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Zhao J, Gao Z. Dynamic changes in microbial communities and flavor during different fermentation stages of proso millet Baijiu, a new product from Shanxi light-flavored Baijiu. Front Microbiol 2024; 15:1333466. [PMID: 38318340 PMCID: PMC10839113 DOI: 10.3389/fmicb.2024.1333466] [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: 11/05/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction Proso millet, a high-quality fermentation material used for Chinese yellow wine production, can produce special flavored substances; however, its role in improving the flavor and altering microbial communities of light-flavored Baijiu during fermentation remain unknown. Thus, we aimed to investigate the effect of proso millet on improving the flavor of light-flavored Baijiu and altering microbial communities during different fermentation stages. Methods The dynamic changes in the microbial communities and flavor of proso millet (50%) + sorghum (50%) mixed fermentation samples were analyzed through intermittent sampling on days 7, 14, 21, and 28 of the fermentation process. Microbial high-throughput sequencing and the analysis of flavor characteristics were conducted through 16S DNA/ ITS amplicon sequencing and gas chromatography (multi-capillary column)-ion mobility spectrometry, respectively. Results Proso millet significantly changed the core flavor compound composition of traditional light-flavored Baijiu from ethyl acetate, ethyl hexanoate, ethyl hexanoate dimer, ethyl butanoate, ethyl lactate, and butyl acetate to oct-2-ene, 2-butanol, propyl propanoate, 2-pentenal, and 4-methylpentanal. The amplicon sequencing analysis revealed that the alpha diversity parameters of bacterial and fungal communities, including the Chao1, Pielou_e, Shannon, and Simpson indices, for proso millet-sorghum mixed fermentation samples were significantly higher than those for sorghum fermentation samples (p < 0.05). Of the 40 most significant microbial genera in two treatments, proso millet significantly increased the abundance of 12 bacterial and 18 fungal genera. Among the 40 most significant bacterial and fungal species, 23 bacterial species belonged to the Lactobacillus genus, whereas the 30 primary fungal species belonged to 28 different genera. The analysis of the relationship between microbial changes and the main flavor compounds of light-flavored Baijiu showed that bacteria from the Weissella, Acinetobacter, Bacteroides, Psychrobacter, Pseudarthrobacter, Lactococcus, Chloroplast, Saccharopolyspora, Psychrobacter, Saccharopolyspora, Pseudonocardiaceae, Bacteroides genera and fungi from the Thermoascus, Aspergillus, Pichia, Rhizomucor, Papiliotrema, Hyphopichia, and Mucor genera significantly inhibited the synthesis of ethyl hexanoate, ethyl butanoate, ethyl lactate ethyl lactate, and butyl acetate but increased the synthesis of ethyl acetate (p < 0.05). Moreover, these microbes exhibited a significantly greater abundance in proso millet-sorghum mixed fermentation samples than in sorghum samples. The synthesis of special flavored compounds in proso millet Baijiu was significantly positively correlated with the presence of fungi from the Rhizopus, Papiliotrema, Wickerhamomyces, Aspergillus, and Thermoascus genera but negative correlated with the presence of bacteria from the Weissella, Acinetobacter, Psychrobacter, Pseudarthrobacter, Bacteroides, and Saccharopolyspora genera. Regarding ethanol content, the low alcohol content of Fenjiu may be due to the significantly high abundance of fungi from the Psathyrella genus and bacteria from the Staphylococcus, Kroppenstedtia, Brevibacterium, and Acetobacter genera during fermentation. In summary, proso millet significantly altered the flavor of light-flavored Baijiu by inducing the formation of a special microbial community; however, it did not increase alcohol concentration. Discussion This study lays the foundation for future research on Baijiu fermentation. Additionally, the study findings may help improve the production efficiency and elevate the quality and flavor of the final product.
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Affiliation(s)
- Jia Zhao
- Department of Biological Science and Technology, Jinzhong University, Jinzhong, China
| | - Zhenfeng Gao
- College of Food Science and Engineering, Shanxi Agriculture University, Jinzhong, China
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Jeffery IB, Cotter PD, Scanlan PD. Collateral Damage in the Human Gut Microbiome - Blastocystis Is Significantly Less Prevalent in an Antibiotic-Treated Adult Population Compared to Non-Antibiotic Treated Controls. Front Cell Infect Microbiol 2022; 12:822475. [PMID: 35281435 PMCID: PMC8913940 DOI: 10.3389/fcimb.2022.822475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/04/2022] [Indexed: 12/14/2022] Open
Abstract
Antibiotics can drive the rapid loss of non-target, phylogenetically diverse microorganisms that inhabit the human gut. This so-called “collateral damage” has myriad consequences for host health and antibiotic mediated changes to the gut microbiota have been implicated in the aetiology of many chronic diseases. To date, studies have largely focused on how antibiotics affect the bacterial fraction of the gut microbiome and their impact on non-bacterial members, including prevalent eukaryal species, such as Blastocystis, remains largely unknown. Here we assessed the prevalence and diversity of Blastocystis in an elderly adult group that were in receipt of antibiotics (n = 86) and an equivalent non-antibiotic treated group (n = 88) using a PCR-based approach. This analysis revealed that although similar subtypes were present in both groups, Blastocystis was significantly less prevalent in the antibiotic-treated group (16%) compared to non-antibiotic treated controls (55%); Fisher’s Exact test, p < 0.0001). Given that antibiotics target structures and molecules of prokaryotic cells to kill or inhibit bacterial populations, the most likely explanation for differences in prevalence between both groups is due to secondary extinctions owing to the potential dependence of Blastocystis on bacteria present in the gut microbiome that were negatively affected by antibiotic treatment. Although further work is required to explore this hypothesis in greater detail, these data clearly show that Blastocystis prevalence in human populations is negatively associated with antibiotic treatment. This finding may be relevant to explaining patterns of variation for this microorganism in different human populations and cohorts of interest.
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Affiliation(s)
- Ian B. Jeffery
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Pauline D. Scanlan
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- *Correspondence: Pauline D. Scanlan,
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Xie H, Wang H, Ji F, Liang Y, Song M, Zhang J. Tetrabromobisphenol A alters soil microbial community via selective antibacterial activity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 164:597-603. [PMID: 30153641 DOI: 10.1016/j.ecoenv.2018.08.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/14/2018] [Accepted: 08/15/2018] [Indexed: 06/08/2023]
Abstract
Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant. Most studies regarding TBBPA have concentrated on its occurrence, distribution, toxicity and degradation in the environment. However, little is known about its ecological effects on soil microbial communities. In this study, we investigated the effect of TBBPA on soil microbial community. Overall, the data suggested that the growth and composition of soil microorganisms were correlated to the TBBPA concentration and exposure time. Phospholipid-derived fatty acid analysis (PLFAs) showed that significant microbial growth inhibitions were 46.1% and 46.9% in 40 mg/kg TBBPA-treated soils after 45-day incubation under aerobic and anaerobic conditions, respectively. Results of PLFAs and llumina sequencing indicated that TBBPA mainly inhibited Gram-positive bacteria, but not Gram-negative bacteria. The selective antibacterial activity of TBBPA toward Gram-positive bacteria was further confirmed in pure bacteria cultures. These data suggested that, in addition to their effect on microbial growth and composition, TBBPA may affect the microbial ecology. Additional research should be carried out to identify the ecological risk of TBBPA in soil.
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Affiliation(s)
- Huijun Xie
- Environment Research Institute, Shandong University, Jinan 250100, China
| | - Haijing Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Jinan 250100, China
| | - Fang Ji
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Yong Liang
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jian Zhang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science & Engineering, Shandong University, Jinan 250100, China
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Urbina H, Breed MF, Zhao W, Lakshmi Gurrala K, Andersson SGE, Ågren J, Baldauf S, Rosling A. Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere. Fungal Biol 2018; 122:231-240. [PMID: 29551197 DOI: 10.1016/j.funbio.2017.12.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/23/2017] [Indexed: 01/16/2023]
Abstract
Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely-studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2. Fungal species diversity was found to decrease from bulk soil to rhizosphere to endosphere. A significant effect of plant genotype on fungal community composition was detected only in the endosphere compartment. Despite A. thaliana being a non-mycorrhizal plant, it hosts a number of known mycorrhiza fungi in its endosphere compartment, which is also colonized by endophytic, pathogenic and saprotrophic fungi. Species in the Archaeorhizomycetes were most abundant in rhizosphere samples suggesting an adaptation to environments with high nutrient turnover for some of these species. We conclude that A. thaliana endosphere fungal communities represent a selected subset of fungi recruited from soil and that plant genotype has small but significant quantitative and qualitative effects on these communities.
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Affiliation(s)
- Hector Urbina
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden; Department of Botany and Plant Pathology, Purdue University, 915 W State St, West Lafayette, IN, 47907, USA
| | - Martin F Breed
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden; School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, SA-5005, Australia
| | - Weizhou Zhao
- Department of Molecular Evolution, Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75124, Uppsala, Sweden
| | - Kanaka Lakshmi Gurrala
- Department of Molecular Evolution, Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75124, Uppsala, Sweden
| | - Siv G E Andersson
- Department of Molecular Evolution, Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75124, Uppsala, Sweden
| | - Jon Ågren
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Sandra Baldauf
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anna Rosling
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
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DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico. MYCOSCIENCE 2016. [DOI: 10.1016/j.myc.2016.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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马 啸, 蔡 慧, 何 彦, 郑 慧, 康 玲, 周 宏, 刘 木. [Longitudinal analysis of vaginal microbiota in women with recurrent vulvovaginal candidiasis]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2016; 37:192-198. [PMID: 28219862 PMCID: PMC6779659 DOI: 10.3969/j.issn.1673-4254.2017.02.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To investigate the vaginal flora in patients with recurrent vulvovaginal candidiasis (RVVC). METHODS Vaginal swabs were collected at different time points from 6 RVVC patients and 5 healthy women of child-bearing age. The dynamic changes, microbiota composition, alpha diversity and beta diversity in the two groups were assessed by analyzing the 16S rRNA V4 hypervariable region amplified from the total genomic DNA from the swabs. RESULTS Lactobacillus was the predominant species in healthy women with similar proportions of L.iners and L.crispatus; small proportions of Gardnerella, Prevotella and other genus were also detected. In some healthy women, the vaginal flora showed a high relative abundance of anaerobic bacteria such as Gardnerella, Prevotella, Atopobium, Sneathia. Compared with the healthy women, patients with RVVC showed a significantly reduced diversity of vaginal flora, where L.iners was the predominant species and the content of L.crispatus decreased significantly. In healthy women, the vaginal flora fluctuated with the menstrual cycle, and the fluctuation was the most prominent during menstruation; the dominant species either alternated regularly or maintain an absolute superiority in the menstrual cycle. The vaginal flora showed attenuated fluctuation in women with RVVC, were highly conserved within the menstrual cycle, and maintained a similar composition in the episodes and intermittent periods. CONCLUSION The vaginal flora of RVVC patients do not undergo regular variations with the menstrual cycle and shows a similar composition between the episodes and intermittent periods. Promoting the production of L.iners or inhibiting the colonization of L.crispatus to restore the composition of the vaginal flora may help in the treatment of RVVC.
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Affiliation(s)
- 啸 马
- 南方医科大学珠江医院 妇产科,广东 广州 510280Department of Obstetrics and Gynecology
- 广东省人民医院//广东省医学科学院妇产科, 广东 广州 510080Department of Obstetrics and Gynecology, Guangdong General Hospital/Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - 慧华 蔡
- 南方医科大学珠江医院 妇产科,广东 广州 510280Department of Obstetrics and Gynecology
| | - 彦 何
- 南方医科大学珠江医院 检验医学部,广东 广州 510280Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - 慧敏 郑
- 南方医科大学珠江医院 检验医学部,广东 广州 510280Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - 玲 康
- 南方医科大学珠江医院 妇产科,广东 广州 510280Department of Obstetrics and Gynecology
- 广东省人民医院//广东省医学科学院妇产科, 广东 广州 510080Department of Obstetrics and Gynecology, Guangdong General Hospital/Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - 宏伟 周
- 南方医科大学珠江医院 检验医学部,广东 广州 510280Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - 木彪 刘
- 南方医科大学珠江医院 妇产科,广东 广州 510280Department of Obstetrics and Gynecology
- 广东省人民医院//广东省医学科学院妇产科, 广东 广州 510080Department of Obstetrics and Gynecology, Guangdong General Hospital/Guangdong Academy of Medical Sciences, Guangzhou 510080, China
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Shifts of microbial community structure in soils of a photovoltaic plant observed using tag-encoded pyrosequencing of 16S rRNA. Appl Microbiol Biotechnol 2015; 100:3735-45. [DOI: 10.1007/s00253-015-7219-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/27/2015] [Accepted: 12/02/2015] [Indexed: 11/26/2022]
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He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW. Erratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. MICROBIOME 2015; 3:34. [PMID: 26229598 PMCID: PMC4520016 DOI: 10.1186/s40168-015-0098-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 07/22/2015] [Indexed: 06/04/2023]
Abstract
[This corrects the article DOI: 10.1186/s40168-015-0081-x.].
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Affiliation(s)
- Yan He
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - J. Gregory Caporaso
- />Department of Biological Sciences, Northern Arizona University, PO Box 5640, Flagstaff, AZ 86011-5640 USA
- />Center for Microbial Genetics and Genomics, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011-4073 USA
| | - Xiao-Tao Jiang
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - Hua-Fang Sheng
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - Susan M. Huse
- />Department of Pathology and Laboratory Science, Warren Alpert Medical School, Brown University, 70 Ship Street, Providence, RI 02912 USA
| | - Jai Ram Rideout
- />Center for Microbial Genetics and Genomics, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011-4073 USA
| | | | - Evguenia Kopylova
- />Department of Pediatrics, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
| | - William A. Walters
- />Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853 USA
| | - Rob Knight
- />Department of Pediatrics, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
- />Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
| | - Hong-Wei Zhou
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
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Composition and temporal stability of the gut microbiota in older persons. ISME JOURNAL 2015; 10:170-82. [PMID: 26090993 PMCID: PMC4681863 DOI: 10.1038/ismej.2015.88] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/01/2015] [Accepted: 04/24/2015] [Indexed: 12/21/2022]
Abstract
The composition and function of the human gut microbiota has been linked to health and disease. We previously identified correlations between habitual diet, microbiota composition gradients and health gradients in an unstratified cohort of 178 elderly subjects. To refine our understanding of diet–microbiota associations and differential taxon abundance, we adapted an iterative bi-clustering algorithm (iterative binary bclustering of gene sets (iBBiG)) and applied it to microbiota composition data from 732 faecal samples from 371 ELDERMET cohort subjects, including longitudinal samples. We thus identified distinctive microbiota configurations associated with ageing in both community and long-stay residential care elderly subjects. Mixed-taxa populations were identified that had clinically distinct associations. Microbiota temporal instability was observed in both community-dwelling and long-term care subjects, particularly in those with low initial microbiota diversity. However, the stability of the microbiota of subjects had little impact on the directional change of the microbiota as observed for long-stay subjects who display a gradual shift away from their initial microbiota. This was not observed in community-dwelling subjects. This directional change was associated with duration in long-stay. Changes in these bacterial populations represent the loss of the health-associated and youth-associated microbiota components and gain of an elderly associated microbiota. Interestingly, community-associated microbiota configurations were impacted more by the use of antibiotics than the microbiota of individuals in long-term care, as the community-associated microbiota showed more loss but also more recovery following antibiotic treatment. This improved definition of gut microbiota composition patterns in the elderly will better inform the design of dietary or antibiotic interventions targeting the gut microbiota.
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Flynn JM, Brown EA, Chain FJJ, MacIsaac HJ, Cristescu ME. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods. Ecol Evol 2015; 5:2252-66. [PMID: 26078860 PMCID: PMC4461425 DOI: 10.1002/ece3.1497] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/05/2015] [Accepted: 03/10/2015] [Indexed: 11/05/2022] Open
Abstract
Metabarcoding has the potential to become a rapid, sensitive, and effective approach for identifying species in complex environmental samples. Accurate molecular identification of species depends on the ability to generate operational taxonomic units (OTUs) that correspond to biological species. Due to the sometimes enormous estimates of biodiversity using this method, there is a great need to test the efficacy of data analysis methods used to derive OTUs. Here, we evaluate the performance of various methods for clustering length variable 18S amplicons from complex samples into OTUs using a mock community and a natural community of zooplankton species. We compare analytic procedures consisting of a combination of (1) stringent and relaxed data filtering, (2) singleton sequences included and removed, (3) three commonly used clustering algorithms (mothur, UCLUST, and UPARSE), and (4) three methods of treating alignment gaps when calculating sequence divergence. Depending on the combination of methods used, the number of OTUs varied by nearly two orders of magnitude for the mock community (60–5068 OTUs) and three orders of magnitude for the natural community (22–22191 OTUs). The use of relaxed filtering and the inclusion of singletons greatly inflated OTU numbers without increasing the ability to recover species. Our results also suggest that the method used to treat gaps when calculating sequence divergence can have a great impact on the number of OTUs. Our findings are particularly relevant to studies that cover taxonomically diverse species and employ markers such as rRNA genes in which length variation is extensive.
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Affiliation(s)
- Jullien M Flynn
- Department of Biology, McGill University 1205 Docteur Penfield, Stewart Biology Building, Montreal, Quebec, Canada, H3A 1B1
| | - Emily A Brown
- Department of Biology, McGill University 1205 Docteur Penfield, Stewart Biology Building, Montreal, Quebec, Canada, H3A 1B1 ; Great Lakes Institute for Environmental Research, University of Windsor Windsor, Ontario, Canada
| | - Frédéric J J Chain
- Department of Biology, McGill University 1205 Docteur Penfield, Stewart Biology Building, Montreal, Quebec, Canada, H3A 1B1
| | - Hugh J MacIsaac
- Great Lakes Institute for Environmental Research, University of Windsor Windsor, Ontario, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University 1205 Docteur Penfield, Stewart Biology Building, Montreal, Quebec, Canada, H3A 1B1
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Yin J, M P, Wang S, Liao SX, Peng X, He Y, Chen YR, Shen HF, Su J, Chen Y, Jiang YX, Zhang GX, Zhou HW. Different Dynamic Patterns of β-Lactams, Quinolones, Glycopeptides and Macrolides on Mouse Gut Microbial Diversity. PLoS One 2015; 10:e0126712. [PMID: 25970622 PMCID: PMC4430517 DOI: 10.1371/journal.pone.0126712] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/07/2015] [Indexed: 11/18/2022] Open
Abstract
The adverse impact of antibiotics on the gut microbiota has attracted extensive interest, particularly due to the development of microbiome research techniques in recent years. However, a direct comparison of the dynamic effects of various types of antibiotics using the same animal model has not been available. In the present study, we selected six antibiotics from four categories with the broadest clinical usage, namely, β-lactams (Ceftriaxone Sodium, Cefoperazone/Sulbactam and meropenem), quinolones (ofloxacin), glycopeptides (vancomycin), and macrolides (azithromycin), to treat BALB/c mice. Stool samples were collected during and after the administration of antibiotics, and microbial diversity was analyzed through Illumina sequencing and bioinformatics analyses using QIIME. Both α and β diversity analyses showed that ceftriaxone sodium, cefoperazone/sulbactam, meropenem and vancomycin changed the gut microbiota dramatically by the second day of antibiotic administration whereas the influence of ofloxacin was trivial. Azithromycin clearly changed the gut microbiota but much less than vancomycin and the β-lactams. In general, the community changes induced by the three β-lactam antibiotics showed consistency in inhibiting Papillibacter, Prevotella and Alistipes while inducing massive growth of Clostridium. The low diversity and high Clostridium level might be an important cause of Clostridium difficile infection after usage of β-lactams. Vancomycin was unique in that it inhibited Firmicutes, mainly the genus Clostridium. On the other hand, it induced the growth of Escherichia and effect lasted for months afterward. Azithromycin and meropenem induced the growth of Enterococcus. These findings will be useful for understanding the potential adverse effects of antibiotics on the gut microbiome and ensuring their better usage.
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Affiliation(s)
- Jia Yin
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China 510515
| | - Prabhakar M
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China 510515
| | - Shan Wang
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China 510515
| | - Shuo-Xi Liao
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China 510515
| | - Xin Peng
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China 510515
| | - Yan He
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China 510515
| | - Yi-Ran Chen
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China 510515
| | - Hua-Fang Shen
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China 510515
| | - Jin Su
- Department of respiration, Nanfang Hospital, Southern Medical University, Guangzhou, China 510515
| | - Ye Chen
- Department of Digestive Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China 510515
| | - Yun-Xia Jiang
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China 510515
| | - Guo-Xia Zhang
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China 510515
- * E-mail: (G-XZ); (H-WZ)
| | - Hong-Wei Zhou
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China 510515
- * E-mail: (G-XZ); (H-WZ)
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First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing. J Appl Genet 2015; 56:393-401. [PMID: 25604266 PMCID: PMC4543427 DOI: 10.1007/s13353-014-0258-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/11/2014] [Accepted: 11/16/2014] [Indexed: 10/26/2022]
Abstract
The digestive systems of mammals harbor a complex gut microbiome, comprising bacteria and other microorganisms that confer metabolic and immunological benefits to the host. Ruminants that digest plant-based foods have a four-compartment stomach consisting of the rumen, reticulum, omasum, and abomasum. The microorganisms in the stomach are essential for providing the host with critical nutrients. However, the majority of these microorganisms are unknown species. The microbiome of the stomach is diverse, and the majority of these organisms cannot be cultured. Next-generation sequencing (NGS) combined with bioinformatic analysis tools have allowed the dissection of the composition of the microbiome in samples collected from a specific environment. In this study, for the first time, the bacterial composition in two compartments, the reticulum and the omasum, of bovine were analyzed using a metagenomic approach and compared to the bacterial composition of the rumen. These data will assist in understanding the biology of ruminants and benefit the agricultural industry. The diversity and composition of the bacterial community in samples collected from the rumen, reticulum, and omasum of bovines in the Changchun Region of Northeast China were analyzed by sequencing the V3 region of the 16S rRNA gene using a barcoded Illumina paired-end sequencing technique, and the primary composition of the microbiome in the rumen, reticulum, and omasum of the bovines was determined. These microbiomes contained 17 phyla and 107 genera in all three samples. Five phyla, Bacteroidetes, Firmicutes, Proteobacteria, Spirochaetes, and Lentisphaerae, were the most abundant taxonomic groups. Additionally, the different stomach compartments harbored different compositions of the microorganisms.
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He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, Edgar RC, Kopylova E, Walters WA, Knight R, Zhou HW. Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. MICROBIOME 2015; 3:20. [PMID: 25995836 PMCID: PMC4438525 DOI: 10.1186/s40168-015-0081-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/03/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. RESULTS Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. CONCLUSIONS As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.
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Affiliation(s)
- Yan He
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - J Gregory Caporaso
- />Department of Biological Sciences, Northern Arizona University, PO Box 5640, Flagstaff, AZ 86011-5640 USA
- />Center for Microbial Genetics and Genomics, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011-4073 USA
| | - Xiao-Tao Jiang
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - Hua-Fang Sheng
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
| | - Susan M Huse
- />Department of Pathology and Laboratory Science, Warren Alpert Medical School, Brown University, 70 Ship Street, Providence, RI 02912 USA
| | - Jai Ram Rideout
- />Center for Microbial Genetics and Genomics, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011-4073 USA
| | | | - Evguenia Kopylova
- />Department of Pediatrics, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
| | - William A Walters
- />Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853 USA
| | - Rob Knight
- />Department of Pediatrics, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
- />Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive MC0763, La Jolla, CA 92093-0763 USA
| | - Hong-Wei Zhou
- />State Key Laboratory of Organ Failure Research, Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, 510515 China
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Liu MB, Xu SR, He Y, Deng GH, Sheng HF, Huang XM, Ouyang CY, Zhou HW. Diverse vaginal microbiomes in reproductive-age women with vulvovaginal candidiasis. PLoS One 2013; 8:e79812. [PMID: 24265786 PMCID: PMC3827160 DOI: 10.1371/journal.pone.0079812] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 10/04/2013] [Indexed: 11/19/2022] Open
Abstract
Vulvovaginal candidiasis (VVC) is one of the most prevalent vaginal infectious diseases, and there are controversial reports regarding the diversity of the associated vaginal microbiota. We determined the vaginal microbial community in patients with VVC, bacterial vaginosis (BV), and mixed infection of VVC and BV using Illumina sequencing of 16S rRNA tags. Our results revealed for the first time the highly variable patterns of the vaginal microbiome from VVC patients. In general, the alpha-diversity results of species richness and evenness showed the following order: normal control < VVC only < mixed BV and VVC infection < BV only. The beta-diversity comparison of community structures also showed an intermediate composition of VVC between the control and BV samples. A detailed comparison showed that, although the control and BV communities had typical patterns, the vaginal microbiota of VVC is complex. The mixed BV and VVC infection group showed a unique pattern, with a relatively higher abundance of Lactobacillus than the BV group and higher abundance of Prevotella, Gardnerella, and Atopobium than the normal control. In contrast, the VVC-only group could not be described by any single profile, ranging from a community structure similar to the normal control (predominated with Lactobacillus) to BV-like community structures (abundant with Gardnerella and Atopobium). Treatment of VVC resulted in inconsistent changes of the vaginal microbiota, with four BV/VVC samples recovering to a higher Lactobacillus level, whereas many VVC-only patients did not. These results will be useful for future studies on the role of vaginal microbiota in VVC and related infectious diseases.
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Affiliation(s)
- Mu-Biao Liu
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Su-Rong Xu
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan He
- Microbial Ecology Lab, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Guan-Hua Deng
- Microbial Ecology Lab, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Hua-Fang Sheng
- Microbial Ecology Lab, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Xue-Mei Huang
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Cai-Yan Ouyang
- Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Hong-Wei Zhou
- Microbial Ecology Lab, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
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He Y, Zhou BJ, Deng GH, Jiang XT, Zhang H, Zhou HW. Comparison of microbial diversity determined with the same variable tag sequence extracted from two different PCR amplicons. BMC Microbiol 2013; 13:208. [PMID: 24034943 PMCID: PMC3848352 DOI: 10.1186/1471-2180-13-208] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 09/12/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deep sequencing of the variable region of 16S rRNA genes has become the predominant tool for studying microbial ecology. As sequencing datasets have accumulated, meta-analysis of sequences obtained with different variable 16S rRNA gene targets and by different sequencing methods has become an intriguing prospect that remains to be evaluated experimentally. RESULTS We amplified a group of fecal samples using both V4F-V6R and V6F-V6R primer sets, excised the same V6 fragment from the two sets of Illumina sequencing data, and compared the resulting data in terms of the α-diversity, β-diversity, and community structure. Principal component analysis (PCA) comparing the microbial community structures of different datasets, including those with simulated sequencing errors, was very reliable. Procrustes analysis showed a high degree of concordance between the different datasets for both abundance-weighted and binary Jaccard distances (P < 0.05), and a meta-analysis of individual datasets resulted in similar conclusions. The Shannon's diversity index was consistent as well, with comparable values obtained for the different datasets and for the meta-analysis of different datasets. In contrast, richness estimators (OTU and Chao) varied significantly, and the meta-analysis of richness estimators was also biased. The community structures of the two datasets were obviously different and led to significant changes in the biomarkers identified by the LEfSe statistical tool. CONCLUSIONS Our results suggest that beta-diversity analysis and Shannon's diversity are relatively reliable for meta-analysis, while community structures and biomarkers are less consistent. These results should be useful for future meta-analyses of microbiomes from different data sources.
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Affiliation(s)
- Yan He
- Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China.
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Jiang XT, Peng X, Deng GH, Sheng HF, Wang Y, Zhou HW, Tam NFY. Illumina sequencing of 16S rRNA tag revealed spatial variations of bacterial communities in a mangrove wetland. MICROBIAL ECOLOGY 2013; 66:96-104. [PMID: 23649297 DOI: 10.1007/s00248-013-0238-8] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/21/2013] [Indexed: 05/19/2023]
Abstract
The microbial community plays an essential role in the high productivity in mangrove wetlands. A proper understanding of the spatial variations of microbial communities will provide clues about the underline mechanisms that structure microbial groups and the isolation of bacterial strains of interest. In the present study, the diversity and composition of the bacterial community in sediments collected from four locations, namely mudflat, edge, bulk, and rhizosphere, within the Mai Po Ramsar Wetland in Hong Kong, SAR, China were compared using the barcoded Illumina paired-end sequencing technique. Rarefaction results showed that the bulk sediment inside the mature mangrove forest had the highest bacterial α-diversity, while the mudflat sediment without vegetation had the lowest. The comparison of β-diversity using principal component analysis and principal coordinate analysis with UniFrac metrics both showed that the spatial effects on bacterial communities were significant. All sediment samples could be clustered into two major groups, inner (bulk and rhizosphere sediments collected inside the mangrove forest) and outer mangrove sediments (the sediments collected at the mudflat and the edge of the mangrove forest). With the linear discriminate analysis scores larger than 3, four phyla, namely Actinobacteria, Acidobacteria, Nitrospirae, and Verrucomicrobia, were enriched in the nutrient-rich inner mangrove sediments, while abundances of Proteobacteria and Deferribacterias were higher in outer mangrove sediments. The rhizosphere effect of mangrove plants was also significant, which had a lower α-diversity, a higher amount of Nitrospirae, and a lower abundance of Proteobacteria than the bulk sediment nearby.
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Affiliation(s)
- Xiao-Tao Jiang
- Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China, 510515
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Comparison of the levels of bacterial diversity in freshwater, intertidal wetland, and marine sediments by using millions of illumina tags. Appl Environ Microbiol 2012; 78:8264-71. [PMID: 23001654 DOI: 10.1128/aem.01821-12] [Citation(s) in RCA: 479] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Sediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched with Acidobacteria, Nitrospira, Verrucomicrobia, Alphaproteobacteria, and Betaproteobacteria. The intertidal sediment had a unique community with diverse primary producers (such as Chloroflexi, Bacillariophyta, Gammaproteobacteria, and Epsilonproteobacteria) as well as saprophytic microbes (such as Actinomycetales, Bacteroidetes, and Firmicutes). The marine sediment had a higher abundance of Gammaproteobacteria and Deltaproteobacteria, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.
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Bonder MJ, Abeln S, Zaura E, Brandt BW. Comparing clustering and pre-processing in taxonomy analysis. ACTA ACUST UNITED AC 2012; 28:2891-7. [PMID: 22962346 DOI: 10.1093/bioinformatics/bts552] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Massively parallel sequencing allows for rapid sequencing of large numbers of sequences in just a single run. Thus, 16S ribosomal RNA (rRNA) amplicon sequencing of complex microbial communities has become possible. The sequenced 16S rRNA fragments (reads) are clustered into operational taxonomic units and taxonomic categories are assigned. Recent reports suggest that data pre-processing should be performed before clustering. We assessed combinations of data pre-processing steps and clustering algorithms on cluster accuracy for oral microbial sequence data. RESULTS The number of clusters varied up to two orders of magnitude depending on pre-processing. Pre-processing using both denoising and chimera checking resulted in a number of clusters that was closest to the number of species in the mock dataset (25 versus 15). Based on run time, purity and normalized mutual information, we could not identify a single best clustering algorithm. The differences in clustering accuracy among the algorithms after the same pre-processing were minor compared with the differences in accuracy among different pre-processing steps. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT bonder.m.j@gmail.com or b.brandt@acta.nl
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Affiliation(s)
- Marc J Bonder
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam-ACTA, University of Amsterdam and VU University Amsterdam, VU University Amsterdam, The Netherlands.
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