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Zhou J, Song W, Tu Q. To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities. Brief Bioinform 2023; 24:6961613. [PMID: 36575570 DOI: 10.1093/bib/bbac594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/22/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.
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Affiliation(s)
- Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China.,Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
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Witney AA, Aller S, Strang BL. Metagenomic profiling of placental tissue suggests DNA virus infection of the placenta is rare. J Gen Virol 2021; 102. [PMID: 34723784 PMCID: PMC8742990 DOI: 10.1099/jgv.0.001677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is widely recognized that pathogens can be transmitted across the placenta from mother to foetus. Recent re-evaluation of metagenomic studies indicates that the placenta has no unique microbiome of commensal bacteria. However, viral transmission across the placenta, including transmission of DNA viruses such as the human herpesviruses, is possible. A fuller understanding of which DNA virus sequence can be found in the placenta is required. We employed a metagenomic analysis to identify viral DNA sequences in placental metagenomes from full-term births (20 births), pre-term births (13 births), births from pregnancies associated with antenatal infections (12 births) or pre-term births with antenatal infections (three births). Our analysis found only a small number of DNA sequences corresponding to the genomes of human herpesviruses in four of the 48 metagenomes analysed. Therefore, our data suggest that DNA virus infection of the placenta is rare and support the concept that the placenta is largely free of pathogen infection.
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Affiliation(s)
- Adam A Witney
- Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Sean Aller
- Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK
| | - Blair L Strang
- Institute for Infection and Immunity, St George's, University of London, London SW17 0RE, UK
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Parks DH, Rigato F, Vera-Wolf P, Krause L, Hugenholtz P, Tyson GW, Wood DLA. Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome. Front Microbiol 2021; 12:643682. [PMID: 33959106 PMCID: PMC8093879 DOI: 10.3389/fmicb.2021.643682] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/11/2021] [Indexed: 12/12/2022] Open
Abstract
A fundamental goal of microbial ecology is to accurately determine the species composition in a given microbial ecosystem. In the context of the human microbiome, this is important for establishing links between microbial species and disease states. Here we benchmark the Microba Community Profiler (MCP) against other metagenomic classifiers using 140 moderate to complex in silico microbial communities and a standardized reference genome database. MCP generated accurate relative abundance estimates and made substantially fewer false positive predictions than other classifiers while retaining a high recall rate. We further demonstrated that the accuracy of species classification was substantially increased using the Microba Genome Database, which is more comprehensive than reference datasets used by other classifiers and illustrates the importance of including genomes of uncultured taxa in reference databases. Consequently, MCP classifies appreciably more reads than other classifiers when using their recommended reference databases. These results establish MCP as best-in-class with the ability to produce comprehensive and accurate species profiles of human gastrointestinal samples.
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Affiliation(s)
| | - Fabio Rigato
- Microba Life Sciences Limited, Brisbane, QLD, Australia
| | | | - Lutz Krause
- Microba Life Sciences Limited, Brisbane, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Gene W. Tyson
- Microba Life Sciences Limited, Brisbane, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
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Luqman A, Zabel S, Rahmdel S, Merz B, Gruenheit N, Harter J, Nieselt K, Götz F. The Neuromodulator-Encoding sadA Gene Is Widely Distributed in the Human Skin Microbiome. Front Microbiol 2020; 11:573679. [PMID: 33335515 PMCID: PMC7736160 DOI: 10.3389/fmicb.2020.573679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/09/2020] [Indexed: 01/01/2023] Open
Abstract
Trace amines (TA) are endogenously produced in mammals, have a low concentration in the central nervous system (CNS), but trigger a variety of neurological effects and intervene in host cell communication. It emerged that neurotransmitters and TA are produced also by the microbiota. As it has been shown that TA contribute to wound healing, we examined the skin microbiome of probands using shotgun metagenomics. The phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were predominant. Since SadA is a highly promiscuous TA-producing decarboxylase in Firmicutes, the skin microbiome was specifically examined for the presence of sadA-homologous genes. By mapping the reads of certain genes, we found that, although there were less reads mapping to sadA than to ubiquitous housekeeping genes (arcC and mutS), normalized reads counts were still >1000 times higher than those of rare control genes (icaA, icaB, and epiA). At protein sequence level SadA homologs were found in at least 7 phyla: Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and Cyanobacteria, and in 23 genera of the phylum Firmicutes. A high proportion of the genera that have a SadA homolog belong to the classical skin and intestinal microbiota. The distribution of sadA in so many different phyla illustrates the importance of horizontal gene transfer (HGT). We show that the sadA gene is widely distributed in the human skin microbiome. When comparing the sadA read counts in the probands, there was no correlation between age and gender, but an enormous difference in the sadA read counts in the microbiome of the individuals. Since sadA is involved in TA synthesis, it is likely that the TA content of the skin is correlated with the amount of TA producing bacteria in the microbiome. In this way, the microbiome-generated TA could influence signal transmission in the epithelial and nervous system.
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Affiliation(s)
- Arif Luqman
- Microbial Genetics, University of Tübingen, Tübingen, Germany.,Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | - Susanne Zabel
- Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Samane Rahmdel
- Department of Food Hygiene and Quality Control, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | | | | | - Kay Nieselt
- Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Friedrich Götz
- Microbial Genetics, University of Tübingen, Tübingen, Germany
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Xing Z, Zhang Y, Li M, Guo C, Mi S. RBUD: A New Functional Potential Analysis Approach for Whole Microbial Genome Shotgun Sequencing. Microorganisms 2020; 8:E1563. [PMID: 33050530 PMCID: PMC7650719 DOI: 10.3390/microorganisms8101563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022] Open
Abstract
Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size.
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Affiliation(s)
- Zhikai Xing
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; (Z.X.); (Y.Z.); (M.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunting Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; (Z.X.); (Y.Z.); (M.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; (Z.X.); (Y.Z.); (M.L.)
| | - Chongye Guo
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; (Z.X.); (Y.Z.); (M.L.)
| | - Shuangli Mi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China; (Z.X.); (Y.Z.); (M.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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