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He Y, Wu W, Wu S, Zheng HM, Li P, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZDX, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Xu JB, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Ma WJ, Zhou HW. Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis. Microbiome 2018; 6:172. [PMID: 30249275 PMCID: PMC6154942 DOI: 10.1186/s40168-018-0557-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/07/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND The metabolic syndrome (MetS) epidemic is associated with economic development, lifestyle transition and dysbiosis of gut microbiota, but these associations are rarely studied at the population scale. Here, we utilised the Guangdong Gut Microbiome Project (GGMP), the largest Eastern population-based gut microbiome dataset covering individuals with different economic statuses, to investigate the relationships between the gut microbiome and host physiology, diet, geography, physical activity and socioeconomic status. RESULTS At the population level, 529 OTUs were significantly associated with MetS. OTUs from Proteobacteria and Firmicutes (other than Ruminococcaceae) were mainly positively associated with MetS, whereas those from Bacteroidetes and Ruminococcaceae were negatively associated with MetS. Two hundred fourteen OTUs were significantly associated with host economic status (140 positive and 74 negative associations), and 157 of these OTUs were also MetS associated. A microbial MetS index was formulated to represent the overall gut dysbiosis of MetS. The values of this index were significantly higher in MetS subjects regardless of their economic status or geographical location. The index values did not increase with increasing personal economic status, although the prevalence of MetS was significantly higher in people of higher economic status. With increased economic status, the study population tended to consume more fruits and vegetables and fewer grains, whereas meat consumption was unchanged. Sedentary time was significantly and positively associated with higher economic status. The MetS index showed an additive effect with sedentary lifestyle, as the prevalence of MetS in individuals with high MetS index values and unhealthy lifestyles was significantly higher than that in the rest of the population. CONCLUSIONS The gut microbiome is associated with MetS and economic status. A prolonged sedentary lifestyle, rather than Westernised dietary patterns, was the most notable lifestyle change in our Eastern population along with economic development. Moreover, gut dysbiosis and a Western lifestyle had an additive effect on increasing MetS prevalence.
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Affiliation(s)
- Yan He
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
| | - Wei Wu
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, 510515 China
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430 China
| | - Shan Wu
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, 510515 China
| | - Hui-Min Zheng
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, 510515 China
| | - Pan Li
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, 510515 China
| | - Hua-Fang Sheng
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
| | - Mu-Xuan Chen
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
| | - Zi-Hui Chen
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430 China
| | - Gui-Yuan Ji
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430 China
| | - Zhong-Dai-Xi Zheng
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, 510515 China
| | - Prabhakar Mujagond
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
| | - Xiao-Jiao Chen
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
| | - Zu-Hua Rong
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
- Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou, 510515 China
| | - Peng Chen
- Department of Pathophysiology, Southern Medical University, Guangzhou, 510515 China
| | - Li-Yi Lyu
- Shenzhen Fun-Poo Biotech Co., Ltd., Shenzhen, 518000 China
| | - Xian Wang
- Shenzhen Fun-Poo Biotech Co., Ltd., Shenzhen, 518000 China
| | - Jia-Bao Xu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, 510515 China
| | - Chong-Bin Wu
- Shenzhen Fun-Poo Biotech Co., Ltd., Shenzhen, 518000 China
| | - Nan Yu
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
| | - Yan-Jun Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430 China
| | - Jia Yin
- Department of Neurology, NanFang Hospital, Southern Medical University, Guangzhou, 510515 China
| | - Jeroen Raes
- Department of Microbiology and Immunology, KU Leuven–University of Leuven, Leuven, Belgium
- VIB, Center for the Biology of Disease, Leuven, Belgium
- Vrije Universiteit Brussel, Faculty of Sciences and Bioengineering Sciences, Microbiology Unit, Brussels, Belgium
| | - Wen-Jun Ma
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430 China
| | - Hong-Wei Zhou
- State Key Laboratory of Organ Failure Research, Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 China
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Zhu XX, Yang XJ, Chao YL, Zheng HM, Sheng HF, Liu HY, He Y, Zhou HW. The Potential Effect of Oral Microbiota in the Prediction of Mucositis During Radiotherapy for Nasopharyngeal Carcinoma. EBioMedicine 2017; 18:23-31. [PMID: 28216066 PMCID: PMC5405060 DOI: 10.1016/j.ebiom.2017.02.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/16/2017] [Accepted: 02/03/2017] [Indexed: 12/17/2022] Open
Abstract
Background Oral mucositis is probably the most debilitating complication that can arise in treating a patient with head and neck cancer. Little is known about the impacts of oral microbiota on the initiation and progression of mucositis. Methods Based on 16S rRNA gene sequencing, dynamic changes in oral bacterial profile as well as correlations between the severity of mucositis and bacterial shifts during radiotherapy were investigated. Findings Our results revealed that bacterial community structure altered progressively during radiation therapy, in parallel with a marked increase in the relative abundance of some Gram-negative bacteria. Patients who eventually developed severe mucositis harbored a significantly lower bacterial alpha diversity and higher abundance of Actinobacillus during the phase of erythema – patchy mucositis. Accordingly, a random forest model for predicting exacerbation of mucositis was generated, which achieved a high predictive accuracy (AUC) of 0.89. Interpretation Oral microbiota changes correlate with the progression and aggravation of radiotherapy-induced mucositis in patients with nasopharyngeal carcinoma. Microbiota-based strategies can be used for the early prediction and prevention of the incidence of severe mucositis during radiotherapy. The oral microbiota of NPC patients are different to that of healthy persons. The biodiversity of oral microbiota changed significantly as mucositis progressed during radiotherapy. Oral microbiota represents a potential strategy for predicting the aggravation of severe mucositis during radiotherapy.
Oral or oropharyngeal mucositis is the most common side effect of radiation therapy for head and neck cancers. In this prospective cohort study, we found that changes in an oral microbial community correlated with the progression and aggravation of radiotherapy-induced mucositis in the patients with nasopharyngeal carcinoma; and patients who eventually developed severe mucositis transiently harbored a notably higher proportion of Actinobacillus during a mild phase of mucositis, which may potentially play a role in the aggravation of severe mucosal lesions. Moreover, our findings also showed that microbiota-based strategies can be used for the early prediction of the incidence of severe mucositis during radiotherapy.
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Affiliation(s)
- Xiao-Xia Zhu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xiao-Jun Yang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yi-Lan Chao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Hui-Min Zheng
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Hua-Fang Sheng
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Hai-Yue Liu
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yan He
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Hong-Wei Zhou
- State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China.
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Wang S, Xia GH, He Y, Liao SX, Yin J, Sheng HF, Zhou HW. [Distribution characteristics of trimethylamine N-oxide and its association with gut microbiota]. Nan Fang Yi Ke Da Xue Xue Bao 2016; 36:455-460. [PMID: 27113169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To analyze the distribution of trimethylamine N-oxide (TMAO) in healthy adults with different risk factors and explore its association with gut microbiota. METHODS We collected fasting blood samples and fresh fecal samples from 181 subjects without atherogenesis in the carotid arteries. Plasma TMAO levels of the subjects were determined using stable isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS). The fecal DNA was extracted, and the 16S rRNA V4 tags were amplified and sequenced by Illumina HiSeq 2000. The association between TMAO and classical cardiovascular risk factors were analyzed. Gut microbial community structure was analyzed with QIIME, and LEfSe was used to identify the biomarkers. RESULTS The median (IQR) TMAO level was 2.66 (1.96-4.91) µmol/L in the subjects. TMAO level was significantly correlated with body mass index and operational taxonomic units (OTU). Individuals with high TMAO levels were found to have abundant Clostridiales, Phascolarctobacterium, Oscillibacter, and Alistipes but less abundant Anaerosprobacter. CONCLUSION Chinese subjects have in general low levels of TMAO. TMAO levels are not significantly correlated with the classical cardiovascular risk factors or the gut microbial structures.
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Affiliation(s)
- Shan Wang
- Department of Environmental Hygiene, School of Public Health and Tropical Medicine, Department of Neurology, Southern Medical University, Guangzhou 510515, China. E-mail:
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Huang YE, Wang Y, He Y, Ji Y, Wang LP, Sheng HF, Zhang M, Huang QT, Zhang DJ, Wu JJ, Zhong M, Zhou HW. Homogeneity of the vaginal microbiome at the cervix, posterior fornix, and vaginal canal in pregnant Chinese women. Microb Ecol 2015; 69:407-14. [PMID: 25230887 DOI: 10.1007/s00248-014-0487-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 08/25/2014] [Indexed: 05/21/2023]
Abstract
The vaginal microbiome is an emerging concern in prenatal health. Because the sampling process of vaginal microbiota may pose potential risks for pregnant women, the choice of sampling site should be carefully considered. However, whether the microbial diversity is different across various sampling sites has been controversial. In the present study, three repeated swabs were collected at the cervix (C), posterior fornix (P), and vaginal canal (V) from 34 Chinese women during different pregnancy stages, and vaginal species were determined using the Illumina sequencing of 16S rRNA tag sequences. The identified microbiomes were classified into four community state types (CSTs): CST I (dominated by L. crispatus), CST II (dominated by L. gasseri), CST III (dominated by L. iners), and CST IV-A (characterized by a low abundance of Lactobacillus, but with proportions of various species previously shown to be associated with bacterial vaginosis). All individuals had consistent CST at the three sampling sites regardless of pregnancy stage and CST group. In addition, there was little heterogeneity across community structures within each individual, as determined by LEfSe, indicating high vaginal microbiome homogeneity at the three sampling sites. The present study also revealed different beta diversity during pregnancy stages. The vaginal microbiome variation among women during trimester T1 (9 ± 2.6 weeks) is larger than that of non-pregnant women and women from other trimesters, as demonstrated by the UniFrac distance (P < 0.05). In particular, the present study is the first one that demonstrates the notably difference of vaginal microbiome of postpartum women compare to women in gestation. These results will be useful for future studies of the vaginal microbiota during pregnancy.
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Affiliation(s)
- Yi-E Huang
- State Key Laboratory of Organ Failure Research, Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, China, 510515
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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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. Microb Ecol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Jiang XT, Zhang H, Sheng HF, Wang Y, He Y, Zou F, Zhou HW. Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons. PLoS One 2012; 7:e30230. [PMID: 22253923 PMCID: PMC3256218 DOI: 10.1371/journal.pone.0030230] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 12/12/2011] [Indexed: 11/18/2022] Open
Abstract
Clustering 16S/18S rRNA amplicon sequences into operational taxonomic units (OTUs) is a critical step for the bioinformatic analysis of microbial diversity. Here, we report a pipeline for selecting OTUs with a relatively low computational demand and a high degree of accuracy. This pipeline is referred to as two-stage clustering (TSC) because it divides tags into two groups according to their abundance and clusters them sequentially. The more abundant group is clustered using a hierarchical algorithm similar to that in ESPRIT, which has a high degree of accuracy but is computationally costly for large datasets. The rarer group, which includes the majority of tags, is then heuristically clustered to improve efficiency. To further improve the computational efficiency and accuracy, two preclustering steps are implemented. To maintain clustering accuracy, all tags are grouped into an OTU depending on their pairwise Needleman-Wunsch distance. This method not only improved the computational efficiency but also mitigated the spurious OTU estimation from ‘noise’ sequences. In addition, OTUs clustered using TSC showed comparable or improved performance in beta-diversity comparisons compared to existing OTU selection methods. This study suggests that the distribution of sequencing datasets is a useful property for improving the computational efficiency and increasing the clustering accuracy of the high-throughput sequencing of PCR amplicons. The software and user guide are freely available at http://hwzhoulab.smu.edu.cn/paperdata/.
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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
| | - Hai Zhang
- NetworkCenter, Southern Medical University, Guangzhou, Guangdong, China
| | - Hua-Fang Sheng
- Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu Wang
- Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Yan He
- Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Fei Zou
- Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Hong-Wei Zhou
- Department of Environmental Health, School of Public Health and Tropical Medicine, Southern Medical University, Guangzhou, Guangdong, China
- * E-mail:
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Abstract
In order to study the role of calmodulin (CaM) in the proliferation of lung cancer cells, the CaM level of the specimens of 40 cases of primary lung cancers and the DNA content of the specimens of 35 cases of primary lung cancers were determined with phosphodiesterase assay and flow cytometry respectively. It was found that the CaM level of lung cancers was significantly higher than that of host lungs, benign lung diseases and normal lungs (p<0.001) and that it was significantly correlated with the histopathological grading and TNM staging of the lung cancers. It was also found that the cellular DNA content of lung cancers, like the CaM level, was also significantly higher than that of benign lung diseases and normal lungs (p<0.001). There was a significant positive correlation between the cellular DNA content and tissue CaM level in lung cancers (r=0.885). It is believed that CaM plays an important role in the proliferation of lung cancer cells through the mechanism of the promotion of an uncontrolled synthesis of DNA in the cells. Consequently, it is inferred that CaM antagonists may be tried as a chemotherapeutic agent for lung cancer.
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Affiliation(s)
- G X Liu
- Department of Respiratory Disease, Southwest Hospital, Third Military Medical University, Gaotanyan, People's Republic of China
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