
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Zhong C, Chen C, Wang L, Ning K. Integrating pan-genome with metagenome for microbial community profiling. Comput Struct Biotechnol J 2021; 19:1458-1466. [PMID: 33841754 PMCID: PMC8010324 DOI: 10.1016/j.csbj.2021.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 02/07/2023] Open
Abstract
Advances in sequencing technology have led to the increased availability of genomes and metagenomes, which has greatly facilitated microbial pan-genome and metagenome analysis in the community. In line with this trend, studies on microbial genomes and phenotypes have gradually shifted from individuals to environmental communities. Pan-genomics and metagenomics are powerful strategies for in-depth profiling study of microbial communities. Pan-genomics focuses on genetic diversity, dynamics, and phylogeny at the multi-genome level, while metagenomics profiles the distribution and function of culture-free microbial communities in special environments. Combining pan-genome and metagenome analysis can reveal the microbial complicated connections from an individual complete genome to a mixture of genomes, thereby extending the catalog of traditional individual genomic profile to community microbial profile. Therefore, the combination of pan-genome and metagenome approaches has become a promising method to track the sources of various microbes and decipher the population-level evolution and ecosystem functions. This review summarized the pan-genome and metagenome approaches, the combined strategies of pan-genome and metagenome, and applications of these combined strategies in studies of microbial dynamics, evolution, and function in communities. We discussed emerging strategies for the study of microbial communities that integrate information in both pan-genome and metagenome. We emphasized studies in which the integrating pan-genome with metagenome approach improved the understanding of models of microbial community profiles, both structural and functional. Finally, we illustrated future perspectives of microbial community profile: more advanced analytical techniques, including big-data based artificial intelligence, will lead to an even better understanding of the patterns of microbial communities.
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Affiliation(s)
- Chaofang Zhong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.,Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Chaoyun Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Lusheng Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, China.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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39
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Câmara PEAS, Carvalho-Silva M, Pinto OHB, Amorim ET, Henriques DK, da Silva TH, Pellizzari F, Convey P, Rosa LH. Diversity and Ecology of Chlorophyta (Viridiplantae) Assemblages in Protected and Non-protected Sites in Deception Island (Antarctica, South Shetland Islands) Assessed Using an NGS Approach. MICROBIAL ECOLOGY 2021; 81:323-334. [PMID: 32860076 DOI: 10.1007/s00248-020-01584-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/24/2020] [Indexed: 05/20/2023]
Abstract
Assessment of the diversity of algal assemblages in Antarctica has until now largely relied on traditional microbiological culture approaches. Here we used DNA metabarcoding through high-throughput sequencing (HTS) to assess the uncultured algal diversity at two sites on Deception Island, Antarctica. The first was a relatively undisturbed site within an Antarctic Specially Protected Area (ASPA 140), and the second was a site heavily impacted by human visitation, the Whalers Bay historic site. We detected 65 distinct algal taxa, 50 from within ASPA 140 and 61 from Whalers Bay. Of these taxa, 46 were common to both sites, and 19 only occurred at one site. Algal richness was about six times greater than reported in previous studies using culture methods. A high proportion of DNA reads obtained was assigned to the highly invasive species Caulerpa webbiana at Whalers Bay, and the potentially pathogenic genus Desmodesmus was found at both sites. Our data demonstrate that important differences exist between these two protected and human-impacted sites on Deception Island in terms of algal diversity, richness, and abundance. The South Shetland Islands have experienced considerable effects of climate change in recent decades, while warming through geothermal activity on Deception Island itself makes this island one of the most vulnerable to colonization by non-native species. The detection of DNA of non-native taxa highlights concerns about how human impacts, which take place primarily through tourism and national research operations, may influence future biological colonization processes in Antarctica.
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Affiliation(s)
| | | | - Otávio H B Pinto
- Departamento de Biologia Celular e Molecular, Universidade de Brasília (UnB), Brasilia, Brazil
| | - Eduardo T Amorim
- Departamento de Botânica, Universidade de Brasília (UnB), Brasilia, Brazil
- Centro Nacional de Conservação da Flora/Instituto de Pesquisas Jardim Botânico do Rio de Janeiro (CNCFlora/JBRJ), Rio de Janeiro, Brazil
| | | | - Thamar Holanda da Silva
- Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Franciane Pellizzari
- Departamento de Ciências Biológicas, Universidade Estadual do Paraná, Paranaguá, Brazil
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Luiz Henrique Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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40
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Sakai Y. Improvements in Extraction Methods of High-molecular-weight DNA from Soils by Modifying Cell Lysis Conditions and Reducing Adsorption of DNA onto Soil Particles. Microbes Environ 2021; 36. [PMID: 34234043 PMCID: PMC8446751 DOI: 10.1264/jsme2.me21017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-molecular-weight DNA (HMW DNA) extracted from soil is useful for examined the functions and diversity of soil organisms, the majority of which are difficult to culture. In the present study, the procedures used to extract HMW DNA from soil samples were improved. The grinding of soil samples with liquid nitrogen followed by a lysozyme treatment at 45°C for 1 h and an incubation with protease and SDS at 50°C for 5 h increased the size and yield of HMW DNA extracted from these samples. In the soil group Andosols, the addition of boiled sonicated salmon DNA was effective for HMW DNA extraction.
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Affiliation(s)
- Yoriko Sakai
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO)
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41
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Biological, Physical and Chemical Properties of Nanosilver Particles Collected from Soil in Asir, Saudi Arabia. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2021. [DOI: 10.1007/s13369-020-04833-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Santana-Pereira ALR, Sandoval-Powers M, Monsma S, Zhou J, Santos SR, Mead DA, Liles MR. Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library. Front Microbiol 2020; 11:585398. [PMID: 33365020 PMCID: PMC7750434 DOI: 10.3389/fmicb.2020.585398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/16/2020] [Indexed: 12/31/2022] Open
Abstract
Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in Escherichia coli from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.
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Affiliation(s)
| | | | - Scott Monsma
- Lucigen Corporation, Middleton, WI, United States
| | - Jinglie Zhou
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Scott R. Santos
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - David A. Mead
- Varigen Biosciences Corporation, Madison, WI, United States
| | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Varigen Biosciences Corporation, Madison, WI, United States
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43
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Mahfouz S, Mansour G, Murphy DJ, Hanano A. Dioxin impacts on lipid metabolism of soil microbes: towards effective detection and bioassessment strategies. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00347-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AbstractDioxins are the most toxic known environmental pollutants and are mainly formed by human activities. Due to their structural stability, dioxins persist for extended periods and can be transported over long distances from their emission sources. Thus, dioxins can be accumulated to considerable levels in both human and animal food chains. Along with sediments, soils are considered the most important reservoirs of dioxins. Soil microorganisms are therefore highly exposed to dioxins, leading to a range of biological responses that can impact the diversity, genetics and functional of such microbial communities. Dioxins are very hydrophobic with a high affinity to lipidic macromolecules in exposed organisms, including microbes. This review summarizes the genetic, molecular and biochemical impacts of dioxins on the lipid metabolism of soil microbial communities and especially examines modifications in the composition and architecture of cell membranes. This will provide a useful scientific benchmark for future attempts at soil ecological risk assessment, as well as in identifying potential dioxin-specific-responsive lipid biomarkers. Finally, potential uses of lipid-sequestering microorganisms as a part of biotechnological approaches to the bio-management of environmental contamination with dioxins are discussed.
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44
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He K, Yan W, Sun C, Liu J, Bai R, Wang T, Qian W. Alterations in the diversity and composition of gut microbiota in weaned piglets infected with Balantioides coli. Vet Parasitol 2020; 288:109298. [PMID: 33171414 DOI: 10.1016/j.vetpar.2020.109298] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/08/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023]
Abstract
Balantioides coli is a ciliated parasite that can cause diarrhea when inhabiting the colon and cecum of pigs and humans. However, information regarding the changes in structure and composition of the gut microbiome in piglets infected with B. coli remains scarce. In this study, 16S rDNA amplicon sequencing was conducted on fecal samples from both B. coli-positive piglets with diarrhea and B. coli-negative piglets without diarrhea. The results showed that Firmicutes and Bacteroidetes were the major phyla in the two groups, and the relative abundance of the phylum Firmicutes, including Ruminococcaceae and Clostridiaceae, was significantly lower in the B. coli-positive samples than in the B. coli-negative ones (p < 0.05). Compared with B. coli-negative samples, Alloprevotella and Faecalibacterium showed distinctly higher relative abundances (p < 0.05) in the B. coli-positive samples, and the abundances of some potential pathogenic bacteria, including Escherichia-Shigella and Campylobacter, were positively correlated with B. coli infection and diarrhea of weaned piglets. In addition, there were statistically significant differences in fecal microbiota diversity and abundances of predicted functional genes between B. coli-colonized and B. coli-negative samples (p < 0.05). Taken together, these findings suggest that there were significant differences in the bacterial community composition, diversity, and functions between the B. coli-positive and B. coli-negative piglets, and the colonization by B. coli may be associated with the dysbiosis of gut microbiota structure in weaned piglets.
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Affiliation(s)
- Kai He
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Wenchao Yan
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China.
| | - Chenyang Sun
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Jie Liu
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Rongzhen Bai
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Tianqi Wang
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Weifeng Qian
- Parasitology Laboratory, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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45
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Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, Suriani NL. Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review. Front Microbiol 2020; 11:580024. [PMID: 33193209 PMCID: PMC7661733 DOI: 10.3389/fmicb.2020.580024] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.
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Affiliation(s)
- Sadaf Kalam
- Department of Biochemistry, St. Ann's College for Women, Hyderabad, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
| | - R Z Sayyed
- Department of Microbiology, PSGVP Mandal's, Arts, Science and Commerce College, Shahada, India
| | - Hesham Ali El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,City of Scientific Research and Technological Applications, New Borg El-Arab, Egypt
| | - Daniel Joe Dailin
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia
| | - Ni Luh Suriani
- Biology Department, Faculty of Mathematics and Natural Science, Udayana University, Bali, Indonesia
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46
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Seasonal Variation and Assessment of Fish Resources in the Yangtze Estuary Based on Environmental DNA. WATER 2020. [DOI: 10.3390/w12102874] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In the past few years, environmental DNA (eDNA) techniques have been used to monitor marine communities. Research indicates that eDNA is an effective tool for monitoring fishery resources. This study analyzed the seasonal variations in fish resources in the Yangtze Estuary, China, using eDNA. A total of 103 water samples were collected from the Yangtze Estuary across the four seasons in 2019—20 samples in February, 28 in May, 28 in August and 27 in November. Our research successfully detected the fishery resources of the Yangtze Estuary. We found significant differences according to the season. The results showed that 59 species were identified in 2019 (20 in February, 16 in May, 5 in August and 45 in November) and fish species varied widely over the four seasons. Furthermore, our samples revealed significant differences in annual fish stocks in the Yangtze Estuary, compared with eDNA data from 2018 and with traditional surveys from past years. Overall, eDNA is a useful emerging tool to assist with monitoring and protecting fish resources for the Yangtze Estuary.
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47
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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48
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Chen R, Wong HL, Kindler GS, MacLeod FI, Benaud N, Ferrari BC, Burns BP. Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats. Front Microbiol 2020; 11:1950. [PMID: 32973707 PMCID: PMC7472256 DOI: 10.3389/fmicb.2020.01950] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/24/2020] [Indexed: 01/27/2023] Open
Abstract
Microbial mats are geobiological multilayered ecosystems that have significant evolutionary value in understanding the evolution of early life on Earth. Shark Bay, Australia has some of the best examples of modern microbial mats thriving under harsh conditions of high temperatures, salinity, desiccation, and ultraviolet (UV) radiation. Microorganisms living in extreme ecosystems are thought to potentially encode for secondary metabolites as a survival strategy. Many secondary metabolites are natural products encoded by a grouping of genes known as biosynthetic gene clusters (BGCs). Natural products have diverse chemical structures and functions which provide competitive advantages for microorganisms and can also have biotechnology applications. In the present study, the diversity of BGC were described in detail for the first time from Shark Bay microbial mats. A total of 1477 BGCs were detected in metagenomic data over a 20 mm mat depth horizon, with the surface layer possessing over 200 BGCs and containing the highest relative abundance of BGCs of all mat layers. Terpene and bacteriocin BGCs were highly represented and their natural products are proposed to have important roles in ecosystem function in these mat systems. Interestingly, potentially novel BGCs were detected from Heimdallarchaeota and Lokiarchaeota, two evolutionarily significant archaeal phyla not previously known to possess BGCs. This study provides new insights into how secondary metabolites from BGCs may enable diverse microbial mat communities to adapt to extreme environments.
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Affiliation(s)
- Ray Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Gareth S Kindler
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Fraser Iain MacLeod
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
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49
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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: 4.8] [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.
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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
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50
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Abstract
Many biological contaminants are disseminated through water, and their occurrence has potential detrimental impacts on public and environmental health. Conventional monitoring tools rely on cultivation and are not robust in addressing modern water quality concerns. This review proposes metagenomics as a means to provide a rapid, nontargeted assessment of biological contaminants in water. When further coupled with appropriate methods (e.g., quantitative PCR and flow cytometry) and bioinformatic tools, metagenomics can provide information concerning both the abundance and diversity of biological contaminants in reclaimed waters. Further correlation between the metagenomic-derived data of selected contaminants and the measurable parameters of water quality can also aid in devising strategies to alleviate undesirable water quality. Here, we review metagenomic approaches (i.e., both sequencing platforms and bioinformatic tools) and studies that demonstrated their use for reclaimed-water quality monitoring. We also provide recommendations on areas of improvement that will allow metagenomics to significantly impact how the water industry performs reclaimed-water quality monitoring in the future.
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Affiliation(s)
- Pei-Ying Hong
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David Mantilla-Calderon
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Changzhi Wang
- Water Desalination and Reuse Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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