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Simpson S, Bettauer V, Ramachandran A, Kraemer S, Mahon S, Medina M, Vallès Y, Dumeaux V, Vallès H, Walsh D, Hallett MT. A metagenomic-based study of two sites from the Barbadian reef system. Coral Reefs 2023; 42:359-366. [PMID: 37009568 PMCID: PMC10060342 DOI: 10.1007/s00338-022-02330-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 11/05/2022] [Indexed: 06/19/2023]
Abstract
UNLABELLED We study the microbiome of sea water collected from two locations of the Barbadian coral reefs. The two sites differ in several environmental and ecological variables including their endogenous benthic community and their proximity to urban development and runoffs from inland watersheds. The composition of the microbial communities was estimated using whole genome DNA shotgun sequencing with adjuvant measurements of chemical and environmental qualities. Although both sites exhibit a similar degree of richness, the less urbanized site (Maycocks reef at Hangman's Bay) has a strong concentration of phototrophs whereas the more urbanized location (Bellairs reef at Folkstone) is enriched for copiotrophs, macroalgal symbionts and marine-related disease-bearing organisms from taxa scattered across the tree of life. Our results are concordant with previous profiles of warm ocean surface waters, suggesting our approach captures the state of each coral reef site, setting the stage for longitudinal studies of marine microbiome dynamics in Barbados. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00338-022-02330-y.
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Affiliation(s)
- S. Simpson
- Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada
| | - V. Bettauer
- Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada
| | - A. Ramachandran
- Department of Biology, Concordia University, Montreal, Canada
| | - S. Kraemer
- Department of Biology, Concordia University, Montreal, Canada
| | - S. Mahon
- Coral Reef Restoration Alliance (CORALL), Bridgetown, Barbados
| | - M. Medina
- Department of Biology, Pennsylvania State University, University Park, PA USA
| | - Y. Vallès
- Department of Biology and Chemical Sciences, University of the West Indies, Cave Hill, Barbados
| | - V. Dumeaux
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Canada
| | - H. Vallès
- Department of Biology and Chemical Sciences, University of the West Indies, Cave Hill, Barbados
| | - D. Walsh
- Department of Biology, Concordia University, Montreal, Canada
| | - M. T. Hallett
- Department of Biochemistry, University of Western Ontario, London, Canada
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2
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Nousias O, Montesanto F. Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea with MetaPhlAn3. Mar Genomics 2021; 59:100866. [PMID: 33812777 DOI: 10.1016/j.margen.2021.100866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022]
Abstract
Microbial communities play fundamental roles in association with marine algae; in fact, they are recognized to be actively involved in growth and morphogenesis of the algae. Porphyra purpurea is a red alga commonly found in the intertidal zone with a high economic value, however little is known about the bacterial species associated with this genus. Here we report the bacterial-associated diversity of P. purpurea in four different localities (Ireland, Italy United Kingdom and the USA) from analyzing eight publicly available metagenomic datasets. These were analyzed with Methaplan3 to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared these results to the 16S rRNA metagenomic analysis pipeline of the MGnify database to evaluate both methods. Kraken2 was used to verify and support the results, as a complementary classification method to Metaphlan3. This approach highlighted the different taxonomic resolution of a 16S rRNA OTU-based method compared to the pan-genome approach deployed by Metaphlan3 and complemented by Kraken2. The results presented here provide valuable preliminary data on the putative host-associated bacterial species of P. purpurea.
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Affiliation(s)
- Orestis Nousias
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Crete, Greece; Department of Biology, University of Crete, Greece.
| | - Federica Montesanto
- Department of Biology, University of Bari Aldo Moro, Via Orabona 4, 70125, Bari, Italy; CoNISMa, Piazzale Flaminio 9, 00197 Roma, Italy.
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3
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Biegert G, El Alam MB, Karpinets T, Wu X, Sims TT, Yoshida-Court K, Lynn EJ, Yue J, Medrano AD, Petrosino J, Mezzari MP, Ajami NJ, Solley T, Ahmed-Kaddar M, Klopp AH, Colbert LE. Diversity and composition of gut microbiome of cervical cancer patients: Do results of 16S rRNA sequencing and whole genome sequencing approaches align? J Microbiol Methods 2021; 185:106213. [PMID: 33785357 DOI: 10.1016/j.mimet.2021.106213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Next generation sequencing has progressed rapidly, characterizing microbial communities beyond culture-based or biochemical techniques. 16S ribosomal RNA gene sequencing (16S) produces reliable taxonomic classifications and relative abundances, while shotgun metagenome sequencing (WMS) allows higher taxonomic and functional resolution at greater cost. The purpose of this study was to determine if 16S and WMS provide congruent information for our patient population from paired fecal microbiome samples. RESULTS Comparative indices were highly congruent between 16S and WMS. The most abundant genera for 16S and WMS data did not overlap. Overlap was observed at the Phylum level, as expected. However, relative abundances correlated poorly between the two methodologies (all P-value>0.05). Hierarchical clustering of both sequencing analyses identified overlapping enterotypes. Both approaches were in agreement with regard to demographic variables. CONCLUSION Diversity, evenness and richness are comparable when using 16S and WMS techniques, however relative abundances of individual genera are not. Clinical associations with diversity and evenness metrics were similarly identified with WMS or 16S.
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Affiliation(s)
- Greyson Biegert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Molly B El Alam
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Travis T Sims
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyoko Yoshida-Court
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erica J Lynn
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jingyan Yue
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrea Delgado Medrano
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Melissa P Mezzari
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Travis Solley
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mustapha Ahmed-Kaddar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ann H Klopp
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Lauren E Colbert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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4
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Wang L, Liu L, Liu X, Xiang M, Zhou L, Huang C, Shen Z, Miao L. The gut microbes, Enterococcus and Escherichia-Shigella, affect the responses of heart valve replacement patients to the anticoagulant warfarin. Pharmacol Res 2020; 159:104979. [PMID: 32505835 DOI: 10.1016/j.phrs.2020.104979] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
Numerous algorithms based on patient genetic variants have been established with the aim of reducing the risk of GI bleeding and thromboembolism during warfarin administration. However, approximately 35 % of individual warfarin sensitivity still remains unexplained. Few of warfarin algorithms take into account gut microbiota profiles. The identification of certain microbiome will provide new targets and new strategies for reducing the risk of bleeding and thromboembolism during warfarin administration. In this study, we collected plasma and stool samples from 200 inpatients undergoing heart valve replacement (HVR), which were classified as low responder (LR), high responder (HR) and normal responder (NR). Significant differences were observed in the diversity and relative abundance of the gut microbiota among the three groups. The genus Escherichia-Shigella was enriched significantly in the LRs (P = 3.189e-11), while the genus Enterococcus was enriched significantly in the HRs (P = 1.249e-11). The amount of VK2 synthesized by gut microbiota in LR group was much higher than that in HR group (P = 0.005). Whole genome shotgun sequencing indicated that the relative abundance of enzymes and modules associated with VK biosynthesis was significantly higher in LRs than in HRs or NRs. The 12 microbial markers were identified through tenfold cross-validation with a random forest model. The results provided a new microbial diagnostic model that can be used to inform modulation of warfarin dosage on the basis of patient intestinal flora composition.
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Abstract
With the developments in high-throughput sequencing (HTS) technologies, researchers have gained a powerful tool to identify structural variants (SVs) in genomes with substantially less cost than before. SVs can be broadly classified into two main categories: balanced rearrangements and copy number variations (CNVs). Many algorithms have been developed to characterize CNVs using HTS data, with focus on different types and size range of variants using different read signatures. Read depth (RD) based tools are more common in characterizing large (>10 kb) CNVs since RD strategy does not rely on the fragment size and read length, which are limiting factors in read pair and split read analysis. Here we provide a guideline for a user friendly tool for detecting large segmental duplications and deletions that can also predict integer copy numbers for duplicated genes.
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Affiliation(s)
- Fatma Kahveci
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey.
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Veeraraghavan B, Devanga Ragupathi NK, Santhanam S, Verghese VP, Inbanathan FY, Livingston C. Whole genome shotgun sequencing of Indian strains of Streptococcus agalactiae. Genom Data 2017; 14:63-65. [PMID: 29021957 PMCID: PMC5633162 DOI: 10.1016/j.gdata.2017.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/26/2017] [Accepted: 10/01/2017] [Indexed: 11/29/2022]
Abstract
Group B streptococcus is known as a leading cause of neonatal infections in developing countries. The present study describes the whole genome shotgun sequences of four Group B Streptococcus (GBS) isolates. Molecular data on clonality is lacking for GBS in India. The present genome report will add important information on the scarce genome data of GBS and will help in deriving comparative genome studies of GBS isolates at global level. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers NHPL00000000 - NHPO00000000.
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Affiliation(s)
- Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, India
| | | | - Sridhar Santhanam
- Department of Neonatology, Christian Medical College, Vellore 632004, India
| | | | | | - Charles Livingston
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, India
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7
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Manku HK, Dhanoa JK, Kaur S, Arora JS, Mukhopadhyay CS. Biocomputational identification and validation of novel microRNAs predicted from bubaline whole genome shotgun sequences. Comput Biol Chem 2017; 70:96-106. [PMID: 28844020 DOI: 10.1016/j.compbiolchem.2017.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/01/2017] [Accepted: 08/07/2017] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are small (19-25 base long), non-coding RNAs that regulate post-transcriptional gene expression by cleaving targeted mRNAs in several eukaryotes. The miRNAs play vital roles in multiple biological and metabolic processes, including developmental timing, signal transduction, cell maintenance and differentiation, diseases and cancers. Experimental identification of microRNAs is expensive and lab-intensive. Alternatively, computational approaches for predicting putative miRNAs from genomic or exomic sequences rely on features of miRNAs viz. secondary structures, sequence conservation, minimum free energy index (MFEI) etc. To date, not a single miRNA has been identified in bubaline (Bubalus bubalis), which is an economically important livestock. The present study aims at predicting the putative miRNAs of buffalo using comparative computational approach from buffalo whole genome shotgun sequencing data (INSDC: AWWX00000000.1). The sequences were blasted against the known mammalian miRNA. The obtained miRNAs were then passed through a series of filtration criteria to obtain the set of predicted (putative and novel) bubaline miRNA. Eight miRNAs were selected based on lowest E-value and validated by real time PCR (SYBR green chemistry) using RNU6 as endogenous control. The results from different trails of real time PCR shows that out of selected 8 miRNAs, only 2 (hsa-miR-1277-5p; bta-miR-2285b) are not expressed in bubaline PBMCs. The potential target genes based on their sequence complementarities were then predicted using miRanda. This work is the first report on prediction of bubaline miRNA from whole genome sequencing data followed by experimental validation. The finding could pave the way to future studies in economically important traits in buffalo.
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8
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Abstract
Metagenomic analysis based on whole genome shotgun sequencing data requires fast protein sequence homology searches for predicting the function of proteins coded on metagenome short reads. However, huge amounts of sequence data cause even general homology search analyses using BLASTX to become difficult in terms of computational cost. GHOSTX is a sequence homology search tool specifically developed for functional annotation of metagenome sequences. The tool is more than 160 times faster than BLASTX and has sufficient search sensitivity for metagenomic analysis. Using this tool, user can perform functional annotation of metagenomic data within a short time and infer metabolic pathways within an environment.
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Affiliation(s)
- Shuji Suzuki
- Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, 152-8550, Tokyo, Japan.,Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Kanagawa, Japan
| | - Takashi Ishida
- Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, 152-8550, Tokyo, Japan.,Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Kanagawa, Japan.,Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, 152-8550, Tokyo, Japan
| | - Masahito Ohue
- Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, 152-8550, Tokyo, Japan.,Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, 152-8550, Tokyo, Japan
| | - Masanori Kakuta
- Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, 152-8550, Tokyo, Japan
| | - Yutaka Akiyama
- Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, 152-8550, Tokyo, Japan. .,Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama, 226-8501, Kanagawa, Japan. .,Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, 152-8550, Tokyo, Japan.
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9
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Ranjan R, Rani A, Metwally A, McGee HS, Perkins DL. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun. 2016;469:967-977. [PMID: 26718401 DOI: 10.1016/j.bbrc.2015.12.083] [Citation(s) in RCA: 477] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/19/2015] [Indexed: 02/08/2023]
Abstract
The human microbiome has emerged as a major player in regulating human health and disease. Translational studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have frequently utilized sequencing of the conserved 16S ribosomal RNA (rRNA) gene. We present a comparative study of an alternative approach using whole genome shotgun sequencing (WGS). In the present study, we analyzed the human fecal microbiome compiling a total of 194.1 × 10(6) reads from a single sample using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads. Our study demonstrates that whole genome shotgun sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection.
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10
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Burrell AS, Disotell TR, Bergey CM. The use of museum specimens with high-throughput DNA sequencers. J Hum Evol 2015; 79:35-44. [PMID: 25532801 PMCID: PMC4312722 DOI: 10.1016/j.jhevol.2014.10.015] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/08/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022]
Abstract
Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists' ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials.
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Affiliation(s)
- Andrew S Burrell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
| | - Todd R Disotell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
| | - Christina M Bergey
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
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