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Special Issue "Metagenomics: a Powerful Lens Viewing the Microbial World"

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry, Molecular Biology and Biophysics".

Deadline for manuscript submissions: closed (30 July 2014)

Special Issue Editor

Guest Editor
Dr. Weizhong Li (Website)

Center for Research in Biological Systems, University of California, San Diego, 9500 Gilman Drive MC 0446, Atkinson Hall, Room 3113, La Jolla, CA 92093-0446, USA
Interests: development of computational and bioinformatics methods; genomics; metagenomics; RNA-seq; system biology; human microbiome; next generation sequence data analysis; development of workflows; high performance computing

Special Issue Information

Dear Colleagues,

Metagenomics has been one of the most fast-developing fields of the last decade. Through culture-independent genomic sequencing, the metagenomics approach offers an unprecedented view of the diverse microbial world in different environments, such as ocean and other water bodies, human and animal body sites, soil, air and many others. At a genomic level, metagenomics reveals the identity, composition and dynamics of microbial communities and interactions with their environments. With the rapid advance of next generation high throughput sequencing technologies, metagenomics approach is now widely utilized by researchers in many disciplines such as ecology, energy, agriculture, biotechnology and medicine. As such a fast-growing field, metagenomics also presents many great challenges that need to be addressed. This Special Issue is intended to provide a snapshot of the state-of-the-art of today’s metagenomics research. We plan to publish original research papers as well as review articles on studies of different microbial environments and systems using the metagenomics approach, novel computational and statistical methods for metagenomics data analysis, and innovative technologies and protocols that expand the existing metagenomics capabilities. We especially encourage topics that discuss and address the imposing challenges in metagenomics, introduce novel methodologies, and provide new insights into the microbial world, for example, accurate species and strain identification and profiling, utilization and integration of multiple omics approaches (e.g. metagenomics, metatranscriptomics, 16S, metaproteomics and metabolomics), in depth investigation of novel habitats, microbiome-based disease models, and so on.

Dr. Weizhong Li
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs).

Keywords

  • metagenomics
  • metagenome
  • microbiome
  • microbiot
  • metatranscriptomics
  • 16S
  • next generation sequencing
  • microbial ecology
  • metagenomics sequence analysis
  • metagenome comparison

Published Papers (8 papers)

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Research

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Open AccessArticle Assessing the Accuracy of Quantitative Molecular Microbial Profiling
Int. J. Mol. Sci. 2014, 15(11), 21476-21491; doi:10.3390/ijms151121476
Received: 25 July 2014 / Revised: 11 November 2014 / Accepted: 14 November 2014 / Published: 21 November 2014
Cited by 4 | PDF Full-text (1107 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The application of high-throughput sequencing in profiling microbial communities is providing an unprecedented ability to investigate microbiomes. Such studies typically apply one of two methods: amplicon sequencing using PCR to target a conserved orthologous sequence (typically the 16S ribosomal RNA gene) or [...] Read more.
The application of high-throughput sequencing in profiling microbial communities is providing an unprecedented ability to investigate microbiomes. Such studies typically apply one of two methods: amplicon sequencing using PCR to target a conserved orthologous sequence (typically the 16S ribosomal RNA gene) or whole (meta)genome sequencing (WGS). Both methods have been used to catalog the microbial taxa present in a sample and quantify their respective abundances. However, a comparison of the inherent precision or bias of the different sequencing approaches has not been performed. We previously developed a metagenomic control material (MCM) to investigate error when performing different sequencing strategies. Amplicon sequencing using four different primer strategies and two 16S rRNA regions was examined (Roche 454 Junior) and compared to WGS (Illumina HiSeq). All sequencing methods generally performed comparably and in good agreement with organism specific digital PCR (dPCR); WGS notably demonstrated very high precision. Where discrepancies between relative abundances occurred they tended to differ by less than twofold. Our findings suggest that when alternative sequencing approaches are used for microbial molecular profiling they can perform with good reproducibility, but care should be taken when comparing small differences between distinct methods. This work provides a foundation for future work comparing relative differences between samples and the impact of extraction methods. We also highlight the value of control materials when conducting microbial profiling studies to benchmark methods and set appropriate thresholds. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
Open AccessArticle Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract Microbiome
Int. J. Mol. Sci. 2014, 15(10), 18819-18839; doi:10.3390/ijms151018819
Received: 28 July 2014 / Revised: 30 September 2014 / Accepted: 11 October 2014 / Published: 20 October 2014
PDF Full-text (833 KB) | HTML Full-text | XML Full-text
Abstract
This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida. Using a modified indirect DNA extraction protocol and performing metagenomic profiling based on specific prokaryotic marker genes, the abundance of bacterial groups [...] Read more.
This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida. Using a modified indirect DNA extraction protocol and performing metagenomic profiling based on specific prokaryotic marker genes, the abundance of bacterial groups was identified from the analyzed metagenome. The members of three significantly abundant phyla of Proteobacteria, Firmicutes and Bacteroidetes were characterized through the literature and their predicted functions towards the host, as well as potential applications in the industrial environment assessed. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
Open AccessArticle Identification of Diversity-Generating Retroelements in Human Microbiomes
Int. J. Mol. Sci. 2014, 15(8), 14234-14246; doi:10.3390/ijms150814234
Received: 21 June 2014 / Revised: 2 August 2014 / Accepted: 6 August 2014 / Published: 15 August 2014
Cited by 3 | PDF Full-text (2950 KB) | HTML Full-text | XML Full-text
Abstract
Diversity-generating retroelements (DGRs) are a unique family of retroelements that confer selective advantages to their hosts by accelerating the evolution of target genes through a specialized, error-prone, reverse transcription process. First identified in a Bordetella phage (BPP-1), which mediates the phage tropism [...] Read more.
Diversity-generating retroelements (DGRs) are a unique family of retroelements that confer selective advantages to their hosts by accelerating the evolution of target genes through a specialized, error-prone, reverse transcription process. First identified in a Bordetella phage (BPP-1), which mediates the phage tropism specificity by generating variability in an involved gene, DGRs were predicted to be present in a larger collection of viral and bacterial species. A minimal DGR system is comprised of a reverse transcriptase (RTase) gene, a template sequence (TR) and a variable region (VR) within a target gene. We developed a computational tool, DGRscan, to allow either de novo identification (based on the prediction of potential template-variable region pairs) or similarity-based searches of DGR systems using known template sequences as the reference. The application of DGRscan to the human microbiome project (HMP) datasets resulted in the identification of 271 non-redundant DGR systems, doubling the size of the collection of known DGR systems. We further identified a large number of putative target genes (651, which share no more than 90% sequence identity at the amino acid level) that are potentially under diversification by the DGR systems. Our study provides the first survey of the DGR systems in the human microbiome, showing that the DGR systems are frequently found in human-associated bacterial communities, although they are of low incidence in individual genomes. Our study also provides functional clues for a large number of genes (reverse transcriptases and target genes) that were previously annotated as proteins of unknown functions or nonspecific functions. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
Figures

Open AccessArticle Exploring Neighborhoods in the Metagenome Universe
Int. J. Mol. Sci. 2014, 15(7), 12364-12378; doi:10.3390/ijms150712364
Received: 31 March 2014 / Revised: 23 June 2014 / Accepted: 25 June 2014 / Published: 14 July 2014
PDF Full-text (1211 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The variety of metagenomes in current databases provides a rapidly growing source of information for comparative studies. However, the quantity and quality of supplementary metadata is still lagging behind. It is therefore important to be able to identify related metagenomes by means [...] Read more.
The variety of metagenomes in current databases provides a rapidly growing source of information for comparative studies. However, the quantity and quality of supplementary metadata is still lagging behind. It is therefore important to be able to identify related metagenomes by means of the available sequence data alone. We have studied efficient sequence-based methods for large-scale identification of similar metagenomes within a database retrieval context. In a broad comparison of different profiling methods we found that vector-based distance measures are well-suitable for the detection of metagenomic neighbors. Our evaluation on more than 1700 publicly available metagenomes indicates that for a query metagenome from a particular habitat on average nine out of ten nearest neighbors represent the same habitat category independent of the utilized profiling method or distance measure. While for well-defined labels a neighborhood accuracy of 100% can be achieved, in general the neighbor detection is severely affected by a natural overlap of manually annotated categories. In addition, we present results of a novel visualization method that is able to reflect the similarity of metagenomes in a 2D scatter plot. The visualization method shows a similarly high accuracy in the reduced space as compared with the high-dimensional profile space. Our study suggests that for inspection of metagenome neighborhoods the profiling methods and distance measures can be chosen to provide a convenient interpretation of results in terms of the underlying features. Furthermore, supplementary metadata of metagenome samples in the future needs to comply with readily available ontologies for fine-grained and standardized annotation. To make profile-based k-nearest-neighbor search and the 2D-visualization of the metagenome universe available to the research community, we included the proposed methods in our CoMet-Universe server for comparative metagenome analysis. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
Figures

Open AccessArticle Generation and Analysis of Expressed Sequence Tags (ESTs) from Halophyte Atriplex canescens to Explore Salt-Responsive Related Genes
Int. J. Mol. Sci. 2014, 15(6), 11172-11189; doi:10.3390/ijms150611172
Received: 20 May 2014 / Revised: 11 June 2014 / Accepted: 12 June 2014 / Published: 23 June 2014
Cited by 4 | PDF Full-text (711 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided [...] Read more.
Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided 343 high-quality ESTs. In an evaluation of 343 valid EST sequences in the cDNA library, 197 unigenes were assembled, among which 190 unigenes (83.1% ESTs) were identified according to their significant similarities with proteins of known functions. All the 343 EST sequences have been deposited in the dbEST GenBank under accession numbers JZ535802 to JZ536144. According to Arabidopsis MIPS functional category and GO classifications, we identified 193 unigenes of the 311 annotations EST, representing 72 non-redundant unigenes sharing similarities with genes related to the defense response. The sets of ESTs obtained provide a rich genetic resource and 17 up-regulated genes related to salt stress resistance were identified by qRT-PCR. Six of these genes may contribute crucially to earlier and later stage salt stress resistance. Additionally, among the 343 unigenes sequences, 22 simple sequence repeats (SSRs) were also identified contributing to the study of A. canescens resources. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
Open AccessArticle A Comprehensive Insight into Tetracycline Resistant Bacteria and Antibiotic Resistance Genes in Activated Sludge Using Next-Generation Sequencing
Int. J. Mol. Sci. 2014, 15(6), 10083-10100; doi:10.3390/ijms150610083
Received: 30 March 2014 / Revised: 9 May 2014 / Accepted: 22 May 2014 / Published: 5 June 2014
Cited by 7 | PDF Full-text (894 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In order to comprehensively investigate tetracycline resistance in activated sludge of sewage treatment plants, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential tetracycline resistant bacteria (TRB) and antibiotic resistance genes (ARGs) in sludge cultured with different concentrations of tetracycline. [...] Read more.
In order to comprehensively investigate tetracycline resistance in activated sludge of sewage treatment plants, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential tetracycline resistant bacteria (TRB) and antibiotic resistance genes (ARGs) in sludge cultured with different concentrations of tetracycline. Pyrosequencing of 16S rRNA gene revealed that tetracycline treatment greatly affected the bacterial community structure of the sludge. Nine genera consisting of Sulfuritalea, Armatimonas, Prosthecobacter, Hyphomicrobium, Azonexus, Longilinea, Paracoccus, Novosphingobium and Rhodobacter were identified as potential TRB in the sludge. Results of qPCR, molecular cloning and metagenomic analysis consistently indicated that tetracycline treatment could increase both the abundance and diversity of the tet genes, but decreased the occurrence and diversity of non-tetracycline ARG, especially sulfonamide resistance gene sul2. Cluster analysis showed that tetracycline treatment at subinhibitory concentrations (5 mg/L) was found to pose greater effects on the bacterial community composition, which may be responsible for the variations of the ARGs abundance. This study indicated that joint use of 454 pyrosequencing and Illumina high-throughput sequencing can be effectively used to explore ARB and ARGs in the environment, and future studies should include an in-depth investigation of the relationship between microbial community, ARGs and antibiotics in sewage treatment plant (STP) sludge. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)

Review

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Open AccessReview Viral Metagenomics on Animals as a Tool for the Detection of Zoonoses Prior to Human Infection?
Int. J. Mol. Sci. 2014, 15(6), 10377-10397; doi:10.3390/ijms150610377
Received: 12 March 2014 / Revised: 24 May 2014 / Accepted: 28 May 2014 / Published: 10 June 2014
Cited by 8 | PDF Full-text (1481 KB) | HTML Full-text | XML Full-text
Abstract
Many human viral infections have a zoonotic, i.e., wild or domestic animal, origin. Several zoonotic viruses are transmitted to humans directly via contact with an animal or indirectly via exposure to the urine or feces of infected animals or the bite [...] Read more.
Many human viral infections have a zoonotic, i.e., wild or domestic animal, origin. Several zoonotic viruses are transmitted to humans directly via contact with an animal or indirectly via exposure to the urine or feces of infected animals or the bite of a bloodsucking arthropod. If a virus is able to adapt and replicate in its new human host, human-to-human transmissions may occur, possibly resulting in an epidemic, such as the A/H1N1 flu pandemic in 2009. Thus, predicting emerging zoonotic infections is an important challenge for public health officials in the coming decades. The recent development of viral metagenomics, i.e., the characterization of the complete viral diversity isolated from an organism or an environment using high-throughput sequencing technologies, is promising for the surveillance of such diseases and can be accomplished by analyzing the viromes of selected animals and arthropods that are closely in contact with humans. In this review, we summarize our current knowledge of viral diversity within such animals (in particular blood-feeding arthropods, wildlife and domestic animals) using metagenomics and present its possible future application for the surveillance of zoonotic and arboviral diseases. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)
Open AccessReview Marine Microbial Metagenomics: From Individual to the Environment
Int. J. Mol. Sci. 2014, 15(5), 8878-8892; doi:10.3390/ijms15058878
Received: 31 March 2014 / Revised: 29 April 2014 / Accepted: 8 May 2014 / Published: 19 May 2014
Cited by 9 | PDF Full-text (222 KB) | HTML Full-text | XML Full-text
Abstract
Microbes are the most abundant biological entities on earth, therefore, studying them is important for understanding their roles in global ecology. The science of metagenomics is a relatively young field of research that has enjoyed significant effort since its inception in 1998. [...] Read more.
Microbes are the most abundant biological entities on earth, therefore, studying them is important for understanding their roles in global ecology. The science of metagenomics is a relatively young field of research that has enjoyed significant effort since its inception in 1998. Studies using next-generation sequencing techniques on single genomes and collections of genomes have not only led to novel insights into microbial genomics, but also revealed a close association between environmental niches and genome evolution. Herein, we review studies investigating microbial genomics (largely in the marine ecosystem) at the individual and community levels to summarize our current understanding of microbial ecology in the environment. Full article
(This article belongs to the Special Issue Metagenomics: a Powerful Lens Viewing the Microbial World)

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