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Zavadska D, Henry N, Auladell A, Berney C, Richter DJ. Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes. PLoS One 2024; 19:e0303697. [PMID: 38843225 PMCID: PMC11156365 DOI: 10.1371/journal.pone.0303697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Two common approaches to study the composition of environmental protist communities are metabarcoding and metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches are used to assemble metagenomic reads into metagenome-assembled genomes (MAGs). Understanding the correspondence between the data produced by these two approaches can help to integrate information between the datasets and to explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent. MAGs do not contain the commonly used barcoding loci, therefore sequence homology approaches cannot be used to match OTUs and MAGs. We made an attempt to match V9 metabarcoding OTUs from the 18S rRNA gene (V9 OTUs) and MAGs from the Tara Oceans expedition based on the correspondence of their relative abundances across the same set of samples. We evaluated several metrics for detecting correspondence between features in these two datasets and developed controls to filter artefacts of data structure and processing. After selecting the best-performing metrics, ranking the V9 OTU/MAG matches by their proportionality/correlation coefficients and applying a set of selection criteria, we identified candidate matches between V9 OTUs and MAGs. In some cases, V9 OTUs and MAGs could be matched with a one-to-one correspondence, implying that they likely represent the same underlying biological entity. More generally, matches we observed could be classified into 4 scenarios: one V9 OTU matches many MAGs; many V9 OTUs match many MAGs; many V9 OTUs match one MAG; one V9 OTU matches one MAG. Notably, we found some instances in which different OTU-MAG matches from the same taxonomic group were not classified in the same scenario, with all four scenarios possible even within the same taxonomic group, illustrating that factors beyond taxonomic lineage influence the relationship between OTUs and MAGs. Overall, each scenario produces a different interpretation of V9 OTUs, MAGs and how they compare in terms of the genomic and ecological diversity they represent.
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Affiliation(s)
- Daryna Zavadska
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Nicolas Henry
- CNRS, FR2424, ABiMS, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Adrià Auladell
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Cédric Berney
- CNRS, UMR7144, AD2M, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Daniel J. Richter
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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2
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Junker R, Valence F, Mistou MY, Chaillou S, Chiapello H. Integration of metataxonomic data sets into microbial association networks highlights shared bacterial community dynamics in fermented vegetables. Microbiol Spectr 2024; 12:e0031224. [PMID: 38747598 DOI: 10.1128/spectrum.00312-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/26/2024] [Indexed: 06/06/2024] Open
Abstract
The management of food fermentation is still largely based on empirical knowledge, as the dynamics of microbial communities and the underlying metabolic networks that produce safe and nutritious products remain beyond our understanding. Although these closed ecosystems contain relatively few taxa, they have not yet been thoroughly characterized with respect to how their microbial communities interact and dynamically evolve. However, with the increased availability of metataxonomic data sets on different fermented vegetables, it is now possible to gain a comprehensive understanding of the microbial relationships that structure plant fermentation. In this study, we applied a network-based approach to the integration of public metataxonomic 16S data sets targeting different fermented vegetables throughout time. Specifically, we aimed to explore, compare, and combine public 16S data sets to identify shared associations between amplicon sequence variants (ASVs) obtained from independent studies. The workflow includes steps for searching and selecting public time-series data sets and constructing association networks of ASVs based on co-abundance metrics. Networks for individual data sets are then integrated into a core network, highlighting significant associations. Microbial communities are identified based on the comparison and clustering of ASV networks using the "stochastic block model" method. When we applied this method to 10 public data sets (including a total of 931 samples) targeting five varieties of vegetables with different sampling times, we found that it was able to shed light on the dynamics of vegetable fermentation by characterizing the processes of community succession among different bacterial assemblages. IMPORTANCE Within the growing body of research on the bacterial communities involved in the fermentation of vegetables, there is particular interest in discovering the species or consortia that drive different fermentation steps. This integrative analysis demonstrates that the reuse and integration of public microbiome data sets can provide new insights into a little-known biotope. Our most important finding is the recurrent but transient appearance, at the beginning of vegetable fermentation, of amplicon sequence variants (ASVs) belonging to Enterobacterales and their associations with ASVs belonging to Lactobacillales. These findings could be applied to the design of new fermented products.
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Affiliation(s)
- Romane Junker
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
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3
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Kazer SW, Match CM, Langan EM, Messou MA, LaSalle TJ, O’Leary E, Marbourg J, Naughton K, von Andrian UH, Ordovas-Montanes J. Primary nasal viral infection rewires the tissue-scale memory response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.11.539887. [PMID: 38562902 PMCID: PMC10983857 DOI: 10.1101/2023.05.11.539887] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The nasal mucosa is frequently the initial site of respiratory viral infection, replication, and transmission. Recent work has started to clarify the independent responses of epithelial, myeloid, and lymphoid cells to viral infection in the nasal mucosa, but their spatiotemporal coordination and relative contributions remain unclear. Furthermore, understanding whether and how primary infection shapes tissue-scale memory responses to secondary challenge is critical for the rational design of nasal-targeting therapeutics and vaccines. Here, we generated a single-cell RNA-sequencing (scRNA-seq) atlas of the murine nasal mucosa sampling three distinct regions before and during primary and secondary influenza infection. Primary infection was largely restricted to respiratory mucosa and induced stepwise changes in cell type, subset, and state composition over time. Type I Interferon (IFN)-responsive neutrophils appeared 2 days post infection (dpi) and preceded transient IFN-responsive/cycling epithelial cell responses 5 dpi, which coincided with broader antiviral monocyte and NK cell accumulation. By 8 dpi, monocyte-derived macrophages (MDMs) expressing Cxcl9 and Cxcl16 arose alongside effector cytotoxic CD8 and Ifng-expressing CD4 T cells. Following viral clearance (14 dpi), rare, previously undescribed Krt13+ nasal immune-interacting floor epithelial (KNIIFE) cells expressing multiple genes with immune communication potential increased concurrently with tissue-resident memory T (TRM)-like cells and early IgG+/IgA+ plasmablasts. Proportionality analysis coupled with cell-cell communication inference, alongside validation by in situ microscopy, underscored the CXCL16-CXCR6 signaling axis between MDMs and effector CD8 T cells 8dpi and KNIIFE cells and TRM cells 14 dpi. Secondary influenza challenge with a homologous or heterologous strain administered 60 dpi induced an accelerated and coordinated myeloid and lymphoid response without epithelial proliferation, illustrating how tissue-scale memory to natural infection engages both myeloid and lymphoid cells to reduce epithelial regenerative burden. Together, this atlas serves as a reference for viral infection in the upper respiratory tract and highlights the efficacy of local coordinated memory responses upon rechallenge.
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Affiliation(s)
- Samuel W. Kazer
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Colette Matysiak Match
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Erica M. Langan
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marie-Angèle Messou
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Thomas J. LaSalle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Health Sciences and Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA
| | - Elise O’Leary
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | | | | - Ulrich H. von Andrian
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
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4
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Greathouse KL, Stone JK, Vargas AJ, Choudhury A, Padgett RN, White JR, Jung A, Harris CC. Co-enrichment of cancer-associated bacterial taxa is correlated with immune cell infiltrates in esophageal tumor tissue. Sci Rep 2024; 14:2574. [PMID: 38296990 PMCID: PMC10831118 DOI: 10.1038/s41598-023-48862-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/30/2023] [Indexed: 02/02/2024] Open
Abstract
Esophageal carcinoma (ESCA) is a leading cause of cancer-related death worldwide, and certain oral and intestinal pathogens have been associated with cancer development and progression. We asked if esophageal microbiomes had shared alterations that could provide novel biomarkers for ESCA risk. We extracted DNA from tumor and non-tumor tissue of 212 patients in the NCI-MD case control study and sequenced the 16S rRNA gene (V3-4), with TCGA ESCA RNA-seq (n = 172) and WGS (n = 123) non-human reads used as validation. We identified four taxa, Campylobacter, Prevotella, Streptococcus, and Fusobacterium as highly enriched in esophageal cancer across all cohorts. Using SparCC, we discovered that Fusobacterium and Prevotella were also co-enriched across all cohorts. We then analyzed immune cell infiltration to determine if these dysbiotic taxa were associated with immune signatures. Using xCell to obtain predicted immune infiltrates, we identified a depletion of megakaryocyte-erythroid progenitor (MEP) cells in tumors with presence of any of the four taxa, along with enrichment of platelets in tumors with Campylobactor or Fusobacterium. Taken together, our results suggest that intratumoral presence of these co-occurring bacterial genera may confer tumor promoting immune alterations that allow disease progression in esophageal cancer.
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Affiliation(s)
- K L Greathouse
- Department of Biology, Baylor University, Waco, TX, USA.
- Nutrition Division, Human Sciences and Design, Baylor University, Waco, TX, USA.
| | - J K Stone
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - A J Vargas
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - A Choudhury
- Department of Biology, Baylor University, Waco, TX, USA
| | - R N Padgett
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - J R White
- Resphera Biosciences, LLC, Baltimore, MD, USA
| | - A Jung
- Department of Biology, Baylor University, Waco, TX, USA
| | - C C Harris
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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5
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Fullerton H, Smith L, Enriquez A, Butterfield D, Wheat CG, Moyer CL. Seafloor incubation experiments at deep-sea hydrothermal vents reveal distinct biogeographic signatures of autotrophic communities. FEMS Microbiol Ecol 2024; 100:fiae001. [PMID: 38200713 PMCID: PMC10808952 DOI: 10.1093/femsec/fiae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/20/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024] Open
Abstract
The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kama'ehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kama'ehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.
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Affiliation(s)
- Heather Fullerton
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - Lindsey Smith
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
| | - Alejandra Enriquez
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - David Butterfield
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington and NOAA/PMEL, John M. Wallace Hall, 3737 Brooklyn Ave NE, Seattle, WA 98105, United States
| | - C Geoffrey Wheat
- Institute of Marine Studies, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Drive, 245 O’Neill Building, PO Box 757220, Fairbanks, Alaska 99775-7220, United States
| | - Craig L Moyer
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
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6
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Chetty A, Blekhman R. Multi-omic approaches for host-microbiome data integration. Gut Microbes 2024; 16:2297860. [PMID: 38166610 PMCID: PMC10766395 DOI: 10.1080/19490976.2023.2297860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
The gut microbiome interacts with the host through complex networks that affect physiology and health outcomes. It is becoming clear that these interactions can be measured across many different omics layers, including the genome, transcriptome, epigenome, metabolome, and proteome, among others. Multi-omic studies of the microbiome can provide insight into the mechanisms underlying host-microbe interactions. As more omics layers are considered, increasingly sophisticated statistical methods are required to integrate them. In this review, we provide an overview of approaches currently used to characterize multi-omic interactions between host and microbiome data. While a large number of studies have generated a deeper understanding of host-microbiome interactions, there is still a need for standardization across approaches. Furthermore, microbiome studies would also benefit from the collection and curation of large, publicly available multi-omics datasets.
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Affiliation(s)
- Ashwin Chetty
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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7
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Xia Y. Statistical normalization methods in microbiome data with application to microbiome cancer research. Gut Microbes 2023; 15:2244139. [PMID: 37622724 PMCID: PMC10461514 DOI: 10.1080/19490976.2023.2244139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/12/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Mounting evidence has shown that gut microbiome is associated with various cancers, including gastrointestinal (GI) tract and non-GI tract cancers. But microbiome data have unique characteristics and pose major challenges when using standard statistical methods causing results to be invalid or misleading. Thus, to analyze microbiome data, it not only needs appropriate statistical methods, but also requires microbiome data to be normalized prior to statistical analysis. Here, we first describe the unique characteristics of microbiome data and the challenges in analyzing them (Section 2). Then, we provide an overall review on the available normalization methods of 16S rRNA and shotgun metagenomic data along with examples of their applications in microbiome cancer research (Section 3). In Section 4, we comprehensively investigate how the normalization methods of 16S rRNA and shotgun metagenomic data are evaluated. Finally, we summarize and conclude with remarks on statistical normalization methods (Section 5). Altogether, this review aims to provide a broad and comprehensive view and remarks on the promises and challenges of the statistical normalization methods in microbiome data with microbiome cancer research examples.
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Affiliation(s)
- Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, USA
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8
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Ewald J, Zhou G, Lu Y, Xia J. Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non-Model Organisms. Curr Protoc 2023; 3:e922. [PMID: 37929753 DOI: 10.1002/cpz1.922] [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: 11/07/2023]
Abstract
ExpressAnalyst is a web-based platform that enables intuitive, end-to-end transcriptomics and proteomics data analysis. Users can start from FASTQ files, gene/protein abundance tables, or gene/protein lists. ExpressAnalyst will perform read quantification, gene expression table processing and normalization, differential expression analysis, or meta-analysis with complex study designs. The results are presented via various interactive visualizations such as volcano plots, heatmaps, networks, and ridgeline charts, with built-in functional enrichment analysis to allow flexible data exploration and understanding. ExpressAnalyst currently contains built-in support for 29 common organisms. For non-model organisms without good reference genomes, it can perform comprehensive transcriptome profiling directly from RNA-seq reads. These common tasks are covered in 11 Basic Protocols. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: RNA-seq count table uploading, processing, and normalization Basic Protocol 2: Differential expression analysis with linear models Basic Protocol 3: Functional analysis with volcano plot, enrichment network, and ridgeline visualization Basic Protocol 4: Hierarchical clustering analysis of transcriptomics data using interactive heatmaps Basic Protocol 5: Cross-species gene expression analysis based on ortholog mapping results Basic Protocol 6: Proteomics and microarray data processing and normalization Basic Protocol 7: Preparing multiple gene expression tables for meta-analysis Basic Protocol 8: Statistical and functional meta-analysis of gene expression data Basic Protocol 9: Functional analysis of transcriptomics signatures Basic Protocol 10: Dose-response and time-series data analysis Basic Protocol 11: RNA-seq reads processing and quantification with and without reference transcriptomes.
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Affiliation(s)
- Jessica Ewald
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
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9
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Li X, Wang C, Zhu X, Ntoukakis V, Cernava T, Jin D. Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance. ENVIRONMENTAL MICROBIOME 2023; 18:78. [PMID: 37876011 PMCID: PMC10594911 DOI: 10.1186/s40793-023-00534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant's defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with differing aphid resistance, grown in the same farmland. RESULTS The bacterial community in both the phyllosphere and endosphere showed significant differences among most wheat cultivars. The phyllosphere was connected to more complex and stable microbial networks than the endosphere in most wheat cultivars. Moreover, the genera Pantoea, Massilia, and Pseudomonas were found to play a major role in shaping the microbial community in the wheat phyllosphere. Additionally, wheat plants showed phenotype-specific associations with the genera Massilia and Pseudomonas. The abundance of the genus Exiguobacterium in the phyllosphere exhibited a significant negative correlation with the aphid hazard grade in the wheat plants. CONCLUSION Communities of leaf-associated microbes in wheat plants were mainly driven by the host genotype. Members of the genus Exiguobacterium may have adverse effects on wheat aphids. Our findings provide new clues supporting the development of aphid control strategies based on phyllosphere microbiome engineering.
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Affiliation(s)
- Xinan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, School of Resource and Environmental Sciences, Henan Institute of Science and Technology, 453003, Xinxiang, China
| | - Chao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China.
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Papoutsoglou G, Tarazona S, Lopes MB, Klammsteiner T, Ibrahimi E, Eckenberger J, Novielli P, Tonda A, Simeon A, Shigdel R, Béreux S, Vitali G, Tangaro S, Lahti L, Temko A, Claesson MJ, Berland M. Machine learning approaches in microbiome research: challenges and best practices. Front Microbiol 2023; 14:1261889. [PMID: 37808286 PMCID: PMC10556866 DOI: 10.3389/fmicb.2023.1261889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Microbiome data predictive analysis within a machine learning (ML) workflow presents numerous domain-specific challenges involving preprocessing, feature selection, predictive modeling, performance estimation, model interpretation, and the extraction of biological information from the results. To assist decision-making, we offer a set of recommendations on algorithm selection, pipeline creation and evaluation, stemming from the COST Action ML4Microbiome. We compared the suggested approaches on a multi-cohort shotgun metagenomics dataset of colorectal cancer patients, focusing on their performance in disease diagnosis and biomarker discovery. It is demonstrated that the use of compositional transformations and filtering methods as part of data preprocessing does not always improve the predictive performance of a model. In contrast, the multivariate feature selection, such as the Statistically Equivalent Signatures algorithm, was effective in reducing the classification error. When validated on a separate test dataset, this algorithm in combination with random forest modeling, provided the most accurate performance estimates. Lastly, we showed how linear modeling by logistic regression coupled with visualization techniques such as Individual Conditional Expectation (ICE) plots can yield interpretable results and offer biological insights. These findings are significant for clinicians and non-experts alike in translational applications.
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Affiliation(s)
- Georgios Papoutsoglou
- Department of Computer Science, University of Crete, Heraklion, Greece
- JADBio Gnosis DA S.A., Science and Technology Park of Crete, Heraklion, Greece
| | - Sonia Tarazona
- Department of Applied Statistics and Operations Research and Quality, Polytechnic University of Valencia, Valencia, Spain
| | - Marta B. Lopes
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
- Research and Development Unit for Mechanical and Industrial Engineering (UNIDEMI), Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology, Caparica, Portugal
| | - Thomas Klammsteiner
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Eliana Ibrahimi
- Department of Biology, University of Tirana, Tirana, Albania
| | - Julia Eckenberger
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Pierfrancesco Novielli
- Department of Soil, Plant, and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- National Institute for Nuclear Physics, Bari Division, Bari, Italy
| | - Alberto Tonda
- UMR 518 MIA-PS, INRAE, Paris-Saclay University, Palaiseau, France
- Complex Systems Institute of Paris Ile-de-France (ISC-PIF) - UAR 3611 CNRS, Paris, France
| | - Andrea Simeon
- BioSense Institute, University of Novi Sad, Novi Sad, Serbia
| | - Rajesh Shigdel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Stéphane Béreux
- MetaGenoPolis, INRAE, Paris-Saclay University, Jouy-en-Josas, France
- MaIAGE, INRAE, Paris-Saclay University, Jouy-en-Josas, France
| | - Giacomo Vitali
- MetaGenoPolis, INRAE, Paris-Saclay University, Jouy-en-Josas, France
| | - Sabina Tangaro
- Department of Soil, Plant, and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- National Institute for Nuclear Physics, Bari Division, Bari, Italy
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Andriy Temko
- Department of Electrical and Electronic Engineering, University College Cork, Cork, Ireland
| | - Marcus J. Claesson
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Magali Berland
- MetaGenoPolis, INRAE, Paris-Saclay University, Jouy-en-Josas, France
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11
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Kneis D, Lemay-St-Denis C, Cellier-Goetghebeur S, Elena AX, Berendonk TU, Pelletier JN, Heß S. Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene. THE ISME JOURNAL 2023; 17:1455-1466. [PMID: 37369703 PMCID: PMC10432401 DOI: 10.1038/s41396-023-01460-7] [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: 01/05/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Trimethoprim (TMP) is a low-cost, widely prescribed antibiotic. Its effectiveness is increasingly challenged by the spread of genes coding for TMP-resistant dihydrofolate reductases: dfrA, and the lesser-known, evolutionarily unrelated dfrB. Despite recent reports of novel variants conferring high level TMP resistance (dfrB10 to dfrB21), the prevalence of dfrB is still unknown due to underreporting, heterogeneity of the analyzed genetic material in terms of isolation sources, and limited bioinformatic processing. In this study, we explored a coherent set of shotgun metagenomic sequences to quantitatively estimate the abundance of dfrB gene variants in aquatic environments. Specifically, we scanned sequences originating from influents and effluents of municipal sewage treatment plants as well as river-borne microbiomes. Our analyses reveal an increased prevalence of dfrB1, dfrB2, dfrB3, dfrB4, dfrB5, and dfrB7 in wastewater microbiomes as compared to freshwater. These gene variants were frequently found in genomic neighborship with other resistance genes, transposable elements, and integrons, indicating their mobility. By contrast, the relative abundances of the more recently discovered variants dfrB9, dfrB10, and dfrB13 were significantly higher in freshwater than in wastewater microbiomes. Moreover, their direct neighborship with other resistance genes or markers of mobile genetic elements was significantly less likely. Our findings suggest that natural freshwater communities form a major reservoir of the recently discovered dfrB gene variants. Their proliferation and mobilization in response to the exposure of freshwater communities to selective TMP concentrations may promote the prevalence of high-level TMP resistance and thus limit the future effectiveness of antimicrobial therapies.
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Affiliation(s)
- David Kneis
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany.
| | - Claudèle Lemay-St-Denis
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Stella Cellier-Goetghebeur
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
| | - Alan X Elena
- TU Dresden, Institute of Hydrobiology, 01062, Dresden, Germany
| | | | - Joelle N Pelletier
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Quebec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
- Department of Biochemistry & Molecular Medicine, University of Montréal, Montréal, QC, H3T 1J4, Canada
- Chemistry Department, University of Montréal, Montréal, QC, H2V 0B3, Canada
| | - Stefanie Heß
- TU Dresden, Institute of Microbiology, 01062, Dresden, Germany
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12
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Stanaway IB, Wallace JC, Hong S, Wilder CS, Green FH, Tsai J, Knight M, Workman T, Vigoren EM, Smith MN, Griffith WC, Thompson B, Shojaie A, Faustman EM. Alteration of oral microbiome composition in children living with pesticide-exposed farm workers. Int J Hyg Environ Health 2023; 248:114090. [PMID: 36516690 PMCID: PMC9898171 DOI: 10.1016/j.ijheh.2022.114090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/30/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Our prior work shows that azinphos-methyl pesticide exposure is associated with altered oral microbiomes in exposed farmworkers. Here we extend this analysis to show the same association pattern is also evident in their children. Oral buccal swab samples were analyzed at two time points, the apple thinning season in spring-summer 2005 for 78 children and 101 adults and the non-spray season in winter 2006 for 62 children and 82 adults. The pesticide exposure for the children were defined by the farmworker occupation of the cohabitating household adult and the blood azinphos-methyl detection of the cohabitating adult. Oral buccal swab 16S rRNA sequencing determined taxonomic microbiota proportional composition from concurrent samples from both adults and children. Analysis of the identified bacteria showed significant proportional changes for 12 of 23 common oral microbiome genera in association with azinphos-methyl detection and farmworker occupation. The most common significantly altered genera had reductions in the abundance of Streptococcus, suggesting an anti-microbial effect of the pesticide. Principal component analysis of the microbiome identified two primary clusters, with association of principal component 1 to azinphos-methyl blood detection and farmworker occupational status of the household. The children's buccal microbiota composition clustered with their household adult in ∼95% of the households. Household adult farmworker occupation and household pesticide exposure is associated with significant alterations in their children's oral microbiome composition. This suggests that parental occupational exposure and pesticide take-home exposure pathways elicit alteration of their children's microbiomes.
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Affiliation(s)
- Ian B Stanaway
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - James C Wallace
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Sungwoo Hong
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Carly S Wilder
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Foad H Green
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Jesse Tsai
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Misty Knight
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Tomomi Workman
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Eric M Vigoren
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Marissa N Smith
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - William C Griffith
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA
| | - Beti Thompson
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ali Shojaie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Elaine M Faustman
- Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA.
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13
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Ullmann T, Peschel S, Finger P, Müller CL, Boulesteix AL. Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering. PLoS Comput Biol 2023; 19:e1010820. [PMID: 36608142 PMCID: PMC9873197 DOI: 10.1371/journal.pcbi.1010820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/24/2023] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
In recent years, unsupervised analysis of microbiome data, such as microbial network analysis and clustering, has increased in popularity. Many new statistical and computational methods have been proposed for these tasks. This multiplicity of analysis strategies poses a challenge for researchers, who are often unsure which method(s) to use and might be tempted to try different methods on their dataset to look for the "best" ones. However, if only the best results are selectively reported, this may cause over-optimism: the "best" method is overly fitted to the specific dataset, and the results might be non-replicable on validation data. Such effects will ultimately hinder research progress. Yet so far, these topics have been given little attention in the context of unsupervised microbiome analysis. In our illustrative study, we aim to quantify over-optimism effects in this context. We model the approach of a hypothetical microbiome researcher who undertakes four unsupervised research tasks: clustering of bacterial genera, hub detection in microbial networks, differential microbial network analysis, and clustering of samples. While these tasks are unsupervised, the researcher might still have certain expectations as to what constitutes interesting results. We translate these expectations into concrete evaluation criteria that the hypothetical researcher might want to optimize. We then randomly split an exemplary dataset from the American Gut Project into discovery and validation sets multiple times. For each research task, multiple method combinations (e.g., methods for data normalization, network generation, and/or clustering) are tried on the discovery data, and the combination that yields the best result according to the evaluation criterion is chosen. While the hypothetical researcher might only report this result, we also apply the "best" method combination to the validation dataset. The results are then compared between discovery and validation data. In all four research tasks, there are notable over-optimism effects; the results on the validation data set are worse compared to the discovery data, averaged over multiple random splits into discovery/validation data. Our study thus highlights the importance of validation and replication in microbiome analysis to obtain reliable results and demonstrates that the issue of over-optimism goes beyond the context of statistical testing and fishing for significance.
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Affiliation(s)
- Theresa Ullmann
- Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-Universität München, München, Germany
- Munich Center for Machine Learning (MCML), München, Germany
- * E-mail:
| | - Stefanie Peschel
- Institute for Asthma and Allergy Prevention, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig-Maximilians-Universität München, München, Germany
| | - Philipp Finger
- Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Christian L. Müller
- Department of Statistics, Ludwig-Maximilians-Universität München, München, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Center for Computational Mathematics, Flatiron Institute, New York, New York, United States of America
| | - Anne-Laure Boulesteix
- Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-Universität München, München, Germany
- Munich Center for Machine Learning (MCML), München, Germany
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14
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Schreiber L, Fortin N, Mazza A, Maynard C, Wasserscheid J, Tremblay J, Lee K, Greer CW. An experimental oil spill at a tidal freshwater wetland along the St. Lawrence River re-visited after 21 years. ENVIRONMENTAL RESEARCH 2023; 216:114456. [PMID: 36181891 DOI: 10.1016/j.envres.2022.114456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
In 1999, a tidal wetland located along the St. Lawrence River close to Ste. Croix de Lotbinière (Quebec, Eastern Canada) was the site of an experimental oil spill. Test plots were established and subjected to an experimental crude oil spill to evaluate natural attenuation, nutrient amendment and vegetation cropping as countermeasures. In 2020, this study re-visited the test plots to investigate residual oil and habitat recovery. Only concentrations of mid-chain length n-alkanes (C10-C36), but not of polycyclic aromatic hydrocarbons (PAHs), were significantly above detection limit, and were detected in both test plot and control sediments. Hydrocarbon, total organic carbon, nitrogen and phosphate contents did not differ significantly between test plot and control sediments. Microbial analyses did not detect significant differences in microbial load, microbial diversity or microbial community composition between test plot and control sediments. Key genes for the aerobic and anaerobic degradation of n-alkanes as well as for the aerobic degradation of PAHs were detected in all sediment samples. Associated gene abundances did not differ significantly between test plot and control sediments. This study shows that oil-exposed test plot sediments of the Ste. Croix wetland can be considered completely recovered after 21 years irrespective of the performed countermeasure.
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Affiliation(s)
- Lars Schreiber
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada.
| | - Nathalie Fortin
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Alberto Mazza
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Christine Maynard
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Jessica Wasserscheid
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON, K1A 0E6, Canada
| | - Charles W Greer
- Energy, Mining and Environment Research Center, National Research Council Canada, 6100 Royalmount Ave, Montreal, QC, H4P 2R2, Canada; Department of Natural Resource Sciences, McGill University, 21111 Lakeshore Rd, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
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15
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Piro VC, Renard BY. Contamination detection and microbiome exploration with GRIMER. Gigascience 2022; 12:giad017. [PMID: 36994872 PMCID: PMC10061425 DOI: 10.1093/gigascience/giad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/06/2023] [Accepted: 03/01/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Contamination detection is a important step that should be carefully considered in early stages when designing and performing microbiome studies to avoid biased outcomes. Detecting and removing true contaminants is challenging, especially in low-biomass samples or in studies lacking proper controls. Interactive visualizations and analysis platforms are crucial to better guide this step, to help to identify and detect noisy patterns that could potentially be contamination. Additionally, external evidence, like aggregation of several contamination detection methods and the use of common contaminants reported in the literature, could help to discover and mitigate contamination. RESULTS We propose GRIMER, a tool that performs automated analyses and generates a portable and interactive dashboard integrating annotation, taxonomy, and metadata. It unifies several sources of evidence to help detect contamination. GRIMER is independent of quantification methods and directly analyzes contingency tables to create an interactive and offline report. Reports can be created in seconds and are accessible for nonspecialists, providing an intuitive set of charts to explore data distribution among observations and samples and its connections with external sources. Further, we compiled and used an extensive list of possible external contaminant taxa and common contaminants with 210 genera and 627 species reported in 22 published articles. CONCLUSION GRIMER enables visual data exploration and analysis, supporting contamination detection in microbiome studies. The tool and data presented are open source and available at https://gitlab.com/dacs-hpi/grimer.
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Affiliation(s)
- Vitor C Piro
- Data Analytics and Computational Statistics, Hasso Plattner Insititute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
| | - Bernhard Y Renard
- Data Analytics and Computational Statistics, Hasso Plattner Insititute, Digital Engineering Faculty, University of Potsdam, Potsdam 14482, Germany
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16
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Lanciano T, Savino A, Porcu F, Cittaro D, Bonchi F, Provero P. Contrast subgraphs allow comparing homogeneous and heterogeneous networks derived from omics data. Gigascience 2022; 12:giad010. [PMID: 36852877 PMCID: PMC9972522 DOI: 10.1093/gigascience/giad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/30/2022] [Accepted: 02/08/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Biological networks are often used to describe the relationships between relevant entities, particularly genes and proteins, and are a powerful tool for functional genomics. Many important biological problems can be investigated by comparing biological networks between different conditions or networks obtained with different techniques. FINDINGS We show that contrast subgraphs, a recently introduced technique to identify the most important structural differences between 2 networks, provide a versatile tool for comparing gene and protein networks of diverse origin. We demonstrate the use of contrast subgraphs in the comparison of coexpression networks derived from different subtypes of breast cancer, coexpression networks derived from transcriptomic and proteomic data, and protein-protein interaction networks assayed in different cell lines. CONCLUSIONS These examples demonstrate how contrast subgraphs can provide new insight in functional genomics by extracting the gene/protein modules whose connectivity is most altered between 2 conditions or experimental techniques.
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Affiliation(s)
| | - Aurora Savino
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Turin 10126, Italy
| | | | - Davide Cittaro
- Center for Omics Sciences, San Raffaele Scientific Institute IRCSS, Milan 20132, Italy
| | | | - Paolo Provero
- Center for Omics Sciences, San Raffaele Scientific Institute IRCSS, Milan 20132, Italy
- Department of Neurosciences “Rita Levi Montalcini,” University of Turin, Turin 10126, Italy
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17
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Acharjee A, Singh U, Choudhury SP, Gkoutos GV. The diagnostic potential and barriers of microbiome based therapeutics. Diagnosis (Berl) 2022; 9:411-420. [PMID: 36000189 DOI: 10.1515/dx-2022-0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/03/2022] [Indexed: 02/07/2023]
Abstract
High throughput technological innovations in the past decade have accelerated research into the trillions of commensal microbes in the gut. The 'omics' technologies used for microbiome analysis are constantly evolving, and large-scale datasets are being produced. Despite of the fact that much of the research is still in its early stages, specific microbial signatures have been associated with the promotion of cancer, as well as other diseases such as inflammatory bowel disease, neurogenerative diareses etc. It has been also reported that the diversity of the gut microbiome influences the safety and efficacy of medicines. The availability and declining sequencing costs has rendered the employment of RNA-based diagnostics more common in the microbiome field necessitating improved data-analytical techniques so as to fully exploit all the resulting rich biological datasets, while accounting for their unique characteristics, such as their compositional nature as well their heterogeneity and sparsity. As a result, the gut microbiome is increasingly being demonstrating as an important component of personalised medicine since it not only plays a role in inter-individual variability in health and disease, but it also represents a potentially modifiable entity or feature that may be addressed by treatments in a personalised way. In this context, machine learning and artificial intelligence-based methods may be able to unveil new insights into biomedical analyses through the generation of models that may be used to predict category labels, and continuous values. Furthermore, diagnostic aspects will add value in the identification of the non invasive markers in the critical diseases like cancer.
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Affiliation(s)
- Animesh Acharjee
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.,Institute of Translational Medicine, University of Birmingham, Birmingham, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham, Birmingham, UK.,MRC Health Data Research UK (HDR UK), Birmingham, UK
| | - Utpreksha Singh
- Department of Health and Life Sciences, Coventry University, Coventry, UK
| | | | - Georgios V Gkoutos
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.,Institute of Translational Medicine, University of Birmingham, Birmingham, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham, Birmingham, UK.,MRC Health Data Research UK (HDR UK), Birmingham, UK.,NIHR Experimental Cancer Medicine Centre, Birmingham, UK
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18
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He J, Shen X, Zhang N, Sun C, Shao Y. Smartphones as an Ecological Niche of Microorganisms: Microbial Activities, Assembly, and Opportunistic Pathogens. Microbiol Spectr 2022; 10:e0150822. [PMID: 36040152 PMCID: PMC9603676 DOI: 10.1128/spectrum.01508-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/11/2022] [Indexed: 12/31/2022] Open
Abstract
Smartphone usage and contact frequency are unprecedentedly high in this era, and they affect humans mentally and physically. However, the characteristics of the microorganisms associated with smartphones and smartphone hygiene habits remain unclear. In this study, using various culture-independent techniques, including high-throughput sequencing, real-time quantitative PCR (RT-qPCR), the ATP bioluminescence system, and electron microscopy, we investigated the structure, assembly, quantity, and dynamic metabolic activity of the bacterial community on smartphone surfaces and the user's dominant and nondominant hands. We found that smartphone microbiotas are more similar to the nondominant hand microbiotas than the dominant hand microbiotas and show significantly decreased phylogenetic diversity and stronger deterministic processes than the hand microbiota. Significant interindividual microbiota differences were observed, contributing to an average owner identification accuracy of 70.6% using smartphone microbiota. Furthermore, it is estimated that approximately 1.75 × 106 bacteria (2.24 × 104/cm2) exist on the touchscreen of a single smartphone, and microbial activities remain stable for at least 48 h. Scanning electron microscopy detected large fragments harboring microorganisms, suggesting that smartphone microbiotas live on the secreta or other substances, e.g., human cell debris and food debris. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. Taken together, our results demonstrate that smartphone surfaces not only are a reservoir of microbes but also provide an ecological niche in which microbiotas, particularly opportunistic pathogens, can survive, be active, and even grow. IMPORTANCE Currently, people spend an average of 4.2 h per day on their smartphones. Due to the COVID-19 pandemic, this figure may still be increasing. The high frequency of smartphone usage may allow microbes, particularly pathogens, to attach to-and even survive on-phone surfaces, potentially causing adverse effects on humans. We employed various culture-independent techniques in this study to evaluate the microbiological features and hygiene of smartphones, including community assembly, bacterial load, and activity. Our data showed that deterministic processes drive smartphone microbiota assembly and that approximately 1.75 × 106 bacteria exist on a single smartphone touchscreen, with activities being stable for at least 48 h. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. This work expands our understanding of the microbial ecology of smartphone surfaces and might facilitate the development of electronic device cleaning/hygiene guidelines to support public health.
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Affiliation(s)
- Jintao He
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoqiang Shen
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Nan Zhang
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Yongqi Shao
- Max Planck Partner Group, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory for Molecular Animal Nutrition, Ministry of Education, Beijing, China
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19
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Lam TJ, Ye Y. Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes. Sci Rep 2022; 12:17482. [PMID: 36261472 PMCID: PMC9581956 DOI: 10.1038/s41598-022-22541-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/17/2022] [Indexed: 01/12/2023] Open
Abstract
The human gut microbiome is composed of a diverse and dynamic population of microbial species which play key roles in modulating host health and physiology. While individual microbial species have been found to be associated with certain disease states, increasing evidence suggests that higher-order microbial interactions may have an equal or greater contribution to host fitness. To better understand microbial community dynamics, we utilize networks to study interactions through a meta-analysis of microbial association networks between healthy and disease gut microbiomes. Taking advantage of the large number of metagenomes derived from healthy individuals and patients with various diseases, together with recent advances in network inference that can deal with sparse compositional data, we inferred microbial association networks based on co-occurrence of gut microbial species and made the networks publicly available as a resource (GitHub repository named GutNet). Through our meta-analysis of inferred networks, we were able to identify network-associated features that help stratify between healthy and disease states such as the differentiation of various bacterial phyla and enrichment of Proteobacteria interactions in diseased networks. Additionally, our findings show that the contributions of taxa in microbial associations are disproportionate to their abundances and that rarer taxa of microbial species play an integral part in shaping dynamics of microbial community interactions. Network-based meta-analysis revealed valuable insights into microbial community dynamics between healthy and disease phenotypes. We anticipate that the healthy and diseased microbiome association networks we inferred will become an important resource for human-related microbiome research.
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Affiliation(s)
- Tony J Lam
- Luddy School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47408, USA
| | - Yuzhen Ye
- Luddy School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47408, USA.
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20
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Espinoza JL, Torralba M, Leong P, Saffery R, Bockmann M, Kuelbs C, Singh S, Hughes T, Craig JM, Nelson KE, Dupont CL. Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries. PNAS NEXUS 2022; 1:pgac239. [PMID: 36712365 PMCID: PMC9802336 DOI: 10.1093/pnasnexus/pgac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022]
Abstract
Dental caries is a microbial disease and the most common chronic health condition, affecting nearly 3.5 billion people worldwide. In this study, we used a multiomics approach to characterize the supragingival plaque microbiome of 91 Australian children, generating 658 bacterial and 189 viral metagenome-assembled genomes with transcriptional profiling and gene-expression network analysis. We developed a reproducible pipeline for clustering sample-specific genomes to integrate metagenomics and metatranscriptomics analyses regardless of biosample overlap. We introduce novel feature engineering and compositionally-aware ensemble network frameworks while demonstrating their utility for investigating regime shifts associated with caries dysbiosis. These methods can be applied when differential abundance modeling does not capture statistical enrichments or the results from such analysis are not adequate for providing deeper insight into disease. We identified which organisms and metabolic pathways were central in a coexpression network as well as how these networks were rewired between caries and caries-free phenotypes. Our findings provide evidence of a core bacterial microbiome that was transcriptionally active in the supragingival plaque of all participants regardless of phenotype, but also show highly diagnostic changes in the ways that organisms interact. Specifically, many organisms exhibit high connectedness with central carbon metabolism to Cardiobacterium and this shift serves a bridge between phenotypes. Our evidence supports the hypothesis that caries is a multifactorial ecological disease.
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Affiliation(s)
- Josh L Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Manolito Torralba
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Pamela Leong
- Epigenetics, Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Richard Saffery
- Epigenetics, Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Michelle Bockmann
- Adelaide Dental School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Claire Kuelbs
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Suren Singh
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Toby Hughes
- Adelaide Dental School, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jeffrey M Craig
- Epigenetics, Murdoch Children's Research Institute and Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia,IMPACT Strategic Research Centre, Deakin University School of Medicine, Geelong, VIC 3220, Australia
| | - Karen E Nelson
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, Rockville, MD 20850, USA
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21
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Espinoza JL, Dupont CL. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. BMC Bioinformatics 2022; 23:419. [PMID: 36224545 PMCID: PMC9554839 DOI: 10.1186/s12859-022-04973-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth's natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ, however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes. RESULTS In this study, we introduce the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge, VEBA is the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes. VEBA implements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone. VEBA includes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification. VEBA also provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally, VEBA is the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genome quality assessments. VEBA's capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives. CONCLUSIONS The VEBA software suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways. VEBA fully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions of VEBA to the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks. VEBA allows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.
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Affiliation(s)
- Josh L. Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037 USA
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037 USA
| | - Chris L. Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037 USA
- Department of Human Biology and Genomic Medicine, J. Craig Venter Institute, La Jolla, CA 92037 USA
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22
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Wang C, Yang Y, Wang Y, Wang D, Xu X, Wang Y, Li L, Yang C, Zhang T. Absolute quantification and genome-centric analyses elucidate the dynamics of microbial populations in anaerobic digesters. WATER RESEARCH 2022; 224:119049. [PMID: 36108398 DOI: 10.1016/j.watres.2022.119049] [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: 06/12/2022] [Revised: 08/25/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic digestion (AD) relies on myriads of functions performed by complex microbial communities in customized settings, thus, a comprehensive investigation on the AD microbiome is central to the fine-tuned control. Most current AD microbiome studies are based on relative abundance, which hinders the interpretation of microbes' dynamics and inter-sample comparisons. Here, we developed an absolute quantification (AQ) approach that integrated cellular spike-ins with metagenomic sequencing to elucidate microbial community variations and population dynamics in four anaerobic digesters. Using this method, 253 microbes were defined as decaying populations with decay rates ranging from -0.05 to -5.85 d-1, wherein, a population from Flavobacteriaceae family decayed at the highest rates of -3.87 to -5.85 d-1 in four digesters. Meanwhile, 25 microbes demonstrated the growing trend in the AD processes with growth rates ranging from 0.11 to 1.77 d-1, and genome-centric analysis assigned some of the populations to the functional niches of hydrolysis, short-chain fatty acids metabolism, and methane generation. Additionally, we observed that the specific activity of methanogens was lower in the prolonged digestion stage, and redundancy analysis revealed that the feedstock composition and the digestion duration were the two key parameters in governing the AD microbial compositions.
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Affiliation(s)
- Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China.
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23
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Watson ER, Mora A, Taherian Fard A, Mar JC. How does the structure of data impact cell-cell similarity? Evaluating how structural properties influence the performance of proximity metrics in single cell RNA-seq data. Brief Bioinform 2022; 23:6712300. [PMID: 36151725 PMCID: PMC9677483 DOI: 10.1093/bib/bbac387] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/26/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022] Open
Abstract
Accurately identifying cell-populations is paramount to the quality of downstream analyses and overall interpretations of single-cell RNA-seq (scRNA-seq) datasets but remains a challenge. The quality of single-cell clustering depends on the proximity metric used to generate cell-to-cell distances. Accordingly, proximity metrics have been benchmarked for scRNA-seq clustering, typically with results averaged across datasets to identify a highest performing metric. However, the 'best-performing' metric varies between studies, with the performance differing significantly between datasets. This suggests that the unique structural properties of an scRNA-seq dataset, specific to the biological system under study, have a substantial impact on proximity metric performance. Previous benchmarking studies have omitted to factor the structural properties into their evaluations. To address this gap, we developed a framework for the in-depth evaluation of the performance of 17 proximity metrics with respect to core structural properties of scRNA-seq data, including sparsity, dimensionality, cell-population distribution and rarity. We find that clustering performance can be improved substantially by the selection of an appropriate proximity metric and neighbourhood size for the structural properties of a dataset, in addition to performing suitable pre-processing and dimensionality reduction. Furthermore, popular metrics such as Euclidean and Manhattan distance performed poorly in comparison to several lessor applied metrics, suggesting that the default metric for many scRNA-seq methods should be re-evaluated. Our findings highlight the critical nature of tailoring scRNA-seq analyses pipelines to the dataset under study and provide practical guidance for researchers looking to optimize cell-similarity search for the structural properties of their own data.
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Affiliation(s)
- Ebony Rose Watson
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Ariane Mora
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Atefeh Taherian Fard
- Corresponding authors. Jessica Cara Mar, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia. Tel.: +614 90 733 703; E-mail: ; Atefeh Taherian Fard, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia. Tel.: +61 7 3346 3894; E-mail:
| | - Jessica Cara Mar
- Corresponding authors. Jessica Cara Mar, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia. Tel.: +614 90 733 703; E-mail: ; Atefeh Taherian Fard, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia. Tel.: +61 7 3346 3894; E-mail:
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24
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Boix-Amorós A, Monaco H, Sambataro E, Clemente JC. Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease. Gut Microbes 2022; 14:2107866. [PMID: 36104776 PMCID: PMC9481095 DOI: 10.1080/19490976.2022.2107866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We present an overview of recent experimental and computational advances in technology used to characterize the microbiome, with a focus on how these developments improve our understanding of inflammatory bowel disease (IBD). Specifically, we present studies that make use of flow cytometry and metabolomics assays to provide a functional characterization of microbial communities. We also describe computational methods for strain-level resolution, temporal series, mycobiome and virome data, co-occurrence networks, and compositional data analysis. In addition, we review novel techniques to therapeutically manipulate the microbiome in IBD. We discuss the benefits and drawbacks of these technologies to increase awareness of specific biases, and to facilitate a more rigorous interpretation of results and their potential clinical application. Finally, we present future lines of research to better characterize the relation between microbial communities and IBD pathogenesis and progression.
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Affiliation(s)
- Alba Boix-Amorós
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Hilary Monaco
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA
| | - Elisa Sambataro
- Department of Biological Sciences, CUNY Hunter College, New York, NY, USA
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY, USA,CONTACT Jose C. Clemente Department of Genetics and Genomic Sciences, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai. New York, NY10029USA
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25
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Boyraz A, Pawlowsky-Glahn V, Egozcue JJ, Acar AC. Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data. Brief Bioinform 2022; 23:6675749. [PMID: 36007229 DOI: 10.1093/bib/bbac328] [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: 02/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Statistical and machine learning techniques based on relative abundances have been used to predict health conditions and to identify microbial biomarkers. However, high dimensionality, sparsity and the compositional nature of microbiome data represent statistical challenges. On the other hand, the taxon grouping allows summarizing microbiome abundance with a coarser resolution in a lower dimension, but it presents new challenges when correlating taxa with a disease. In this work, we present a novel approach that groups Operational Taxonomical Units (OTUs) based only on relative abundances as an alternative to taxon grouping. The proposed procedure acknowledges the compositional data making use of principal balances. The identified groups are called Principal Microbial Groups (PMGs). The procedure reduces the need for user-defined aggregation of $\textrm{OTU}$s and offers the possibility of working with coarse group of $\textrm{OTU}$s, which are not present in a phylogenetic tree. PMGs can be used for two different goals: (1) as a dimensionality reduction method for compositional data, (2) as an aggregation procedure that provides an alternative to taxon grouping for construction of microbial balances afterward used for disease prediction. We illustrate the procedure with a cirrhosis study data. PMGs provide a coherent data analysis for the search of biomarkers in human microbiota. The source code and demo data for PMGs are available at: https://github.com/asliboyraz/PMGs.
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Affiliation(s)
- Aslı Boyraz
- Department of Computer Programming, Recep Tayyip Erdoğan University, Ardeşen Vocational School, Rize, 53400, Turkey
| | - Vera Pawlowsky-Glahn
- Department of Computer Sciences, Applied Mathematics and Statistics, University of Girona, Campus Montilivi, 17003 Girona, Spain
| | - Juan José Egozcue
- Department of Civil and Environmental Engineering, Universitat Politécnica de Catalunya, Barcelona, 08034, Spain
| | - Aybar Can Acar
- Department of Medical Informatics, Middle East Technical University, Ankara Turkey
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26
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Lin H, Eggesbø M, Peddada SD. Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data. Nat Commun 2022; 13:4946. [PMID: 35999204 PMCID: PMC9399263 DOI: 10.1038/s41467-022-32243-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
It is well-known that human gut microbiota form an ecosystem where microbes interact with each other. Due to complex underlying interactions, some microbes may correlate nonlinearly. There are no measures in the microbiome literature we know of that quantify these nonlinear relationships. Here, we develop a methodology called Sparse Estimation of Correlations among Microbiomes (SECOM) for estimating linear and nonlinear relationships among microbes while maintaining the sparsity. SECOM accounts for both sample and taxon-specific biases in its model. Its statistical properties are evaluated analytically and by comprehensive simulation studies. We test SECOM in two real data sets, namely, forehead and palm microbiome data from college-age adults, and Norwegian infant gut microbiome data. Given that forehead and palm are related to skin, as desired, SECOM discovers each genus to be highly correlated between the two sites, but that is not the case with any of the competing methods. It is well-known that infant gut evolves as the child grows. Using SECOM, for the first time in the literature, we characterize temporal changes in correlations among bacterial families during a baby's first year after birth.
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Affiliation(s)
- Huang Lin
- Biostatistics and Bioinformatics Branch, Eunice Shriver Kennedy NICHD, NIH, Bethesda, MD, USA
| | | | - Shyamal Das Peddada
- Biostatistics and Bioinformatics Branch, Eunice Shriver Kennedy NICHD, NIH, Bethesda, MD, USA.
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27
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Perrone MR, Romano S, De Maria G, Tundo P, Bruno AR, Tagliaferro L, Maffia M, Fragola M. Compositional Data Analysis of 16S rRNA Gene Sequencing Results from Hospital Airborne Microbiome Samples. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10107. [PMID: 36011742 PMCID: PMC9408509 DOI: 10.3390/ijerph191610107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 06/15/2023]
Abstract
The compositional analysis of 16S rRNA gene sequencing datasets is applied to characterize the bacterial structure of airborne samples collected in different locations of a hospital infection disease department hosting COVID-19 patients, as well as to investigate the relationships among bacterial taxa at the genus and species level. The exploration of the centered log-ratio transformed data by the principal component analysis via the singular value decomposition has shown that the collected samples segregated with an observable separation depending on the monitoring location. More specifically, two main sample clusters were identified with regards to bacterial genera (species), consisting of samples mostly collected in rooms with and without COVID-19 patients, respectively. Human pathogenic genera (species) associated with nosocomial infections were mostly found in samples from areas hosting patients, while non-pathogenic genera (species) mainly isolated from soil were detected in the other samples. Propionibacterium acnes, Staphylococcus pettenkoferi, Corynebacterium tuberculostearicum, and jeikeium were the main pathogenic species detected in COVID-19 patients' rooms. Samples from these locations were on average characterized by smaller richness/evenness and diversity than the other ones, both at the genus and species level. Finally, the ρ metrics revealed that pairwise positive associations occurred either between pathogenic or non-pathogenic taxa.
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Affiliation(s)
- Maria Rita Perrone
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Salvatore Romano
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
| | - Giuseppe De Maria
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Italy
| | - Paolo Tundo
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Italy
| | - Anna Rita Bruno
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Italy
| | - Luigi Tagliaferro
- Presidio Ospedaliero Santa Caterina Novella, Azienda Sanitaria Locale Lecce, 73013 Galatina, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Mattia Fragola
- Department of Mathematics and Physics, University of Salento, 73100 Lecce, Italy
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28
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Gaio D, DeMaere MZ, Anantanawat K, Eamens GJ, Falconer L, Chapman TA, Djordjevic S, Darling AE. Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig. PLoS One 2022; 17:e0270372. [PMID: 35749534 PMCID: PMC9232140 DOI: 10.1371/journal.pone.0270372] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.
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Affiliation(s)
- Daniela Gaio
- iThree Institute, University of Technology Sydney, Ultimo, Australia
- * E-mail:
| | | | - Kay Anantanawat
- iThree Institute, University of Technology Sydney, Ultimo, Australia
| | - Graeme J. Eamens
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Linda Falconer
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Toni A. Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Steven Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, Australia
| | - Aaron E. Darling
- iThree Institute, University of Technology Sydney, Ultimo, Australia
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29
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Møller TE, Le Moine Bauer S, Hannisdal B, Zhao R, Baumberger T, Roerdink DL, Dupuis A, Thorseth IH, Pedersen RB, Jørgensen SL. Mapping Microbial Abundance and Prevalence to Changing Oxygen Concentration in Deep-Sea Sediments Using Machine Learning and Differential Abundance. Front Microbiol 2022; 13:804575. [PMID: 35663876 PMCID: PMC9158483 DOI: 10.3389/fmicb.2022.804575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/09/2022] [Indexed: 12/28/2022] Open
Abstract
Oxygen constitutes one of the strongest factors explaining microbial taxonomic variability in deep-sea sediments. However, deep-sea microbiome studies often lack the spatial resolution to study the oxygen gradient and transition zone beyond the oxic-anoxic dichotomy, thus leaving important questions regarding the microbial response to changing conditions unanswered. Here, we use machine learning and differential abundance analysis on 184 samples from 11 sediment cores retrieved along the Arctic Mid-Ocean Ridge to study how changing oxygen concentrations (1) are predicted by the relative abundance of higher taxa and (2) influence the distribution of individual Operational Taxonomic Units. We find that some of the most abundant classes of microorganisms can be used to classify samples according to oxygen concentration. At the level of Operational Taxonomic Units, however, representatives of common classes are not differentially abundant from high-oxic to low-oxic conditions. This weakened response to changing oxygen concentration suggests that the abundance and prevalence of highly abundant OTUs may be better explained by other variables than oxygen. Our results suggest that a relatively homogeneous microbiome is recruited to the benthos, and that the microbiome then becomes more heterogeneous as oxygen drops below 25 μM. Our analytical approach takes into account the oft-ignored compositional nature of relative abundance data, and provides a framework for extracting biologically meaningful associations from datasets spanning multiple sedimentary cores.
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Affiliation(s)
- Tor Einar Møller
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Sven Le Moine Bauer
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Bjarte Hannisdal
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - Rui Zhao
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tamara Baumberger
- Cooperative Institute for Marine Ecosystem and Resources Studies, Oregon State University, Newport, OR, United States
| | - Desiree L Roerdink
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | | | - Ingunn H Thorseth
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Rolf Birger Pedersen
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Steffen Leth Jørgensen
- Department of Earth Science, University of Bergen, Bergen, Norway.,Centre for Deep Sea Research, University of Bergen, Bergen, Norway
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30
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Guseva K, Darcy S, Simon E, Alteio LV, Montesinos-Navarro A, Kaiser C. From diversity to complexity: Microbial networks in soils. SOIL BIOLOGY & BIOCHEMISTRY 2022; 169:108604. [PMID: 35712047 PMCID: PMC9125165 DOI: 10.1016/j.soilbio.2022.108604] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 05/07/2023]
Abstract
Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research. Analysing microbial networks in soils opens a window to a better understanding of the complexity of microbial communities. However, this approach is unfortunately often used to draw conclusions which are far beyond the scientific evidence it can provide, which has damaged its reputation for soil microbial analysis. In this Perspectives Paper, we would like to sharpen the view for the real potential of microbial co-occurrence analysis in soils, and at the same time raise awareness regarding its limitations and the many ways how it can be misused or misinterpreted.
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Affiliation(s)
- Ksenia Guseva
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Corresponding author.
| | - Sean Darcy
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Eva Simon
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Lauren V. Alteio
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alicia Montesinos-Navarro
- Centro de Investigaciones sobre Desertificación (CIDE, CSIC-UV-GV), Carretera de Moncada-Náquera Km 4.5, 46113, Moncada, Valencia, Spain
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Corresponding author.
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31
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The Translational Landscape of SARS-CoV-2-infected Cells Reveals Suppression of Innate Immune Genes. mBio 2022; 13:e0081522. [PMID: 35604092 PMCID: PMC9239271 DOI: 10.1128/mbio.00815-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes a number of strategies to modulate viral and host mRNA translation. Here, we used ribosome profiling in SARS-CoV-2-infected model cell lines and primary airway cells grown at an air-liquid interface to gain a deeper understanding of the translationally regulated events in response to virus replication. We found that SARS-CoV-2 mRNAs dominate the cellular mRNA pool but are not more efficiently translated than cellular mRNAs. SARS-CoV-2 utilized a highly efficient ribosomal frameshifting strategy despite notable accumulation of ribosomes within the slippery sequence on the frameshifting element. In a highly permissive cell line model, although SARS-CoV-2 infection induced the transcriptional upregulation of numerous chemokine, cytokine, and interferon-stimulated genes, many of these mRNAs were not translated efficiently. The impact of SARS-CoV-2 on host mRNA translation was more subtle in primary cells, with marked transcriptional and translational upregulation of inflammatory and innate immune responses and downregulation of processes involved in ciliated cell function. Together, these data reveal the key role of mRNA translation in SARS-CoV-2 replication and highlight unique mechanisms for therapeutic development.
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Bakir-Gungor B, Hacılar H, Jabeer A, Nalbantoglu OU, Aran O, Yousef M. Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods. PeerJ 2022; 10:e13205. [PMID: 35497193 PMCID: PMC9048649 DOI: 10.7717/peerj.13205] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/10/2022] [Indexed: 01/12/2023] Open
Abstract
The tremendous boost in next generation sequencing and in the "omics" technologies makes it possible to characterize the human gut microbiome-the collective genomes of the microbial community that reside in our gastrointestinal tract. Although some of these microorganisms are considered to be essential regulators of our immune system, the alteration of the complexity and eubiotic state of microbiota might promote autoimmune and inflammatory disorders such as diabetes, rheumatoid arthritis, Inflammatory bowel diseases (IBD), obesity, and carcinogenesis. IBD, comprising Crohn's disease and ulcerative colitis, is a gut-related, multifactorial disease with an unknown etiology. IBD presents defects in the detection and control of the gut microbiota, associated with unbalanced immune reactions, genetic mutations that confer susceptibility to the disease, and complex environmental conditions such as westernized lifestyle. Although some existing studies attempt to unveil the composition and functional capacity of the gut microbiome in relation to IBD diseases, a comprehensive picture of the gut microbiome in IBD patients is far from being complete. Due to the complexity of metagenomic studies, the applications of the state-of-the-art machine learning techniques became popular to address a wide range of questions in the field of metagenomic data analysis. In this regard, using IBD associated metagenomics dataset, this study utilizes both supervised and unsupervised machine learning algorithms, (i) to generate a classification model that aids IBD diagnosis, (ii) to discover IBD-associated biomarkers, (iii) to discover subgroups of IBD patients using k-means and hierarchical clustering approaches. To deal with the high dimensionality of features, we applied robust feature selection algorithms such as Conditional Mutual Information Maximization (CMIM), Fast Correlation Based Filter (FCBF), min redundancy max relevance (mRMR), Select K Best (SKB), Information Gain (IG) and Extreme Gradient Boosting (XGBoost). In our experiments with 100-fold Monte Carlo cross-validation (MCCV), XGBoost, IG, and SKB methods showed a considerable effect in terms of minimizing the microbiota used for the diagnosis of IBD and thus reducing the cost and time. We observed that compared to Decision Tree, Support Vector Machine, Logitboost, Adaboost, and stacking ensemble classifiers, our Random Forest classifier resulted in better performance measures for the classification of IBD. Our findings revealed potential microbiome-mediated mechanisms of IBD and these findings might be useful for the development of microbiome-based diagnostics.
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Affiliation(s)
- Burcu Bakir-Gungor
- Department of Computer Engineering, Abdullah Gul University, Kayseri, Turkey
| | - Hilal Hacılar
- Department of Computer Engineering, Abdullah Gul University, Kayseri, Turkey
| | - Amhar Jabeer
- Department of Computer Engineering, Abdullah Gul University, Kayseri, Turkey
| | | | - Oya Aran
- TETAM, Bogazici University, Istanbul, Turkey
| | - Malik Yousef
- Zefat Academic College, Zefat, Israel,Galilee Digital Health Research Center, Zefat Academic College, Zefat, Israel
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Zhao R, Zhao F, Zheng S, Li X, Wang J, Xu K. Bacteria, Protists, and Fungi May Hold Clues of Seamount Impact on Diversity and Connectivity of Deep-Sea Pelagic Communities. Front Microbiol 2022; 13:773487. [PMID: 35464911 PMCID: PMC9024416 DOI: 10.3389/fmicb.2022.773487] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/22/2022] [Indexed: 12/22/2022] Open
Abstract
The topography and hydrography around seamounts have a strong influence on plankton biogeography. The intrinsic properties of various biological taxa inherently also shape their distribution. Therefore, it is hypothesized that different pelagic groups respond differently to effects of seamounts regarding their distribution and connectivity patterns. Herein, bacterial, protist, and fungal diversity was investigated across the water column around the Kocebu Guyot in the western Pacific Ocean. A higher connectivity was detected for bacteria than for protists and an extremely low connectivity for fungi, which might be attributed to parasitic and commensal interactions of many fungal taxa. The seamount enhanced the vertical connectivity of bacterial and protist communities, but significantly reduced protist connectivity along horizontal dimension. Such effects provide ecological opportunities for eukaryotic adaption and diversification. All the bacterial, protist, and fungal communities were more strongly affected by deterministic than stochastic processes. Drift appeared to have a more significant role in influencing the fungal community than other groups. Our study indicates the impact of seamounts on the pelagic community distribution and connectivity and highlights the mechanism of horizontally restricted dispersal combined with vertical mixing, which promotes the diversification of eukaryotic life.
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Affiliation(s)
- Rongjie Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Shan Zheng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xuegang Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jianing Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Attia S, Russel J, Mortensen MS, Madsen JS, Sørensen SJ. Unexpected diversity among small-scale sample replicates of defined plant root compartments. THE ISME JOURNAL 2022; 16:997-1003. [PMID: 34759302 PMCID: PMC8940884 DOI: 10.1038/s41396-021-01094-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/08/2021] [Accepted: 08/13/2021] [Indexed: 12/19/2022]
Abstract
Community assembly processes determine patterns of species distribution and abundance which are central to the ecology of microbiomes. When studying plant root microbiome assembly, it is typical to sample at the whole plant root system scale. However, sampling at these relatively large spatial scales may hinder the observability of intermediate processes. To study the relative importance of these processes, we employed millimetre-scale sampling of the cell elongation zone of individual roots. Both the rhizosphere and rhizoplane microbiomes were examined in fibrous and taproot model systems, represented by wheat and faba bean, respectively. Like others, we found that the plant root microbiome assembly is mainly driven by plant selection. However, based on variability between replicate millimetre-scale samples and comparisons with randomized null models, we infer that either priority effects during early root colonization or variable selection among replicate plant roots also determines root microbiome assembly.
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Affiliation(s)
- Sally Attia
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark ,grid.31451.320000 0001 2158 2757Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Jakob Russel
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin S. Mortensen
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark ,grid.10306.340000 0004 0606 5382Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Jonas S. Madsen
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J. Sørensen
- grid.5254.60000 0001 0674 042XSection of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Revitalization of Total Petroleum Hydrocarbon Contaminated Soil Remediated by Landfarming. TOXICS 2022; 10:toxics10030147. [PMID: 35324772 PMCID: PMC8951262 DOI: 10.3390/toxics10030147] [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: 02/17/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023]
Abstract
Soil health deteriorates through the contamination and remediation processes, resulting in the limitation of the reuse and recycling of the remediated soils. Therefore, soil health should be recovered for the intended purposes of reuse and recycling. This study aimed to evaluate the applicability and effectiveness of several amendments to revitalize total petroleum hydrocarbon contaminated soils remediated by the landfarming process. Ten inorganic, organic, and biological amendments were investigated for their dosage and duration, and nine physicochemical, four fertility, and seven microbial (soil enzyme activity) factors were compared before and after the treatment of amendments. Finally, the extent of recovery was quantitatively estimated, and the significance of results was confirmed with statistical methods, such as simple regression and correlation analyses assisted by principal component analysis. The landfarming process is considered a somewhat environmentally friendly remediation technology to minimize the adverse effect on soil quality, but four soil properties—such as water holding capacity (WHC), exchangeable potassium (Ex. K), nitrate-nitrogen (NO3-N), available phosphorus (Av. P), and urease—were confirmed to deteriorate through the landfarming process. The WHC was better improved by organic agents, such as peat moss, biochar, and compost. Zeolite was evaluated as the most effective material for improving Ex. K content. The vermicompost showed the highest efficacy in recovering the NO3-N content of the remediated soil. Chlorella, vermicompost, and compost were investigated for their ability to enhance urease activity effectively. Although each additive showed different effectiveness according to different soil properties, their effect on overall soil properties should be considered for cost-effectiveness and practical implementation. Their overall effect was evaluated using statistical methods, and the results showed that compost, chlorella, and vermicompost were the most relevant amendments for rehabilitating the overall health of the remediated soil for the reuse and/or recycling of agricultural purposes. This study highlighted how to practically improve the health of remediated soils for the reuse and recycling of agricultural purposes.
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Boente C, Albuquerque MTD, Gallego JR, Pawlowsky-Glahn V, Egozcue JJ. Compositional baseline assessments to address soil pollution: An application in Langreo, Spain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152383. [PMID: 34952083 DOI: 10.1016/j.scitotenv.2021.152383] [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: 08/17/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Potentially Toxic Elements (PTEs) are contaminants with high toxicity and complex geochemical behaviour and, therefore, high PTEs contents in soil may affect ecosystems and/or human health. However, before addressing the measurement of soil pollution, it is necessary to understand what is meant by pollution-free soil. Often, this background, or pollution baseline, is undefined or only partially known. Since the concentration of chemical elements is compositional, as the attributes vary together, here we present a novel approach to build compositional indicators based on Compositional Data (CoDa) principles. The steps of this new methodology are: 1) Exploratory data analysis through variation matrix, biplots or CoDa dendrograms; 2) Selection of geological background in terms of a trimmed subsample that can be assumed as non-pollutant; 3) Computing the spread Aitchison distance from each sample point to the trimmed sample; 4) Performing a compositional balance able to predict the Aitchison distance computed in step 3.Identifying a compositional balance, including pollutant and non-pollutant elements, with sparsity and simplicity as properties, is crucial for the construction of a Compositional Pollution Indicator (CI). Here we explored a database of 150 soil samples and 37 chemical elements from the contaminated region of Langreo, Northwestern Spain. There were obtained three Cis: the first two using elements obtained through CoDa analysis, and the third one selecting a list of pollutants and non-pollutants based on expert knowledge and previous studies. The three indicators went through a Stochastic Sequential Gaussian simulation. The results of the 100 computed simulations are summarized through mean image maps and probability maps of exceeding a given threshold, thus allowing characterization of the spatial distribution and variability of the CIs. A better understanding of the trends of relative enrichment and PTEs fate is discussed.
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Affiliation(s)
- C Boente
- Department of Mining, Mechanic, Energetic and Construction Engineering, ETSI, University of Huelva, 21071 Huelva, Spain; CIQSO-Center for Research in Sustainable Chemistry, Associate Unit CSIC-University of Huelva, Atmospheric Pollution, Campus El Carmen s/n, 21071 Huelva, Spain.
| | - M T D Albuquerque
- CERNAS | QRural, Instituto Politécnico de Castelo Branco and ICT, Universidade de Évora, Portugal.
| | - J R Gallego
- Environmental Biogeochemistry & Raw Materials Group and INDUROT, Campus de Mieres, University of Oviedo, C/Gonzalo Gutiérrez Quirós, S/N, 33600 Mieres, Spain.
| | - V Pawlowsky-Glahn
- Dpt. Computer Science, Applied Mathematics and Statistics, University of Girona, Spain.
| | - J J Egozcue
- Dpt. Civil and Environmental Engineering, Technical University of Catalonia, Barcelona, Spain.
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López-García A, Saborío-Montero A, Gutiérrez-Rivas M, Atxaerandio R, Goiri I, García-Rodríguez A, Jiménez-Montero JA, González C, Tamames J, Puente-Sánchez F, Serrano M, Carrasco R, Óvilo C, González-Recio O. Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle. Gigascience 2022; 11:6514927. [PMID: 35077540 PMCID: PMC8848325 DOI: 10.1093/gigascience/giab088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/18/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Background Mitigating the effects of global warming has become the main challenge for humanity in recent decades. Livestock farming contributes to greenhouse gas emissions, with an important output of methane from enteric fermentation processes, mostly in ruminants. Because ruminal microbiota is directly involved in digestive fermentation processes and methane biosynthesis, understanding the ecological relationships between rumen microorganisms and their active metabolic pathways is essential for reducing emissions. This study analysed whole rumen metagenome using long reads and considering its compositional nature in order to disentangle the role of rumen microbes in methane emissions. Results The β-diversity analyses suggested a subtle association between methane production and overall microbiota composition (0.01 < R2 < 0.02). Differential abundance analysis identified 36 genera and 279 KEGGs as significantly associated with methane production (Padj < 0.05). Those genera associated with high methane production were Eukaryota from Alveolata and Fungi clades, while Bacteria were associated with low methane emissions. The genus-level association network showed 2 clusters grouping Eukaryota and Bacteria, respectively. Regarding microbial gene functions, 41 KEGGs were found to be differentially abundant between low- and high-emission animals and were mainly involved in metabolic pathways. No KEGGs included in the methane metabolism pathway (ko00680) were detected as associated with high methane emissions. The KEGG network showed 3 clusters grouping KEGGs associated with high emissions, low emissions, and not differentially abundant in either. A deeper analysis of the differentially abundant KEGGs revealed that genes related with anaerobic respiration through nitrate degradation were more abundant in low-emission animals. Conclusions Methane emissions are largely associated with the relative abundance of ciliates and fungi. The role of nitrate electron acceptors can be particularly important because this respiration mechanism directly competes with methanogenesis. Whole metagenome sequencing is necessary to jointly consider the relative abundance of Bacteria, Archaea, and Eukaryota in the statistical analyses. Nutritional and genetic strategies to reduce CH4 emissions should focus on reducing the relative abundance of Alveolata and Fungi in the rumen. This experiment has generated the largest ONT ruminal metagenomic dataset currently available.
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Affiliation(s)
- Adrián López-García
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Alejandro Saborío-Montero
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain.,Escuela de Zootecnia y Centro de Investigación en Nutrición Animal, Universidad de Costa Rica, 11501 San José, Costa Rica
| | - Mónica Gutiérrez-Rivas
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Raquel Atxaerandio
- NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario. Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Idoia Goiri
- NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario. Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Aser García-Rodríguez
- NEIKER - Instituto Vasco de Investigación y Desarrollo Agrario. Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Jose A Jiménez-Montero
- Confederación de Asociaciones de Frisona Española (CONAFE), Ctra. de Andalucía km 23600 Valdemoro, 28340 Madrid, Spain
| | - Carmen González
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Javier Tamames
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, 28049 Madrid, Spain
| | - Fernando Puente-Sánchez
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, 28049 Madrid, Spain
| | - Magdalena Serrano
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Rafael Carrasco
- Departamento de Periodismo y Nuevos Medios, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Cristina Óvilo
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Crta. de la Coruña km 7.5, 28040 Madrid, Spain.,Departamento de Producción Agraria, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
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Choi TJ, Malik A, An HE, Kim JI, Dinh Do T, Kim CB. Seasonal Diversity of Microeukaryotes in the Han River, Korea Through 18S rRNA Gene Metabarcoding. Evol Bioinform Online 2022; 18:11769343221074688. [PMID: 35095269 PMCID: PMC8793432 DOI: 10.1177/11769343221074688] [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: 08/30/2021] [Accepted: 12/21/2021] [Indexed: 11/15/2022] Open
Abstract
Freshwater ecosystems contain a large diversity of microeukaryotes that play important roles in maintaining their structure. Microeukaryote communities vary in composition and abundance on the basis of temporal and environmental variables and may serve as useful bioindicators of environmental changes. In the present study, 18S rRNA metabarcoding was employed to investigate the seasonal diversity of microeukaryote communities during four seasons in the Han River, Korea. In total, 882 unique operational taxonomic units (OTUs) were detected, including various diatoms, metazoans (e.g., arthropods and rotifers), chlorophytes, and fungi. Although alpha diversity revealed insignificant differences based on seasons, beta diversity exhibited a prominent variation in the community composition as per seasons. The analysis revealed that the diversity of microeukaryotes was primarily driven by seasonal changes in the prevailing conditions of environmental water temperature and dissolved oxygen. Moreover, potential indicator OTUs belonging to diatoms and chlorophytes were associated with seasonal and environmental factors. This analysis was a preliminary study that established a continuous monitoring system using metabarcoding. This approach could be an effective tool to manage the Han River along with other freshwater ecosystems in Korea.
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Affiliation(s)
- Tae-June Choi
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Adeel Malik
- Institute of Intelligence Informatics Technology, Sangmyung University, Seoul, Republic of Korea
| | - Hyung-Eun An
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Jung-Il Kim
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Thinh Dinh Do
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
| | - Chang-Bae Kim
- Department of Biotechnology, Sangmyung University, Seoul, Republic of Korea
- Chang-Bae Kim, Department of Biotechnology, Sangmyung University, Seoul, 03016 Republic of Korea.
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Auladell A, Barberán A, Logares R, Garcés E, Gasol JM, Ferrera I. Seasonal niche differentiation among closely related marine bacteria. THE ISME JOURNAL 2022; 16:178-189. [PMID: 34285363 PMCID: PMC8692485 DOI: 10.1038/s41396-021-01053-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023]
Abstract
Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.
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Affiliation(s)
- Adrià Auladell
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, USA
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
- Center for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, WA, Australia.
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, Fuengirola, Málaga, Spain.
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40
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Alenazi A. A review of compositional data analysis and recent advances. COMMUN STAT-THEOR M 2021. [DOI: 10.1080/03610926.2021.2014890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Abdulaziz Alenazi
- Department of Mathematics, College of Science, Northern Border University, Arar, Saudi Arabia
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41
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Nabwera HM, Espinoza JL, Worwui A, Betts M, Okoi C, Sesay AK, Bancroft R, Agbla SC, Jarju S, Bradbury RS, Colley M, Jallow AT, Liu J, Houpt ER, Prentice AM, Antonio M, Bernstein RM, Dupont CL, Kwambana-Adams BA. Interactions between fecal gut microbiome, enteric pathogens, and energy regulating hormones among acutely malnourished rural Gambian children. EBioMedicine 2021; 73:103644. [PMID: 34695658 PMCID: PMC8550991 DOI: 10.1016/j.ebiom.2021.103644] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The specific roles that gut microbiota, known pathogens, and host energy-regulating hormones play in the pathogenesis of non-edematous severe acute malnutrition (marasmus SAM) and moderate acute malnutrition (MAM) during outpatient nutritional rehabilitation are yet to be explored. METHODS We applied an ensemble of sample-specific (intra- and inter-modality) association networks to gain deeper insights into the pathogenesis of acute malnutrition and its severity among children under 5 years of age in rural Gambia, where marasmus SAM is most prevalent. FINDINGS Children with marasmus SAM have distinct microbiome characteristics and biologically-relevant multimodal biomarkers not observed among children with moderate acute malnutrition. Marasmus SAM was characterized by lower microbial richness and biomass, significant enrichments in Enterobacteriaceae, altered interactions between specific Enterobacteriaceae and key energy regulating hormones and their receptors. INTERPRETATION Our findings suggest that marasmus SAM is characterized by the collapse of a complex system with nested interactions and key associations between the gut microbiome, enteric pathogens, and energy regulating hormones. Further exploration of these systems will help inform innovative preventive and therapeutic interventions. FUNDING The work was supported by the UK Medical Research Council (MRC; MC-A760-5QX00) and the UK Department for International Development (DFID) under the MRC/DFID Concordat agreement; Bill and Melinda Gates Foundation (OPP 1066932) and the National Institute of Medical Research (NIMR), UK. This network analysis was supported by NIH U54GH009824 [CLD] and NSF OCE-1558453 [CLD].
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Affiliation(s)
- Helen M Nabwera
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Josh L Espinoza
- J. Craig Venture Institute, 4120 Capricorn Ln, La Jolla, CA 92037, USA; Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Archibald Worwui
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Modupeh Betts
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Catherine Okoi
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Abdul K Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Rowan Bancroft
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Schadrac C Agbla
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | | | - Mariama Colley
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Amadou T Jallow
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Jie Liu
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Fajara, Banjul, PO Box 273, The Gambia; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Robin M Bernstein
- Growth and Development Lab, Department of Anthropology, University of Colorado, Boulder, CO, United States of America
| | | | - Brenda A Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, United Kingdom.
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Gordon-Rodriguez E, Quinn TP, Cunningham JP. Learning sparse log-ratios for high-throughput sequencing data. Bioinformatics 2021; 38:157-163. [PMID: 34498030 PMCID: PMC8696089 DOI: 10.1093/bioinformatics/btab645] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/09/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION The automatic discovery of sparse biomarkers that are associated with an outcome of interest is a central goal of bioinformatics. In the context of high-throughput sequencing (HTS) data, and compositional data (CoDa) more generally, an important class of biomarkers are the log-ratios between the input variables. However, identifying predictive log-ratio biomarkers from HTS data is a combinatorial optimization problem, which is computationally challenging. Existing methods are slow to run and scale poorly with the dimension of the input, which has limited their application to low- and moderate-dimensional metagenomic datasets. RESULTS Building on recent advances from the field of deep learning, we present CoDaCoRe, a novel learning algorithm that identifies sparse, interpretable and predictive log-ratio biomarkers. Our algorithm exploits a continuous relaxation to approximate the underlying combinatorial optimization problem. This relaxation can then be optimized efficiently using the modern ML toolbox, in particular, gradient descent. As a result, CoDaCoRe runs several orders of magnitude faster than competing methods, all while achieving state-of-the-art performance in terms of predictive accuracy and sparsity. We verify the outperformance of CoDaCoRe across a wide range of microbiome, metabolite and microRNA benchmark datasets, as well as a particularly high-dimensional dataset that is outright computationally intractable for existing sparse log-ratio selection methods. AVAILABILITY AND IMPLEMENTATION The CoDaCoRe package is available at https://github.com/egr95/R-codacore. Code and instructions for reproducing our results are available at https://github.com/cunningham-lab/codacore. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Thomas P Quinn
- Applied Artificial Intelligence Institute, Deakin University, Geelong, VIC 3126, Australia
| | - John P Cunningham
- Department of Statistics, Columbia University, New York, NY 10025, USA
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43
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Harikumar H, Quinn TP, Rana S, Gupta S, Venkatesh S. Personalized single-cell networks: a framework to predict the response of any gene to any drug for any patient. BioData Min 2021; 14:37. [PMID: 34353329 PMCID: PMC8340371 DOI: 10.1186/s13040-021-00263-w] [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: 01/21/2021] [Accepted: 05/10/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The last decade has seen a major increase in the availability of genomic data. This includes expert-curated databases that describe the biological activity of genes, as well as high-throughput assays that measure gene expression in bulk tissue and single cells. Integrating these heterogeneous data sources can generate new hypotheses about biological systems. Our primary objective is to combine population-level drug-response data with patient-level single-cell expression data to predict how any gene will respond to any drug for any patient. METHODS We take 2 approaches to benchmarking a "dual-channel" random walk with restart (RWR) for data integration. First, we evaluate how well RWR can predict known gene functions from single-cell gene co-expression networks. Second, we evaluate how well RWR can predict known drug responses from individual cell networks. We then present two exploratory applications. In the first application, we combine the Gene Ontology database with glioblastoma single cells from 5 individual patients to identify genes whose functions differ between cancers. In the second application, we combine the LINCS drug-response database with the same glioblastoma data to identify genes that may exhibit patient-specific drug responses. CONCLUSIONS Our manuscript introduces two innovations to the integration of heterogeneous biological data. First, we use a "dual-channel" method to predict up-regulation and down-regulation separately. Second, we use individualized single-cell gene co-expression networks to make personalized predictions. These innovations let us predict gene function and drug response for individual patients. Taken together, our work shows promise that single-cell co-expression data could be combined in heterogeneous information networks to facilitate precision medicine.
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Affiliation(s)
- Haripriya Harikumar
- Applied Artificial Intelligence Institute, Deakin University, Geelong, Australia.
- Institute for Health Transformation, Deakin University, Geelong, Australia.
| | - Thomas P Quinn
- Applied Artificial Intelligence Institute, Deakin University, Geelong, Australia.
| | - Santu Rana
- Applied Artificial Intelligence Institute, Deakin University, Geelong, Australia
| | - Sunil Gupta
- Applied Artificial Intelligence Institute, Deakin University, Geelong, Australia
| | - Svetha Venkatesh
- Applied Artificial Intelligence Institute, Deakin University, Geelong, Australia
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44
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Stevens BR, Roesch L, Thiago P, Russell JT, Pepine CJ, Holbert RC, Raizada MK, Triplett EW. Depression phenotype identified by using single nucleotide exact amplicon sequence variants of the human gut microbiome. Mol Psychiatry 2021; 26:4277-4287. [PMID: 31988436 DOI: 10.1038/s41380-020-0652-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/15/2022]
Abstract
Single nucleotide exact amplicon sequence variants (ASV) of the human gut microbiome were used to evaluate if individuals with a depression phenotype (DEPR) could be identified from healthy reference subjects (NODEP). Microbial DNA in stool samples obtained from 40 subjects were characterized using high throughput microbiome sequence data processed via DADA2 error correction combined with PIME machine-learning de-noising and taxa binning/parsing of prevalent ASVs at the single nucleotide level of resolution. Application of ALDEx2 differential abundance analysis with assessed effect sizes and stringent PICRUSt2 predicted metabolic pathways. This multivariate machine-learning approach significantly differentiated DEPR (n = 20) vs. NODEP (n = 20) (PERMANOVA P < 0.001) based on microbiome taxa clustering and neurocircuit-relevant metabolic pathway network analysis for GABA, butyrate, glutamate, monoamines, monosaturated fatty acids, and inflammasome components. Gut microbiome dysbiosis using ASV prevalence data may offer the diagnostic potential of using human metaorganism biomarkers to identify individuals with a depression phenotype.
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Affiliation(s)
- Bruce R Stevens
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, USA. .,Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL, USA. .,Division of Gastroenterology, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA.
| | - Luiz Roesch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA.,Centro Interdisciplinar de Pesquisas em Biotecnologia-CIP-Biotec, Universidade Federal do Pampa, São Gabriel, Bagé, Brazil
| | - Priscila Thiago
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Jordan T Russell
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Carl J Pepine
- Division of Cardiovascular Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Richard C Holbert
- Department of Psychiatry, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mohan K Raizada
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
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45
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Peschel S, Müller CL, von Mutius E, Boulesteix AL, Depner M. NetCoMi: network construction and comparison for microbiome data in R. Brief Bioinform 2021; 22:bbaa290. [PMID: 33264391 PMCID: PMC8293835 DOI: 10.1093/bib/bbaa290] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/24/2020] [Accepted: 10/07/2020] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Estimating microbial association networks from high-throughput sequencing data is a common exploratory data analysis approach aiming at understanding the complex interplay of microbial communities in their natural habitat. Statistical network estimation workflows comprise several analysis steps, including methods for zero handling, data normalization and computing microbial associations. Since microbial interactions are likely to change between conditions, e.g. between healthy individuals and patients, identifying network differences between groups is often an integral secondary analysis step. Thus far, however, no unifying computational tool is available that facilitates the whole analysis workflow of constructing, analysing and comparing microbial association networks from high-throughput sequencing data. RESULTS Here, we introduce NetCoMi (Network Construction and comparison for Microbiome data), an R package that integrates existing methods for each analysis step in a single reproducible computational workflow. The package offers functionality for constructing and analysing single microbial association networks as well as quantifying network differences. This enables insights into whether single taxa, groups of taxa or the overall network structure change between groups. NetCoMi also contains functionality for constructing differential networks, thus allowing to assess whether single pairs of taxa are differentially associated between two groups. Furthermore, NetCoMi facilitates the construction and analysis of dissimilarity networks of microbiome samples, enabling a high-level graphical summary of the heterogeneity of an entire microbiome sample collection. We illustrate NetCoMi's wide applicability using data sets from the GABRIELA study to compare microbial associations in settled dust from children's rooms between samples from two study centers (Ulm and Munich). AVAILABILITY R scripts used for producing the examples shown in this manuscript are provided as supplementary data. The NetCoMi package, together with a tutorial, is available at https://github.com/stefpeschel/NetCoMi. CONTACT Tel:+49 89 3187 43258; stefanie.peschel@mail.de. SUPPLEMENTARY INFORMATION Supplementary data are available at Briefings in Bioinformatics online.
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Affiliation(s)
- Stefanie Peschel
- Institute for Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Christian L Müller
- Department of Statistics, LMU München, Munich, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Center for Computational Mathematics, Flatiron Institute, New York, USA
| | - Erika von Mutius
- Institute for Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Dr von Hauner Children’s Hospital, LMU München, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Anne-Laure Boulesteix
- Institute for Medical Information Processing, Biometry and Epidemiology, LMU München, Munich, Germany
| | - Martin Depner
- Institute for Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
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46
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Henson MA. Interrogation of the perturbed gut microbiota in gouty arthritis patients through in silico metabolic modeling. Eng Life Sci 2021; 21:489-501. [PMID: 34257630 PMCID: PMC8257998 DOI: 10.1002/elsc.202100003] [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: 01/09/2021] [Revised: 03/26/2021] [Accepted: 05/01/2021] [Indexed: 12/13/2022] Open
Abstract
Recent studies have shown perturbed gut microbiota associated with gouty arthritis, a metabolic disease characterized by an imbalance between uric acid production and excretion. To mechanistically investigate altered microbiota metabolism associated with gout disease, 16S rRNA gene amplicon sequence data from stool samples of gout patients and healthy controls were computationally analyzed through bacterial community metabolic models. Patient-specific community models constructed with the metagenomics modeling pipeline, mgPipe, were used to perform k-means clustering of samples according to their metabolic capabilities. The clustering analysis generated statistically significant partitioning of samples into a Bacteroides-dominated, high gout cluster and a Faecalibacterium-elevated, low gout cluster. The high gout cluster was predicted to allow elevated synthesis of the amino acids D-alanine and L-alanine and byproducts of branched-chain amino acid catabolism, while the low gout cluster allowed higher production of butyrate, the sulfur-containing amino acids L-cysteine and L-methionine, and the L-cysteine catabolic product H2S. By expanding the capabilities of mgPipe to provide taxa-level resolution of metabolite exchange rates, acetate, D-lactate and succinate exchanged from Bacteroides to Faecalibacterium were predicted to enhance butyrate production in the low gout cluster. Model predictions suggested that sulfur-containing amino acid metabolism generally and H2S more specifically could be novel gout disease markers.
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Affiliation(s)
- Michael A. Henson
- Department of Chemical Engineering and the Institute for Applied Life SciencesUniversity of MassachusettsAmherstMAUSA
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47
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Stewart AG, Satlin MJ, Schlebusch S, Isler B, Forde BM, Paterson DL, Harris PNA. Completing the Picture-Capturing the Resistome in Antibiotic Clinical Trials. Clin Infect Dis 2021; 72:e1122-e1129. [PMID: 33354717 DOI: 10.1093/cid/ciaa1877] [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: 09/01/2020] [Indexed: 11/12/2022] Open
Abstract
Despite the accepted dogma that antibiotic use is the largest contributor to antimicrobial resistance (AMR) and human microbiome disruption, our knowledge of specific antibiotic-microbiome effects remains basic. Detection of associations between new or old antimicrobials and specific AMR burden is patchy and heterogeneous. Various microbiome analysis tools are available to determine antibiotic effects on microbial communities in vivo. Microbiome analysis of treatment groups in antibiotic clinical trials, powered to measure clinically meaningful endpoints would greatly assist the antibiotic development pipeline and clinician antibiotic decision making.
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Affiliation(s)
- Adam G Stewart
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia.,Department of Infectious Diseases, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Michael J Satlin
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Sanmarié Schlebusch
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia.,Department of Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Forensic and Scientific Services, Health Support Queensland, Queensland Health, Brisbane, Australia
| | - Burcu Isler
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Queensland, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
| | - David L Paterson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia.,Department of Infectious Diseases, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
| | - Patrick N A Harris
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women's Hospital Campus, Brisbane, Australia.,Department of Microbiology, Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
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48
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Murdock SA, Tunnicliffe V, Boschen-Rose RE, Juniper SK. Emergent "core communities" of microbes, meiofauna and macrofauna at hydrothermal vents. ISME COMMUNICATIONS 2021; 1:27. [PMID: 36739470 PMCID: PMC9723782 DOI: 10.1038/s43705-021-00031-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
Assessment of ecosystem health entails consideration of species interactions within and between size classes to determine their contributions to ecosystem function. Elucidating microbial involvement in these interactions requires tools to distil diverse microbial information down to relevant, manageable elements. We used covariance ratios (proportionality) between pairs of species and patterns of enrichment to identify "core communities" of likely interacting microbial (<64 µm), meiofaunal (64 µm to 1 mm) and macrofaunal (>1 mm) taxa within assemblages hosted by a foundation species, the hydrothermal vent tubeworm Ridgeia piscesae. Compared with samples from co-located hydrothermal fluids, microbial communities within R. piscesae assemblages are hotspots of taxonomic richness and are high in novelty (unclassified OTUs) and in relative abundance of Bacteroidetes. We also observed a robust temperature-driven distinction in assemblage composition above and below ~25 °C that spanned micro to macro size classes. The core high-temperature community included eight macro- and meiofaunal taxa and members of the Bacteroidetes and Epsilonbacteraeota, particularly the genera Carboxylicivirga, Nitratifractor and Arcobacter. The core low-temperature community included more meiofaunal species in addition to Alpha- and Gammaproteobacteria, and Actinobacteria. Inferred associations among high-temperature core community taxa suggest increased reliance on species interactions under more severe hydrothermal conditions. We propose refinement of species diversity to "core communities" as a tool to simplify investigations of relationships between taxonomic and functional diversity across domains and scales by narrowing the taxonomic scope.
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Affiliation(s)
- S A Murdock
- School of Earth & Ocean Sciences, University of Victoria, Victoria, Canada.
| | - V Tunnicliffe
- School of Earth & Ocean Sciences, University of Victoria, Victoria, Canada
- Department of Biology, University of Victoria, Victoria, Canada
| | - R E Boschen-Rose
- Department of Biology, University of Victoria, Victoria, Canada
- Ocean & Earth Science, University of Southampton, Southampton, UK
| | - S K Juniper
- School of Earth & Ocean Sciences, University of Victoria, Victoria, Canada
- Ocean Networks Canada, University of Victoria, Victoria, Canada
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49
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Schreiber L, Fortin N, Tremblay J, Wasserscheid J, Sanschagrin S, Mason J, Wright CA, Spear D, Johannessen SC, Robinson B, King T, Lee K, Greer CW. In situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditions. FEMS Microbiol Ecol 2021; 97:fiab082. [PMID: 34124756 PMCID: PMC8213973 DOI: 10.1093/femsec/fiab082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/11/2021] [Indexed: 12/30/2022] Open
Abstract
Douglas Channel and the adjacent Hecate Strait (British Columbia, Canada) are part of a proposed route to ship diluted bitumen (dilbit). This study presents how two types of dilbit naturally degrade in this environment by using an in situ microcosm design based on dilbit-coated beads. We show that dilbit-associated n-alkanes were microbially biodegraded with estimated half-lives of 57-69 days. n-Alkanes appeared to be primarily degraded using the aerobic alkB, ladA and CYP153 pathways. The loss of dilbit polycyclic aromatic hydrocarbons (PAHs) was slower than of n-alkanes, with half-lives of 89-439 days. A biodegradation of PAHs could not be conclusively determined, although a significant enrichment of the phnAc gene (a marker for aerobic PAH biodegradation) was observed. PAH degradation appeared to be slower in Hecate Strait than in Douglas Channel. Microcosm-associated microbial communities were shaped by the presence of dilbit, deployment location and incubation time but not by dilbit type. Metagenome-assembled genomes of putative dilbit-degraders were obtained and could be divided into populations of early, late and continuous degraders. The majority of the identified MAGs could be assigned to the orders Flavobacteriales, Methylococcales, Pseudomonadales and Rhodobacterales. A high proportion of the MAGs represent currently unknown lineages or lineages with currently no cultured representative.
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Affiliation(s)
- Lars Schreiber
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Nathalie Fortin
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Julien Tremblay
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Jessica Wasserscheid
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Sylvie Sanschagrin
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
| | - Jennifer Mason
- Centre for Offshore Oil, Gas and Energy Research (COOGER), Bedford Institute of Oceanography, Fisheries and Oceans Canada (DFO), 1 Challenger Drive, P.O. Box 1006, Dartmouth, NS B2Y 4A2, Canada
| | - Cynthia A Wright
- Institute of Ocean Sciences, Fisheries and Oceans Canada (DFO), 9860 West Saanich Road, P.O. Box 6000, Sidney, BC V8L 4B2, Canada
| | - David Spear
- Institute of Ocean Sciences, Fisheries and Oceans Canada (DFO), 9860 West Saanich Road, P.O. Box 6000, Sidney, BC V8L 4B2, Canada
| | - Sophia C Johannessen
- Institute of Ocean Sciences, Fisheries and Oceans Canada (DFO), 9860 West Saanich Road, P.O. Box 6000, Sidney, BC V8L 4B2, Canada
| | - Brian Robinson
- Centre for Offshore Oil, Gas and Energy Research (COOGER), Bedford Institute of Oceanography, Fisheries and Oceans Canada (DFO), 1 Challenger Drive, P.O. Box 1006, Dartmouth, NS B2Y 4A2, Canada
| | - Thomas King
- Centre for Offshore Oil, Gas and Energy Research (COOGER), Bedford Institute of Oceanography, Fisheries and Oceans Canada (DFO), 1 Challenger Drive, P.O. Box 1006, Dartmouth, NS B2Y 4A2, Canada
| | - Kenneth Lee
- Ecosystem Science, Fisheries and Oceans Canada (DFO), 200 Kent St, Ottawa,ON K1A 0E6, Canada
| | - Charles W Greer
- Energy, Mining and Environment Research Center, National Research Council of Canada (NRC), 6100 Royalmount Ave, Montreal, QC H4P 2R2, Canada
- Department of Natural Resource Sciences, McGill University, Macdonald-Stewart Building, McGill, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
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50
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Cinek O, Kramna L, Odeh R, Alassaf A, Ibekwe MAU, Ahmadov G, Elmahi BME, Mekki H, Lebl J, Abdullah MA. Eukaryotic viruses in the fecal virome at the onset of type 1 diabetes: A study from four geographically distant African and Asian countries. Pediatr Diabetes 2021; 22:558-566. [PMID: 33786936 DOI: 10.1111/pedi.13207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Studies of the fecal virome in type 1 diabetes (T1D) have been limited to populations of Europe and the United States. We therefore sought to characterize the stool virome in children after onset of T1D and in matched control subjects from four geographically distant African and Asian countries. METHODS Samples of stool were collected from 73 children and adolescents shortly after T1D onset (Azerbaijan 19, Jordan 20, Nigeria 14, Sudan 20) and 105 matched control subjects of similar age and locale. Metagenomic sequencing of the DNA and RNA virome was performed, and virus positivity was defined as more than 0.001% of reads of the sample. Selected viruses were also quantified using real-time PCR. Conditional logistic regression was used to model associations with eukaryotic virus positivity. RESULTS Signals of 387 different viral species were detected; at least one eukaryotic virus was detected in 71% case and 65% control samples. Neither of observed eukaryotic virus species or genera differed in frequency between children with T1D and controls. There was a suggestive association of the total count of different viral genera per sample between cases (1.45 genera) and controls (1.10 genera, OR 1.24, 95%CI 0.98-1.57), and an unplanned subanalysis suggested marginally more frequent endogenous retrovirus signal in cases (in 28.8% vs. in 8.6% controls, OR = 4.55, 95%CI 1.72-12). CONCLUSIONS No clear and consistent association with T1D was observed in the fecal viromes from four distant non-European populations. The finding of borderline associations of human endogenous retroviruses merits further exploration.
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Affiliation(s)
- Ondrej Cinek
- Department of Pediatrics, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Lenka Kramna
- Department of Pediatrics, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Mary Ann Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | | | - Bashir Mukhtar Elwasila Elmahi
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Sudan Childhood Diabetes Center, Khartoum, Sudan
| | - Hanan Mekki
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Jan Lebl
- Department of Pediatrics, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Mohammed Ahmed Abdullah
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Sudan Childhood Diabetes Center, Khartoum, Sudan
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