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Graham AS, Patel F, Little F, van der Kouwe A, Kaba M, Holmes MJ. Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.591068. [PMID: 38798511 PMCID: PMC11118338 DOI: 10.1101/2024.05.13.591068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Introduction Short-read amplicon sequencing studies have typically focused on 1-2 variable regions of the 16S rRNA gene. Species-level resolution is limited in these studies, as each variable region enables the characterisation of a different subsection of the microbiome. Although long-read sequencing techniques take advantage of all 9 variable regions by sequencing the entire 16S rRNA gene, they are substantially more expensive. This work assessed the feasibility of accurate species-level resolution and reproducibility using a relatively new sequencing kit and bioinformatics pipeline developed for short-read sequencing of multiple variable regions of the 16S rRNA gene. In addition, we evaluated the potential impact of different sample collection methods on our outcomes. Methods Using xGen™ 16S Amplicon Panel v2 kits, sequencing of all 9 variable regions of the 16S rRNA gene was carried out on an Illumina MiSeq platform. Mock cells and mock DNA for 8 bacterial species were included as extraction and sequencing controls respectively. Within-run and between-run replicate samples, and pairs of stool and rectal swabs collected at 0-5 weeks from the same participants, were incorporated. Observed relative abundances of each species were compared to theoretical abundances provided by ZymoBIOMICS. Paired Wilcoxon rank sum tests and distance-based intraclass correlation coefficients were used to statistically compare alpha and beta diversity measures, respectively, for pairs of replicates and stool/rectal swab sample pairs. Results Using multiple variable regions of the 16S ribosomal Ribonucleic Acid (rRNA) gene, we found that we could accurately identify taxa to a species level and obtain highly reproducible results at a species level. Yet, the microbial profiles of stool and rectal swab sample pairs differed substantially despite being collected concurrently from the same infants. Conclusion This protocol provides an effective means for studying infant gut microbial samples at a species level. However, sample collection approaches need to be accounted for in any downstream analysis.
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Affiliation(s)
- Amy S Graham
- Imaging Sciences, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Human Biology, Division of Biomedical Engineering, University of Cape Town, Cape Town, South Africa
| | - Fadheela Patel
- Department of Pathology, Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Francesca Little
- Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
| | - Andre van der Kouwe
- Athinoula A. Martinos Centre for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Mamadou Kaba
- Department of Pathology, Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Martha J Holmes
- Imaging Sciences, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Human Biology, Division of Biomedical Engineering, University of Cape Town, Cape Town, South Africa
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
- ImageTech, Simon Fraser University, Surrey, BC, Canada
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Tsugawa H, Ishihara T, Ogasa K, Iwanami S, Hori A, Takahashi M, Yamada Y, Satoh-Takayama N, Ohno H, Minoda A, Arita M. A lipidome landscape of aging in mice. NATURE AGING 2024; 4:709-726. [PMID: 38609525 DOI: 10.1038/s43587-024-00610-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 03/07/2024] [Indexed: 04/14/2024]
Abstract
Understanding the molecular mechanisms of aging is crucial for enhancing healthy longevity. We conducted untargeted lipidomics across 13 biological samples from mice at various life stages (2, 12, 19 and 24 months) to explore the potential link between aging and lipid metabolism, considering sex (male or female) and microbiome (specific pathogen-free or germ-free) dependencies. By analyzing 2,704 molecules from 109 lipid subclasses, we characterized common and tissue-specific lipidome alterations associated with aging. For example, the levels of bis(monoacylglycero)phosphate containing polyunsaturated fatty acids increased in various organs during aging, whereas the levels of other phospholipids containing saturated and monounsaturated fatty acids decreased. In addition, we discovered age-dependent sulfonolipid accumulation, absent in germ-free mice, correlating with Alistipes abundance determined by 16S ribosomal RNA gene amplicon sequencing. In the male kidney, glycolipids such as galactosylceramides, galabiosylceramides (Gal2Cer), trihexosylceramides (Hex3Cer), and mono- and digalactosyldiacylglycerols were detected, with two lipid classes-Gal2Cer and Hex3Cer-being significantly enriched in aged mice. Integrated analysis of the kidney transcriptome revealed uridine diphosphate galactosyltransferase 8A (UGT8a), alkylglycerone phosphate synthase and fatty acyl-coenzyme A reductase 1 as potential enzymes responsible for the male-specific glycolipid biosynthesis in vivo, which would be relevant to sex dependency in kidney diseases. Inhibiting UGT8 reduced the levels of these glycolipids and the expression of inflammatory cytokines in the kidney. Our study provides a valuable resource for clarifying potential links between lipid metabolism and aging.
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Affiliation(s)
- Hiroshi Tsugawa
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Molecular and Cellular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
| | - Tomoaki Ishihara
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Pharmacy, Nagasaki International University, Sasebo, Japan
| | - Kota Ogasa
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Seigo Iwanami
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Aya Hori
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mikiko Takahashi
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yutaka Yamada
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Naoko Satoh-Takayama
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Aki Minoda
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Molecular and Cellular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan.
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan.
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Valencia EM, Maki KA, Dootz JN, Barb JJ. Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines. Sci Data 2024; 11:81. [PMID: 38233447 PMCID: PMC10794705 DOI: 10.1038/s41597-023-02877-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
Shotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be daunting due to the wide variety of tools available. Here, we assessed publicly available shotgun metagenomics processing packages/pipelines including bioBakery, Just a Microbiology System (JAMS), Whole metaGenome Sequence Assembly V2 (WGSA2), and Woltka using 19 publicly available mock community samples and a set of five constructed pathogenic gut microbiome samples. Also included is a workflow for labelling bacterial scientific names with NCBI taxonomy identifiers for better resolution in assessing results. The Aitchison distance, a sensitivity metric, and total False Positive Relative Abundance were used for accuracy assessments for all pipelines and mock samples. Overall, bioBakery4 performed the best with most of the accuracy metrics, while JAMS and WGSA2, had the highest sensitivities. Furthermore, bioBakery is commonly used and only requires a basic knowledge of command line usage. This work provides an unbiased assessment of shotgun metagenomics packages and presents results assessing the performance of the packages using mock community sequence data.
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Affiliation(s)
- E Michael Valencia
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, 20814, USA
| | - Katherine A Maki
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, 20814, USA
| | - Jennifer N Dootz
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Jennifer J Barb
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, 20814, USA.
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Haider D, Hall MW, LaRoche J, Beiko RG. Mock microbial community meta-analysis using different trimming of amplicon read lengths. Environ Microbiol 2024; 26:e16566. [PMID: 38149467 DOI: 10.1111/1462-2920.16566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
Abstract
Trimming of sequencing reads is a pre-processing step that aims to discard sequence segments such as primers, adapters and low quality nucleotides that will interfere with clustering and classification steps. We evaluated the impact of trimming length of paired-end 16S and 18S rRNA amplicon reads on the ability to reconstruct the taxonomic composition and relative abundances of communities with a known composition in both even and uneven proportions. We found that maximizing read retention maximizes recall but reduces precision by increasing false positives. The presence of expected taxa was accurately predicted across broad trim length ranges but recovering original relative proportions remains a difficult challenge. We show that parameters that maximize taxonomic recovery do not simultaneously maximize relative abundance accuracy. Trim length represents one of several experimental parameters that have non-uniform impact across microbial clades, making it a difficult parameter to optimize. This study offers insights, guidelines, and helps researchers assess the significance of their decisions when trimming raw reads in a microbiome analysis based on overlapping or non-overlapping paired-end amplicons.
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Affiliation(s)
- Diana Haider
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Michael W Hall
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie LaRoche
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Robert G Beiko
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
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Cao R, Dong X, Zhao Y, Yin J. Effects of blister blight disease on endophytic microbial diversity and community structure in tea ( Camellia sinensis) leaves. 3 Biotech 2023; 13:421. [PMID: 38037657 PMCID: PMC10684454 DOI: 10.1007/s13205-023-03846-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/04/2023] [Indexed: 12/02/2023] Open
Abstract
In this study, metagenomic sequencing technology was employed to analyze the ITS1 region sequence of the ITS rDNA gene of endophytic fungi and 16S sequence of endophytic bacteria in tea leaves with varying degrees of infection by tea blister blight disease as well as healthy tea leaves. Subsequently, a comparative analysis was conducted on the endophytic microbial diversity and the community structure in tea leaves. The findings of this investigation reveal a shift in the dominant endophytic fungal genera from Ascomycota to Basidiomycota as the disease progressed. Furthermore, a negative correlation was observed between Exobasidium and Talaromyce, with Talaromyce exhibiting potential as an antagonist against the disease. Meanwhile, our findings reveal that Proteobacteria, Firmicutes, and Actinobacteria were the three most abundant bacteria phyla in tea leaves. As the disease progressed, there was an increase in the relative abundance of Actinobacteria, while Variovorax, Sphingomonas, and Pseudomonas were found to have higher abundance in later stages. The diversity analysis results indicated that the endophytic microbial diversity and the community structure in tea leaves in the diseased group were lower than those in the healthy control group. In general, blister blight disease altered the community structure of endophytic microorganisms in tea leaves, resulting in a few species with high abundance. The study lays a foundation for investigating the pathogenic mechanism of tea blister disease and establishing a theoretical basis for controlling diseases in tea trees.
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Affiliation(s)
- Rui Cao
- College of Tea Science, Guizhou University, Guiyang, 550025 China
| | - Xuan Dong
- College of Tea Science, Guizhou University, Guiyang, 550025 China
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guiyang, 550025 China
| | - Yichen Zhao
- College of Tea Science, Guizhou University, Guiyang, 550025 China
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guiyang, 550025 China
| | - Jie Yin
- College of Tea Science, Guizhou University, Guiyang, 550025 China
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