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Zhang J, Lu X, Cheng Z, Zou D, Shi W, Wang T. Alterations of conjunctival microbiota associated with orthokeratology lens wearing in myopic children. BMC Microbiol 2023; 23:397. [PMID: 38087200 PMCID: PMC10717905 DOI: 10.1186/s12866-023-03042-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 10/03/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Orthokeratology (OK) lens wear increases the risk of bacterial infection, but little is known about the microbiota of the conjunctival sac in myopic children wearing OK lenses. This study aimed to investigate the changes of conjunctival microbiota in children after treatment with OK lenses using 16 S rDNA sequencing. METHODS Twenty-eight myopic children who had been continuously wearing OK lenses for 12 to 13 months were enrolled in this prospective study. Twenty-two gender- and age-matched myopic children who had not worn OK lenses or discontinued OK lens wear at least 1 year ago were recruited as controls. Conjunctival swabs from each participant were collected for exploration of the microbiota profiles, targeting the V3-V4 regions of the 16 S rRNA gene by MiSeq sequencing. The differences in the microbial community structure and diversity were also compared between groups. RESULTS The bacterial alpha diversity indices in the OK lens group were not different from those in the non-wearer group (P > 0.05, Wilcoxon test), while beta diversity examined using principle coordinate analysis of unweighted UniFrac divided the two groups into different clusters. Proteobacteria, Bacteroidetes, and Firmicutes were the abundant phyla in the conjunctival sac microbiota in both groups (P < 0.05, Mann-Whitney U test). Among children in the OK lens group, the Linear discriminant analysis Effect Size identified the compositional changes in OK lens-associated bacteria. Key functional genera such as Blautia, Parasutterella, and Muribaculum were enriched, whereas Brevundimonas, Acinetobacter, Proteus, and Agathobacter decreased significantly (P < 0.05, Mann-Whitney U test). Phylogenetic investigation of communities by reconstruction of unobserved states also showed altered bacterial metabolic pathways in OK lens-associated microbiota. Moreover, using receiver operating characteristic curves, Brevundimonas, Acinetobacter, Proteus, and Agathobacter alone (the area under the curve was all > 0.7500) or in combination (the area under the curve was 0.9058) were revealed to discriminate OK lens wearers from controls. CONCLUSIONS The relative abundance of the microbial community in the conjunctival sac of myopic children can alter after OK lens wear. Brevundimonas, Acinetobacter, Proteus, and Agathobacter may be candidate biomarkers to distinguish between OK lens wearers and non-wearers.
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Affiliation(s)
- Ju Zhang
- Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Qingdao, China
| | - Xiuhai Lu
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China
| | - Zhiwei Cheng
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China
| | - Dulei Zou
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Qingdao, China
- Medical College, Qingdao University, Qingdao, China
| | - Weiyun Shi
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China.
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Qingdao, China.
| | - Ting Wang
- Eye Hospital of Shandong First Medical University (Shandong Eye Hospital), 372 Jingsi Road, Jinan, 250021, China.
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Qingdao, China.
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Cheng Y, An N, Ishaq HM, Xu J. Ocular microbial dysbiosis and its linkage with infectious keratitis patients in Northwest China: A cross-sectional study. Microb Pathog 2023; 184:106371. [PMID: 37741304 DOI: 10.1016/j.micpath.2023.106371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
OBJECTIVES To evaluate the alteration of ocular surface microbiome of patients with infectious keratitis in northwest of China. METHODS The corneal scrapings, eyelid margin and conjunctiva samples were collected from 57 participants, who were divided into bacterial keratitis, fungal keratitis, viral keratitis and control group. The V3-V4 region of bacterial 16S rDNA in each sample was amplified and sequenced on the Illumina HiSeq 2500 sequencing platform, and the differences among different groups were compared bioinformatically. RESULTS Significant alterations of the microbiome were observed in alpha-diversity and beta-diversity analysis between the keratitis groups and the control group (p < 0.05). There was no significant differences between eyelid margin and conjunctiva samples in Alpha-Diversity analysis, but a significant difference between eyelid margin and corneal scraping samples in the keratitis group (p < 0.05, independent t-test). The abundances of Bacillus, Megamonas, Acinetobacter, and Rhodococcu were significantly elevated, while the abundance of Staphylococcus was decreased in the keratitis group compared to the control group. CONCLUSIONS The abundance of the ocular microbiome in patients with bacterial keratitis, fungal keratitis, or viral keratitis was significantly higher than those in the control group. Keratitis patients may have ecological disorder on ocular surface microbiome compared with controls. We believe that the conjunctiva and eyelid margin microbiome combined analysis can more comprehensively reflect the composition and abundance of ocular surface microbiome.
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Affiliation(s)
- Yan Cheng
- Department of Microbiology and Immunology, Key Laboratory of Environment and Genes Related to Diseases of Chinese Ministry of Education, School of Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Na An
- The Fist Affiliated Hospital of Northwestern University, Department of Ophthalmology, The Xi'an Fist Hospital, Shaanxi Institute of Ophthalmology, China
| | - Hafiz Muhammad Ishaq
- Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture Multan, Pakistan
| | - Jiru Xu
- Department of Microbiology and Immunology, Key Laboratory of Environment and Genes Related to Diseases of Chinese Ministry of Education, School of Medicine, Xi'an Jiaotong University, Xi'an, China.
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Asao K, Hashida N, Motooka D, Tsukamoto T, Nakamura S, Maruyama K, Nishida K. Fungal dysbiosis and decreased tear mucin at the conjunctiva in patients with conjunctival mucosa-associated lymphoid tissue lymphoma. BMJ Open Ophthalmol 2023; 8:e001360. [PMID: 37777252 PMCID: PMC10546124 DOI: 10.1136/bmjophth-2023-001360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/13/2023] [Indexed: 10/02/2023] Open
Abstract
OBJECTIVE This study aimed to examine the differences in the fungal microbiome between patients with conjunctival mucosa-associated lymphoid tissue (MALT) and healthy controls using metagenomic analysis. METHODS AND ANALYSIS This case-control study was conducted at Osaka University Hospital in Osaka, Japan, from April 2015 to March 2022. Twenty-five consecutive patients with conjunctival MALT lymphoma and 25 healthy volunteers were included. Metagenomic analysis using Internal Transcribed Spacer (ITS)1 deep sequencing and hierarchical clustering was performed to investigate differences in the fungal microbiome. To assess tear environmental change, we measured tear mucin concentrations using ELISA. RESULTS Detailed analyses showed fungal dysbiosis and changes in β-diversity within the conjunctiva of patients with conjunctival MALT lymphoma. Hierarchical clustering revealed that the participants could be divided into three clusters according to the Malassezia abundance: cluster I (Malassezia abundance above 70%), cluster II (Malassezia abundance 25%-70%) and cluster II (Malassezia abundance below 25%). Most patients were included in cluster I, whereas most of healthy controls were included in cluster III. The differences were significant. Tear mucin concentrations were significantly lower in patients with MALT compared with healthy controls. CONCLUSION The metagenomic analysis using ITS1 deep sequencing was useful for identifying the differences in commensal fungi between patients with MALT lymphoma and healthy individuals. The increased prevalence of the Malassezia genus and the decreased levels of tear mucin can lead to an allergic response of the conjunctiva, resulting in the pathogenesis associated with conjunctival MALT lymphoma. Therefore, it may be beneficial to initiate treatment when a high abundance Malassezia is detected.
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Affiliation(s)
- Kazunobu Asao
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Noriyasu Hashida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Teruhisa Tsukamoto
- Biology and Translational Research Unit, Department of Medical Innovations, New Drug Research Division, Otsuka Pharmaceutical. Co. Ltd, Naruto, Tokushima, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kazuichi Maruyama
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Vision Informatics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kohji Nishida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
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Ashby NS, Johnson TJ, Castillo-Ronquillo Y, Payne CJ, Davenport C, Hoopes PC, Moshirfar M. Cutibacterium (Formerly Propionibacterium ) acnes Keratitis: A Review. Eye Contact Lens 2023; 49:212-218. [PMID: 36888541 DOI: 10.1097/icl.0000000000000975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
ABSTRACT Infectious keratitis is a devastating cause of vision loss worldwide. Cutibacterium acnes ( C. acnes ), a commensal bacterium of the skin and ocular surface, is an underrecognized but important cause of bacterial keratitis. This review presents the most comprehensive and up-to-date information for clinicians regarding the risk factors, incidence, diagnosis, management, and prognosis of C. acnes keratitis (CAK). Risk factors are similar to those of general bacterial keratitis and include contact lens use, past ocular surgery, and trauma. The incidence of CAK may be approximately 10%, ranging from 5% to 25% in growth-positive cultures. Accurate diagnosis requires anaerobic blood agar and a long incubation period (≥7 days). Typical clinical presentation includes small (<2 mm) ulcerations with deep stromal infiltrate causing an anterior chamber cell reaction. Small, peripheral lesions are usually resolved, and patients recover a high visual acuity. Severe infections causing VA of 20/200 or worse are common and often do not significantly improve even after treatment. Vancomycin is considered the most potent antibiotic against CAK, although other antibiotics such as moxifloxacin and ceftazidime are more commonly used as first-line treatment.
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Affiliation(s)
- Nathaniel S Ashby
- Creighton University School of Medicine (N.S.A.), Omaha, NE; Spencer Fox Eccles School of Medicine at the University of Utah (T.J.J.), Salt Lake City, UT; Hoopes Vision Research Center (Y.C.-R., C.J.P., C.D., P.C.H., M.M.), Hoopes Vision, Draper, UT; Case Western Reserve University School of Medicine (C.J.P.), Cleveland, OH; John A. Moran Eye Center (M.M.), Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, Salt Lake City, UT; and Utah Lions Eye Bank (M.M.), Murray, UT
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Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms. Int J Mol Sci 2022; 23:ijms232214223. [PMID: 36430699 PMCID: PMC9697482 DOI: 10.3390/ijms232214223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
Amplicon sequencing of bacterial or fungal marker sequences is currently the main method for the study of endophytic microorganisms in plants. However, it cannot obtain all types of microorganisms, including bacteria, fungi, protozoa, etc., in samples, nor compare the relative content between endophytic microorganisms and plants and between different types of endophytes. Therefore, it is necessary to develop a better analysis strategy for endophytic microorganism investigation. In this study, a new analysis strategy was developed to obtain endophytic microbiome information from plant transcriptome data. Results showed that the new strategy can obtain the composition of microbial communities and the relative content between plants and endophytic microorganisms, and between different types of endophytic microorganisms from the plant transcriptome data. Compared with the amplicon sequencing method, more endophytic microorganisms and relative content information can be obtained with the new strategy, which can greatly broaden the research scope and save the experimental cost. Furthermore, the advantages and effectiveness of the new strategy were verified with different analysis of the microbial composition, correlation analysis, inoculant content test, and repeatability test.
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Jing D, Jiang X, Ren X, Su J, Huang C, Yang J, Hao R, Li X. Metagenomic nanopore sequencing of ocular microbiome in patients with meibomian gland dysfunction. Front Med (Lausanne) 2022; 9:1045990. [PMID: 36438054 PMCID: PMC9682043 DOI: 10.3389/fmed.2022.1045990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/26/2022] [Indexed: 07/30/2023] Open
Abstract
PURPOSE To explore the composition of the ocular microbiome in patients with Meibomian gland dysfunction (MGD) using metagenomic nanopore sequencing. METHODS A total of 98 participants were recruited from September to December 2021, including 86 patients with MGD and 12 controls. Symptoms and signs of dry eye were assessed, and bacterial samples in the conjunctival sac (CS) and meibomian gland (MG) secretions were then identified by bacterial culture identification and metagenomic nanopore sequencing. RESULTS The positive rate of CS bacterial culture in the MGD group was significantly higher than that in the normal group. A more complex composition of bacterial genera was detected in the mild and moderate MGD groups than in the control. However, the severe MGD groups had the simplest composition of bacteria. Metagenomic nanopore sequencing detected more species of bacteria than traditional culture. CONCLUSION The CS and MG of MGD patients may have different degrees of bacterial microbiota imbalance. Metagenomic nanopore sequencing technology provides a new way for us to understand the composition of "real-world" ocular surface microorganisms.
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Affiliation(s)
- Dalan Jing
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Xiaodan Jiang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Xiaotong Ren
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Jie Su
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Chen Huang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
- Medical Research Center, Peking University Third Hospital, Beijing, China
| | - Jiarui Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Ran Hao
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xuemin Li
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
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Chen X, Yang F, Bai C, Shi Q, Hu S, Tang X, Peng L, Ding H. Bacillus velezensis Strain GUMT319 Reshapes Soil Microbiome Biodiversity and Increases Grape Yields. BIOLOGY 2022; 11:biology11101486. [PMID: 36290389 PMCID: PMC9598471 DOI: 10.3390/biology11101486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022]
Abstract
Bacillus velezensis strain GUMT319 is a rhizobacteria biocontrol agent that can control tobacco black shank disease. We took GUMT319 as a biological fertilizer on Vitis vinifera L. The test group was treated with GUMT319 for one year and the control group had a water treatment. Yields of GUMT319-treated grape groups were significantly increased compared to the controls. The average length and width of single grape fruit, weight of 100 grape fruits, the sugar/acid ratio, and the content of vitamin C were all increased in the GUMT319-treated grape group. The pH of the soil was higher and the contents of alkaline hydrolyzable nitrogen and available potassium were significantly lower in the GUMT319-treated groups than the controls. The soil microbial community composition was evaluated by 16S rDNA high-throughput sequencing, and the Shannon index and Simpson index all showed that soil microbes were more abundant in the GUMT319-treated group. These results indicate that GUMT319 is not only a biocontrol agent, but also a plant growth-promoting rihizobacteria. It can increase the yield of grape by altering the physical and chemical properties and the microbial community composition of the soil.
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Affiliation(s)
- Xiangru Chen
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Fang Yang
- Sino Green Agri-Biotech Co., Ltd., Beijing 102101, China
| | - Chunwei Bai
- Tonghe Zhiyuan (Beijing) Environmental Protection Technology Co., Ltd., Beijing 100036, China
| | - Qianrui Shi
- Liangshan Yi Autonomous Prefecture Bureau of Agriculture and Rural Affairs, Xichang 615000, China
| | - Shan Hu
- College of Tobacco Science, Guizhou University, Guiyang 550025, China
| | - Xianying Tang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Lijuan Peng
- College of Tobacco Science, Guizhou University, Guiyang 550025, China
| | - Haixia Ding
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
- Correspondence:
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Ting DSJ, Chodosh J, Mehta JS. Achieving diagnostic excellence for infectious keratitis: A future roadmap. Front Microbiol 2022; 13:1020198. [PMID: 36262329 PMCID: PMC9576146 DOI: 10.3389/fmicb.2022.1020198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 02/02/2023] Open
Affiliation(s)
- Darren S. J. Ting
- Academic Ophthalmology, School of Medicine, University of Nottingham, Nottingham, United Kingdom,Department of Ophthalmology, Queen's Medical Centre, Nottingham, United Kingdom
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear and Harvard Medical School, Boston, MA, United States
| | - Jodhbir S. Mehta
- Department of Cornea & Refractive Surgery, Singapore National Eye Centre, Singapore, Singapore,Singapore Eye Research Institute, Singapore, Singapore,*Correspondence: Jodhbir S. Mehta
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