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Huang Y, Cao J, Zhu M, Wang Z, Jin Z, Xiong Z. Nontoxigenic Bacteroides fragilis: A double-edged sword. Microbiol Res 2024; 286:127796. [PMID: 38870618 DOI: 10.1016/j.micres.2024.127796] [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: 09/23/2023] [Revised: 04/12/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024]
Abstract
The contribution of commensal microbes to human health and disease is unknown. Bacteroides fragilis (B. fragilis) is an opportunistic pathogen and a common colonizer of the human gut. Nontoxigenic B. fragilis (NTBF) and enterotoxigenic B. fragilis (ETBF) are two kinds of B. fragilis. NTBF has been shown to affect the host immune system and interact with gut microbes and pathogenic microbes. Previous studies indicated that certain strains of B. fragilis have the potential to serve as probiotics, based on their observed relationship with the immune system. However, several recent studies have shown detrimental effects on the host when beneficial gut bacteria are found in the digestive system or elsewhere. In some pathological conditions, NTBF may have adverse reactions. This paper presents a comprehensive analysis of NTBF ecology from the host-microbe perspective, encompassing molecular disease mechanisms analysis, bacteria-bacteria interaction, bacteria-host interaction, and the intricate ecological context of the gut. Our review provides much-needed insights into the precise application of NTBF.
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Affiliation(s)
- Yumei Huang
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiali Cao
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengpei Zhu
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ziwen Wang
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ze Jin
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhifan Xiong
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Spörri L, Uldry AC, Kreuzer M, Herzog EL, Zinkernagel MS, Unterlauft JD, Zysset-Burri DC. Exploring the Ocular Surface Microbiome and Tear Proteome in Glaucoma. Int J Mol Sci 2024; 25:6257. [PMID: 38892444 PMCID: PMC11172891 DOI: 10.3390/ijms25116257] [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: 03/30/2024] [Revised: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Although glaucoma is a leading cause of irreversible blindness worldwide, its pathogenesis is incompletely understood, and intraocular pressure (IOP) is the only modifiable risk factor to target the disease. Several associations between the gut microbiome and glaucoma, including the IOP, have been suggested. There is growing evidence that interactions between microbes on the ocular surface, termed the ocular surface microbiome (OSM), and tear proteins, collectively called the tear proteome, may also play a role in ocular diseases such as glaucoma. This study aimed to find characteristic features of the OSM and tear proteins in patients with glaucoma. The whole-metagenome shotgun sequencing of 32 conjunctival swabs identified Actinobacteria, Firmicutes, and Proteobacteria as the dominant phyla in the cohort. The species Corynebacterium mastitidis was only found in healthy controls, and their conjunctival microbiomes may be enriched in genes of the phospholipase pathway compared to glaucoma patients. Despite these minor differences in the OSM, patients showed an enrichment of many tear proteins associated with the immune system compared to controls. In contrast to the OSM, this emphasizes the role of the proteome, with a potential involvement of immunological processes in glaucoma. These findings may contribute to the design of new therapeutic approaches targeting glaucoma and other associated diseases.
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Affiliation(s)
- Livia Spörri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
| | | | - Marco Kreuzer
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, 3012 Bern, Switzerland;
| | - Elio L. Herzog
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Martin S. Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
| | - Jan D. Unterlauft
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
| | - Denise C. Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
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3
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Omar WEW, Singh G, McBain AJ, Cruickshank F, Radhakrishnan H. Gut Microbiota Profiles in Myopes and Nonmyopes. Invest Ophthalmol Vis Sci 2024; 65:2. [PMID: 38691091 PMCID: PMC11077909 DOI: 10.1167/iovs.65.5.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024] Open
Abstract
Purpose To identify compositional differences in the gut microbiome of nonmyopes (NM) and myopes using 16S ribosomal RNA sequencing and to investigate whether the microbiome may contribute to the onset or progression of the condition. Methods Faecal samples were collected from 52 adult participants, of whom 23 were NM, 8 were progressive myopes (PM), and 21 were stable myopes (SM). The composition of the gut microbiota in each group was analysed using 16S ribosomal RNA gene sequencing. Results There were no significant differences in alpha and beta diversity between the three groups (NM, PM, and SM). However, the distributions of Bifidobacterium, Bacteroides, Megamonas, Faecalibacterium, Coprococcus, Dorea, Roseburia, and Blautia were significantly higher in the myopes (SM and PM combined) when compared with emmetropes. The myopes exhibited significantly greater abundance of bacteria that are linked to the regulation of dopaminergic signalling, such as Clostridium, Ruminococcus, Bifidobacterium, and Bacteroides. Individuals with stable myopia were found to have a significantly higher proportion of Prevotella copri than those with progressive myopia. Bifidobacterium adolescentis, a gamma-aminobutyric acid (GABA)-producing bacterium, was significantly higher in all myopes than in NM and, in the comparison between SM and PM, it is significantly higher in SM. B. uniformis and B. fragilis, both GABA-producing Bacteroides, were present in relatively high abundance in all myopes and in SM compared with PM, respectively. Conclusions The presence of bacteria related to dopamine effect and GABA-producing bacteria in the gut microbiome of myopes may suggest a role of these microorganisms in the onset and progression of myopia.
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Affiliation(s)
- Wan E. W. Omar
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Faculty of Health Sciences, Centre for Optometry Studies, Universiti Teknologi MARA (UiTM), Selangor, Malaysia
| | - Gurdeep Singh
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Andrew J. McBain
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Fiona Cruickshank
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Hema Radhakrishnan
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
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4
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Labetoulle M, Baudouin C, Benitez Del Castillo JM, Rolando M, Rescigno M, Messmer EM, Aragona P. How gut microbiota may impact ocular surface homeostasis and related disorders. Prog Retin Eye Res 2024; 100:101250. [PMID: 38460758 DOI: 10.1016/j.preteyeres.2024.101250] [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: 10/06/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
Changes in the bacterial flora in the gut, also described as gut microbiota, are readily acknowledged to be associated with several systemic diseases, especially those with an inflammatory, neuronal, psychological or hormonal factor involved in the pathogenesis and/or the perception of the disease. Maintaining ocular surface homeostasis is also based on all these four factors, and there is accumulating evidence in the literature on the relationship between gut microbiota and ocular surface diseases. The mechanisms involved are mostly interconnected due to the interaction of central and peripheral neuronal networks, inflammatory effectors and the hormonal system. A better understanding of the influence of the gut microbiota on the maintenance of ocular surface homeostasis, and on the onset or persistence of ocular surface disorders could bring new insights and help elucidate the epidemiology and pathology of ocular surface dynamics in health and disease. Revealing the exact nature of these associations could be of paramount importance for developing a holistic approach using highly promising new therapeutic strategies targeting ocular surface diseases.
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Affiliation(s)
- Marc Labetoulle
- Ophthalmology Départment, Hopital Bicetre, APHP, Université Paris-Saclay, IDMIT Infrastructure, Fontenay-aux-Roses Cedex, France; Hôpital National de la Vision des Quinze, Vingts, IHU ForeSight, Paris Saclay University, Paris, France.
| | - Christophe Baudouin
- Hôpital National de la Vision des Quinze, Vingts, IHU ForeSight, Paris Saclay University, Paris, France
| | - Jose M Benitez Del Castillo
- Departamento de Oftalmología, Hospital Clínico San Carlos, Clínica Rementeria, Instituto Investigaciones Oftalmologicas Ramon Castroviejo, Universidad Complutense, Madrid, Spain
| | - Maurizio Rolando
- Ocular Surface and Dry Eye Center, ISPRE Ophthalmics, Genoa, Italy
| | - Maria Rescigno
- IRCCS Humanitas Research Hospital, via Manzoni 56, Rozzano, 20089, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, Pieve Emanuele, 20090, MI, Italy
| | | | - Pasquale Aragona
- Department of Biomedical Sciences, Ophthalmology Clinic, University of Messina, Messina, Italy
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5
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Ghenciu LA, Faur AC, Bolintineanu SL, Salavat MC, Maghiari AL. Recent Advances in Diagnosis and Treatment Approaches in Fungal Keratitis: A Narrative Review. Microorganisms 2024; 12:161. [PMID: 38257986 PMCID: PMC10820712 DOI: 10.3390/microorganisms12010161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Fungal keratitis represents a potentially sight-threatening infection associated with poor prognosis, as well as financial burden. Novel diagnostic methods include polymerase-chain-reaction (PCR)-based approaches, metagenomic deep sequences, in vivo confocal microscopy, and antifungal susceptibility testing. The ideal therapeutic approaches and outcomes have been widely discussed in recent times, with early therapy being of the utmost importance for the preservation of visual acuity, minimizing corneal damage and reducing the scar size. However, combination therapy can be more efficacious compared to monotherapy. Understanding the pathogenesis, early diagnosis, and prevention strategies can be of great importance. In this narrative, we discuss the recent progress that may aid our understanding of the diagnosis, treatment, and prevention of mycotic keratitis.
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Affiliation(s)
- Laura Andreea Ghenciu
- Department III Functional Sciences, Victor Babes University of Medicine and Pharmacy, E. Murgu Sq., no. 2, 300041 Timisoara, Romania;
- Department IX Surgery, Discipline of Ophtalmology, Victor Babes University of Medicine and Pharmacy, E. Murgu Sq., no. 2, 300041 Timisoara, Romania;
| | - Alexandra Corina Faur
- Department of Anatomy and Embryology, Victor Babes University of Medicine and Pharmacy, E. Murgu Sq., no. 2, 300041 Timisoara, Romania; (S.L.B.); (A.L.M.)
| | - Sorin Lucian Bolintineanu
- Department of Anatomy and Embryology, Victor Babes University of Medicine and Pharmacy, E. Murgu Sq., no. 2, 300041 Timisoara, Romania; (S.L.B.); (A.L.M.)
| | - Madalina Casiana Salavat
- Department IX Surgery, Discipline of Ophtalmology, Victor Babes University of Medicine and Pharmacy, E. Murgu Sq., no. 2, 300041 Timisoara, Romania;
| | - Anca Laura Maghiari
- Department of Anatomy and Embryology, Victor Babes University of Medicine and Pharmacy, E. Murgu Sq., no. 2, 300041 Timisoara, Romania; (S.L.B.); (A.L.M.)
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Li C, Lu P. Association of Gut Microbiota with Age-Related Macular Degeneration and Glaucoma: A Bidirectional Mendelian Randomization Study. Nutrients 2023; 15:4646. [PMID: 37960299 PMCID: PMC10650403 DOI: 10.3390/nu15214646] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
The objective of this study was to examine the correlation between gut microbiota and both age-related macular degeneration (AMD) and glaucoma. Mendelian randomization studies were conducted utilizing the data sourced from the genome-wide association study (GWAS) database for the gut microbiome, AMD, and glaucoma. Single nucleotide polymorphism (SNP) estimates were summarized through five Mendelian randomization (MR) methods. We utilized Cochran's Q statistic to evaluate the heterogeneity of the instrumental variables (IVs). Additionally, we employed a "leave-one-out" approach to verify the stability of our findings. Inverse variance weighted (IVW) suggests that Eubacterium (oxidoreducens group) and Parabacteroides had a protective effect on AMD. Both weighted median and IVW suggest that Lachnospiraceae (NK4A136 group) and Ruminococcaceae (UCG009) had a protective effect on AMD. However, both weighted median and IVW suggest that Dorea had a risk effect on AMD. Similarly, The IVW of Eubacterium (ventriosum group) showed a risk effect on AMD. The weighted median of Eubacterium (nodatum group), Lachnospiraceae (NC2004 group), and Roseburia had a risk effect on glaucoma. IVW suggested that Ruminococcaceae (UCG004) had a risk effect on glaucoma. Reverse MR analysis found a causal link between Eubacterium (nodatum group) and glaucoma. No causal relationships were found between AMD or glaucoma and the other mentioned bacterial groups. No significant heterogeneity or evidence of horizontal pleiotropy was detected. This study found that certain gut bacteria had protective effects on AMD, while others may be risk factors for AMD or glaucoma. Likewise, reverse MR found that glaucoma led to an increased abundance of certain gut bacteria. Further trials are needed to clarify the specific mechanisms involved.
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Affiliation(s)
| | - Peirong Lu
- The First Affiliated Hospital of Soochow University, Pinghai Road 899, Suzhou 215005, China;
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7
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Russell MW, Muste JC, Kuo BL, Wu AK, Singh RP. Clinical trials targeting the gut-microbiome to effect ocular health: a systematic review. Eye (Lond) 2023; 37:2877-2885. [PMID: 36918627 PMCID: PMC10516887 DOI: 10.1038/s41433-023-02462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 11/21/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
Clinical trials targeting the gut microbiome to mitigate ocular disease are now on the horizon. A review of clinical data thus far is essential to determine future directions in this novel promising field. This review examines recent clinical trials that support the plausibility of a gut-eye axis, and may form the basis of novel clinical interventions. PubMed was queried for English language clinical studies examining the relationships between gut microbiota and ocular pathology. 25 studies were extracted from 828 candidate publications, which suggest that gut imbalance is associated with ocular pathology. Of these, only four interventional studies exist which suggest probiotic supplementation or fecal microbiota transplant can reduce symptoms of chalazion or uveitis. The gut-eye axis appears to hold clinical relevance, but current data is limited in sample size and design. Further investigation via longitudinal clinical trials may be warranted.
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Affiliation(s)
- Matthew W Russell
- Center for Ophthalmic Bioinformatics, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH, USA
| | - Justin C Muste
- Center for Ophthalmic Bioinformatics, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Blanche L Kuo
- Center for Ophthalmic Bioinformatics, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Anna K Wu
- Center for Ophthalmic Bioinformatics, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rishi P Singh
- Center for Ophthalmic Bioinformatics, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA.
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Marsaux B, Moens F, Marzorati M, Van de Wiele T. The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME ® Model. J Fungi (Basel) 2023; 9:877. [PMID: 37754985 PMCID: PMC10532570 DOI: 10.3390/jof9090877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 09/28/2023] Open
Abstract
From the estimated 2.2 to 3.8 million fungal species existing on Earth, only a minor fraction actively colonizes the human gastrointestinal tract. In fact, these fungi only represent 0.1% of the gastrointestinal biosphere. Despite their low abundance, fungi play dual roles in human health-both beneficial and detrimental. Fungal infections are often associated with bacterial dysbiosis following antibiotic use, yet our understanding of gut fungi-bacteria interactions remains limited. Here, we used the SHIME® gut model to explore the colonization of human fecal-derived fungi across gastrointestinal compartments. We accounted for the high inter-individual microbial diversity by using fecal samples from healthy adults, healthy babies, and Crohn's disease patients. Using quantitative Polymerase Chain Reaction and targeted next-generation sequencing, we demonstrated that SHIME®-colonized mycobiomes change upon loss of transient colonizers. In addition, SHIME® reactors from Crohn's disease patients contained comparable bacterial levels as healthy adults but higher fungal concentrations, indicating unpredictable correlations between fungal levels and total bacterial counts. Our findings rather link higher bacterial α-diversity to limited fungal growth, tied to colonization resistance. Hence, while healthy individuals had fewer fungi engrafting the colonic reactors, low α-diversity in impaired (Crohn's disease patients) or immature (babies) microbiota was associated with greater fungal abundance. To validate, antibiotic-treated healthy colonic microbiomes demonstrated increased fungal colonization susceptibility, and bacterial taxa that were negatively correlated with fungal expansion were identified. In summary, fungal colonization varied individually and transiently, and bacterial resistance to fungal overgrowth was more related with specific bacterial genera than total bacterial load. This study sheds light on fungal-bacterial dynamics in the human gut.
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Affiliation(s)
- Benoît Marsaux
- ProDigest B.V., Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (F.M.); (M.M.); (T.V.d.W.)
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Frédéric Moens
- ProDigest B.V., Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (F.M.); (M.M.); (T.V.d.W.)
| | - Massimo Marzorati
- ProDigest B.V., Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (F.M.); (M.M.); (T.V.d.W.)
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tom Van de Wiele
- ProDigest B.V., Technologiepark-Zwijnaarde 82, 9052 Ghent, Belgium; (F.M.); (M.M.); (T.V.d.W.)
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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Fu X, Tan H, Huang L, Chen W, Ren X, Chen D. Gut microbiota and eye diseases: a bibliometric study and visualization analysis. Front Cell Infect Microbiol 2023; 13:1225859. [PMID: 37621873 PMCID: PMC10445766 DOI: 10.3389/fcimb.2023.1225859] [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: 05/31/2023] [Accepted: 07/17/2023] [Indexed: 08/26/2023] Open
Abstract
Introduction Recently the role of gut microbial dysbiosis in many ocular disorders, including but not limited to uveitis, age-related macular degeneration (AMD), diabetic retinopathy (DR), dry eye, keratitis and orbitopathy is a hot research topic in the field. Targeting gut microbiota to treat these diseases has become an unstoppable trend. Bibliometric study and visualization analysis have become essential methods for literature analysis in the medical research field. We aim to depict this area's research hotspots and future directions by bibliometric software and methods. Methods We search all the related publications from the Web of Science Core Collection. Then, CiteSpace was applied to analyze and visualize the country distributions, dual-map overlay of journals, keyword bursts, and co-cited references. VOSviewer was employed to identify authors, co-cited authors, journals and co-cited journals and display the keyword co-occurrence networks. Results A total of 284 relevant publications were identified from 2009 to 2023. The number of studies has been small in the first five years and has grown steadily since 2016. These studies were completed by 1,376 authors from 41 countries worldwide, with the United States in the lead. Lin P has published the most papers while Horai R is the most co-cited author. The top journal and co-cited journal are both Investigative Ophthalmology & Visual Science. In the keyword co-occurrence network, except gut microbiota, inflammation becomes the keyword with the highest frequency. Co-citation analyses reveal that gut dysbiosis is involved in common immune- and inflammation-mediated eye diseases, including uveitis, diabetic retinopathy, age-related macular degeneration, dry eye, and Graves' orbitopathy, and the study of microbiomes is no longer limited to the bacterial populations. Therapeutic strategies that target the gut microbiota, such as probiotics, healthy diet patterns, and fecal microbial transplantation, are effective and critical to future research. Conclusions In conclusion, the bibliometric analysis displays the research hotspots and developmental directions of the involvement of gut microbiota in the pathogenesis and treatment of some ocular diseases. It provides an overview of this field's dynamic evolution and structural relationships.
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Affiliation(s)
- Xiangyu Fu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Haishan Tan
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Huang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Wenyue Chen
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiang Ren
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Danian Chen
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
- Research Laboratory of Ophthalmology and Vision Sciences, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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Zhang H, Mo Y. The gut-retina axis: a new perspective in the prevention and treatment of diabetic retinopathy. Front Endocrinol (Lausanne) 2023; 14:1205846. [PMID: 37469982 PMCID: PMC10352852 DOI: 10.3389/fendo.2023.1205846] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023] Open
Abstract
Diabetic retinopathy (DR) is a microvascular lesion that occurs as a complication of diabetes mellitus. Many studies reveal that retinal neurodegeneration occurs early in its pathogenesis, and abnormal retinal function can occur in patients without any signs of microvascular abnormalities. The gut microbiota is a large, diverse colony of microorganisms that colonize the human intestine. Studies indicated that the gut microbiota is involved in the pathophysiological processes of DR and plays an important role in its development. On the one hand, numerous studies demonstrated the involvement of gut microbiota in retinal neurodegeneration. On the other hand, alterations in gut bacteria in RD patients can cause or exacerbate DR. The present review aims to underline the critical relationship between gut microbiota and DR. After a brief overview of the composition, function, and essential role of the gut microbiota in ocular health, and the review explores the concept of the gut-retina axis and the conditions of the gut-retina axis crosstalk. Because gut dysbiosis has been associated with DR, the review intends to determine changes in the gut microbiome in DR, the hypothesized mechanisms linking to the gut-retina axis, and its predictive potential.
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Affiliation(s)
- Haiyan Zhang
- Chengdu University of Traditional Chinese Medicine, Sichuan, China
| | - Ya Mo
- Chengdu University of Traditional Chinese Medicine, Sichuan, China
- Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Sichuan, China
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Markoulli M, Ahmad S, Arcot J, Arita R, Benitez-Del-Castillo J, Caffery B, Downie LE, Edwards K, Flanagan J, Labetoulle M, Misra SL, Mrugacz M, Singh S, Sheppard J, Vehof J, Versura P, Willcox MDP, Ziemanski J, Wolffsohn JS. TFOS Lifestyle: Impact of nutrition on the ocular surface. Ocul Surf 2023; 29:226-271. [PMID: 37100346 DOI: 10.1016/j.jtos.2023.04.003] [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: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/28/2023]
Abstract
Nutrients, required by human bodies to perform life-sustaining functions, are obtained from the diet. They are broadly classified into macronutrients (carbohydrates, lipids, and proteins), micronutrients (vitamins and minerals) and water. All nutrients serve as a source of energy, provide structural support to the body and/or regulate the chemical processes of the body. Food and drinks also consist of non-nutrients that may be beneficial (e.g., antioxidants) or harmful (e.g., dyes or preservatives added to processed foods) to the body and the ocular surface. There is also a complex interplay between systemic disorders and an individual's nutritional status. Changes in the gut microbiome may lead to alterations at the ocular surface. Poor nutrition may exacerbate select systemic conditions. Similarly, certain systemic conditions may affect the uptake, processing and distribution of nutrients by the body. These disorders may lead to deficiencies in micro- and macro-nutrients that are important in maintaining ocular surface health. Medications used to treat these conditions may also cause ocular surface changes. The prevalence of nutrition-related chronic diseases is climbing worldwide. This report sought to review the evidence supporting the impact of nutrition on the ocular surface, either directly or as a consequence of the chronic diseases that result. To address a key question, a systematic review investigated the effects of intentional food restriction on ocular surface health; of the 25 included studies, most investigated Ramadan fasting (56%), followed by bariatric surgery (16%), anorexia nervosa (16%), but none were judged to be of high quality, with no randomized-controlled trials.
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Affiliation(s)
- Maria Markoulli
- School of Optometry and Vision Science, UNSW Sydney, NSW, Australia.
| | - Sumayya Ahmad
- Icahn School of Medicine of Mt. Sinai, New York, NY, USA
| | - Jayashree Arcot
- Food and Health, School of Chemical Engineering, UNSW Sydney, Australia
| | - Reiko Arita
- Department of Ophthalmology, Itoh Clinic, Saitama, Japan
| | | | | | - Laura E Downie
- Department of Optometry and Vision Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Katie Edwards
- School of Optometry and Vision Science, Queensland University of Technology, Brisbane, Australia
| | - Judith Flanagan
- School of Optometry and Vision Science, UNSW Sydney, NSW, Australia; Vision CRC, USA
| | - Marc Labetoulle
- Ophthalmology Department, Hospital Bicêtre, APHP, Paris-Saclay University, Le Kremlin-Bicêtre, France; IDMIT (CEA-Paris Saclay-Inserm U1184), Fontenay-aux-Roses, France
| | - Stuti L Misra
- Department of Ophthalmology, New Zealand National Eye Centre, The University of Auckland, Auckland, New Zealand
| | | | - Sumeer Singh
- Department of Optometry and Vision Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - John Sheppard
- Virginia Eye Consultants, Norfolk, VA, USA; Eastern Virginia Medical School, Norfolk, VA, USA
| | - Jelle Vehof
- Departments of Ophthalmology and Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK; Department of Ophthalmology, Vestfold Hospital Trust, Tønsberg, Norway
| | - Piera Versura
- Cornea and Ocular Surface Analysis - Translation Research Laboratory, Ophthalmology Unit, DIMEC Alma Mater Studiorum Università di Bologna, Italy; IRCCS AOU di Bologna Policlinico di Sant'Orsola, Bologna, Italy
| | - Mark D P Willcox
- School of Optometry and Vision Science, UNSW Sydney, NSW, Australia
| | - Jillian Ziemanski
- School of Optometry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - James S Wolffsohn
- College of Health & Life Sciences, School of Optometry, Aston University, Birmingham, UK
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12
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Das T, Padakandla SR, Shivaji S, Jayasudha R, Takkar B. Intraocular Microbiome in Diabetes and Diabetic Retinopathy: A Pilot Study. Ophthalmol Ther 2023; 12:1109-1126. [PMID: 36719607 PMCID: PMC10011241 DOI: 10.1007/s40123-023-00660-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/18/2023] [Indexed: 02/01/2023] Open
Abstract
INTRODUCTION The objective of this study was to compare the microbiome in the aqueous humour and gut of people with diabetes mellitus (DM) with and without diabetic retinopathy (DR). METHODS This was a prospective controlled study. The study included 17 people undergoing intraocular surgery in their naïve eyes. Stool samples were obtained in the perioperative period; aqueous humour samples of sufficient quantity were obtained in 12 people during intraocular surgery. Dietary information was obtained using a previously validated questionnaire. The gut and aqueous humour samples were assessed for microbiome using 16S rRNA gene sequencing coupled with QIIME and R software. RESULTS Aqueous humour was analysed in 12 people: 4 each healthy controls, people with DM, and people with DR. There were minor differences at the phyla levels, but the aqueous humour microbiomes of healthy controls, DM, and DR formed three distinct clusters on heat map analysis with discriminatory genera. This genera-level clustering was more apparent for the intraocular than the gut microbiome. In people with DM and DR, we identified genera unique to the eye or the gut. There was a consistent reduction in the abundance of anti-inflammatory bacteria in people with DR than DM. CONCLUSIONS There is a difference in intraocular and gut microbiome regardless of disease or health. Our preliminary findings indicate distinctive features of the intraocular microbiome in people with DR compared with those without it. While this distinctiveness appears more evident in aqueous humour than in the gut, it needs further confirmation with larger studies.
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Affiliation(s)
- Taraprasad Das
- Anant Bajaj Retina Institute-Srimati Kanuri Santhamma Centre for Vitreoretinal Diseases, L V Prasad Eye Institute, Hyderabad, India
| | | | - Sisinthy Shivaji
- Prof. Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | | | - Brijesh Takkar
- Anant Bajaj Retina Institute-Srimati Kanuri Santhamma Centre for Vitreoretinal Diseases, L V Prasad Eye Institute, Hyderabad, India
- Indian Health Outcomes, Public Health, and Economics Research (IHOPE) Centre, L V Prasad Eye Institute, Hyderabad, India
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13
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Chiang MC, Chern E. Ocular surface microbiota: Ophthalmic infectious disease and probiotics. Front Microbiol 2022; 13:952473. [PMID: 36060740 PMCID: PMC9437450 DOI: 10.3389/fmicb.2022.952473] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, increasing studies have emphasized the importance of commensal bacteria in humans, including microbiota in the oral cavity, gut, vagina, or skin. Ocular surface microbiota (OSM) is gaining great importance as new methodologies for bacteria DNA sequencing have been published. This review outlines the current understanding and investigation of OSM and introduces the new concept of the gut–eye axis. Moreover, we have collected current studies that focus on the relationship between ophthalmic infectious disease and alterations in the OSM or human gut microbiota. Finally, we discuss the current application of probiotics in ophthalmic infectious disease, its limitations to date, and futural directions.
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Affiliation(s)
- Ming-Cheng Chiang
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Edward Chern
- niChe Lab for Stem Cell and Regenerative Medicine, Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- *Correspondence: Edward Chern
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14
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Thakur PS, Aggarwal D, Takkar B, Shivaji S, Das T. Evidence Suggesting the Role of Gut Dysbiosis in Diabetic Retinopathy. Invest Ophthalmol Vis Sci 2022; 63:21. [PMID: 35877085 PMCID: PMC9339698 DOI: 10.1167/iovs.63.8.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Gut dysbiosis has been identified and tested in human trials for its role in diabetes mellitus (DM). The gut-retina axis could be a potential target for retardation of diabetic retinopathy (DR), a known complication of DM. This study reviews the evidence suggesting gut dysbiosis in DR. Methods The published literature in the past 5 years was reviewed using predetermined keywords and articles. The review intended to determine changes in gut microbiome in DR, the hypothesized mechanisms linking to the gut-retina axis, its predictive potential for progression of DR, and the possible therapeutic targets. Results The gut microbiota of people with DM differ from those without it, and the gut microbiota of people with DR differ from those without it. The difference is more significant in the former (DM versus no DM) and less significant in the latter (DM without DR versus DM with DR). Early research has suggested mechanisms of the gut-retina axis, but these are not different from known changes in the gut microbiome of people with DM. The current evidence on the predictive value of the gut microbiome in the occurrence and progression of DR is low. Therapeutic avenues targeting the gut-retina axis include lifestyle changes, pharmacologic inhibitors, probiotics, and fecal microbiota transplantation. Conclusions Investigating the therapeutic utility of the gut ecosystem for DM and its complications like DR is an emerging area of research. The gut-retina axis could be a target for retardation of DR but needs longitudinal regional studies adjusting for dietary habits.
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Affiliation(s)
- Pratima Singh Thakur
- Anant Bajaj Retina Institute-Srimati Kanuri Santhamma Centre for Vitreoretinal Diseases, L V Prasad Eye Institute, Hyderabad, India
| | - David Aggarwal
- Anant Bajaj Retina Institute-Srimati Kanuri Santhamma Centre for Vitreoretinal Diseases, L V Prasad Eye Institute, Hyderabad, India
| | - Brijesh Takkar
- Anant Bajaj Retina Institute-Srimati Kanuri Santhamma Centre for Vitreoretinal Diseases, L V Prasad Eye Institute, Hyderabad, India.,Indian Health Outcomes, Public Health, and Economics Research (IHOPE) Centre, L V Prasad Eye Institute, Hyderabad, India.,https://orcid.org/0000-0001-5779-7645
| | - Sisinthy Shivaji
- Prof. Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India.,https://orcid.org/0000-0003-0376-4658
| | - Taraprasad Das
- Anant Bajaj Retina Institute-Srimati Kanuri Santhamma Centre for Vitreoretinal Diseases, L V Prasad Eye Institute, Hyderabad, India.,https://orcid.org/0000-0002-1295-4528
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15
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Thakur S, Sheppard JD. Gut Microbiome and Its Influence On Ocular Surface and Ocular Surface Diseases. Eye Contact Lens 2022; 48:278-282. [PMID: 35580364 DOI: 10.1097/icl.0000000000000905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2022] [Indexed: 12/25/2022]
Abstract
ABSTRACT The gut microbiome plays a substantial immunologic and pathophysiologic role in maintaining the health of the host, and dysregulation of this dynamic ecosystem has been associated with several inflammatory conditions. Many studies have explored the influence of gut microbiota on the ocular surface and whether gut microbiota impact the pathophysiology of ophthalmic conditions. These findings have highlighted the advantages of enhancing gut microbes through probiotics, prebiotics, diet, vitamin supplementations, and fecal microbial transplant in clinical practice. The purpose of this review article was to provide an up-to-date overview of the knowledge on this topic. Further exploration of this area of research is important to help guide new therapeutic targets to develop treatment and prevention of certain ocular surface diseases.
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Affiliation(s)
- Shambhawi Thakur
- Eastern Virginia Medical School (S.T.), Norfolk, VA; and Virginia Eye Consultants (J.D.S.), Norfolk, VA
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16
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Vasishta S, Ganesh K, Umakanth S, Joshi MB. Ethnic disparities attributed to the manifestation in and response to type 2 diabetes: insights from metabolomics. Metabolomics 2022; 18:45. [PMID: 35763080 PMCID: PMC9239976 DOI: 10.1007/s11306-022-01905-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 04/13/2022] [Indexed: 11/21/2022]
Abstract
Type 2 diabetes (T2D) associated health disparities among different ethnicities have long been known. Ethnic variations also exist in T2D related comorbidities including insulin resistance, vascular complications and drug response. Genetic heterogeneity, dietary patterns, nutrient metabolism and gut microbiome composition attribute to ethnic disparities in both manifestation and progression of T2D. These factors differentially regulate the rate of metabolism and metabolic health. Metabolomics studies have indicated significant differences in carbohydrate, lipid and amino acid metabolism among ethnicities. Interestingly, genetic variations regulating lipid and amino acid metabolism might also contribute to inter-ethnic differences in T2D. Comprehensive and comparative metabolomics analysis between ethnicities might help to design personalized dietary regimen and newer therapeutic strategies. In the present review, we explore population based metabolomics data to identify inter-ethnic differences in metabolites and discuss how (a) genetic variations, (b) dietary patterns and (c) microbiome composition may attribute for such differences in T2D.
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Affiliation(s)
- Sampara Vasishta
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, 576104, Manipal, India
| | - Kailash Ganesh
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, 576104, Manipal, India
| | | | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, 576104, Manipal, India.
- Manipal School of Life Sciences, Planetarium Complex Manipal Academy of Higher Education Manipal, 576104, Manipal, India.
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17
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Shi G, Lin Y, Wu Y, Zhou J, Cao L, Chen J, Li Y, Tan N, Zhong S. Bacteroides fragilis Supplementation Deteriorated Metabolic Dysfunction, Inflammation, and Aorta Atherosclerosis by Inducing Gut Microbiota Dysbiosis in Animal Model. Nutrients 2022; 14:nu14112199. [PMID: 35684000 PMCID: PMC9183096 DOI: 10.3390/nu14112199] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
Background: The gut microbial ecosystem is an important factor that regulates host health and the onset of chronic diseases, such as inflammatory bowel diseases, obesity, hyperlipidemia, and diabetes mellitus, which are important risk factors for atherosclerosis. However, the links among diet, microbiota composition, and atherosclerotic progression are unclear. Methods and results: Four-week-old mice (-/- mice, C57Bl/6) were randomly divided into two groups, namely, supplementation with culture medium (control, CTR) and Bacteroides fragilis (BFS), and were fed a high-fat diet. The gut microbiota abundance in feces was evaluated using the 16S rDNA cloning library construction, sequencing, and bioinformatics analysis. The atherosclerotic lesion was estimated using Oil Red O staining. Levels of CD36, a scavenger receptor implicated in atherosclerosis, and F4/80, a macrophage marker in small intestine, were quantified by quantitative real-time PCR. Compared with the CTR group, the BFS group showed increased food intake, fasting blood glucose level, body weight, low-density lipoprotein level, and aortic atherosclerotic lesions. BFS dramatically reduced Lactobacillaceae (LAC) abundance and increased Desulfovibrionaceae (DSV) abundance. The mRNA expression levels of CD36 and F4/80 in small intestine and aorta tissue in the BFS group were significantly higher than those in the CTR group. Conclusions: gut microbiota dysbiosis was induced by BFS. It was characterized by reduced LAC and increased DSV abundance and led to the deterioration of glucose/lipid metabolic dysfunction and inflammatory response, which likely promoted aorta plaque formation and the progression of atherosclerosis.
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Affiliation(s)
- Guoxiang Shi
- Guangdong Provincial Key Laboratory of Coronary, Department of Pharmacy, Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou 510080, China; (G.S.); (Y.L.); (Y.W.); (J.Z.); (J.C.)
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Jiangxi Hypertension Research Institute, Nanchang 335100, China
| | - Yubi Lin
- Guangdong Provincial Key Laboratory of Coronary, Department of Pharmacy, Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou 510080, China; (G.S.); (Y.L.); (Y.W.); (J.Z.); (J.C.)
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523710, China
| | - Yuanyuan Wu
- Guangdong Provincial Key Laboratory of Coronary, Department of Pharmacy, Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou 510080, China; (G.S.); (Y.L.); (Y.W.); (J.Z.); (J.C.)
| | - Jing Zhou
- Guangdong Provincial Key Laboratory of Coronary, Department of Pharmacy, Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou 510080, China; (G.S.); (Y.L.); (Y.W.); (J.Z.); (J.C.)
| | - Lixiang Cao
- School of Medicine, Sun Yat-sen University, Guangzhou 510317, China;
| | - Jiyan Chen
- Guangdong Provincial Key Laboratory of Coronary, Department of Pharmacy, Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou 510080, China; (G.S.); (Y.L.); (Y.W.); (J.Z.); (J.C.)
| | - Yong Li
- Department of Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510317, China
- Correspondence: (Y.L.); (N.T.); (S.Z.); Tel.: +8620-83827812-60298 (S.Z.)
| | - Ning Tan
- Guangdong Provincial Key Laboratory of Coronary, Department of Pharmacy, Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou 510080, China; (G.S.); (Y.L.); (Y.W.); (J.Z.); (J.C.)
- Correspondence: (Y.L.); (N.T.); (S.Z.); Tel.: +8620-83827812-60298 (S.Z.)
| | - Shilong Zhong
- Guangdong Provincial Key Laboratory of Coronary, Department of Pharmacy, Heart Disease Prevention, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Guangzhou 510080, China; (G.S.); (Y.L.); (Y.W.); (J.Z.); (J.C.)
- Correspondence: (Y.L.); (N.T.); (S.Z.); Tel.: +8620-83827812-60298 (S.Z.)
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18
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Jayasudha R, Chakravarthy SK, Prashanthi GS, Sharma S, Garg P, Murthy SI, Shivaji S. Mycobiomes of the Ocular Surface in Bacterial Keratitis Patients. FRONTIERS IN OPHTHALMOLOGY 2022; 2:894739. [PMID: 38983567 PMCID: PMC11182091 DOI: 10.3389/fopht.2022.894739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/06/2022] [Indexed: 07/11/2024]
Abstract
Inflammation of the cornea is known as keratitis, and bacteria, fungi, protozoans, and viruses are the etiological agents of this disease. Delayed treatment of keratitis could result in loss of vision and, under certain severity conditions, the removal of an eye and its associated structures. In the current study, the ocular surface (conjunctiva and cornea) mycobiomes of individuals with bacterial keratitis were compared with the ocular mycobiome (conjunctiva) of healthy individuals, free of any ocular morbidity. Mycobiomes were generated through NGS approach using conjunctival swabs and corneal scrapings as the source of DNA from which ITS2 was amplified and sequenced, as a proxy to identify fungi. The results indicated significant changes in the alpha-diversity indices and in the abundance at the phylum and genera level. Hierarchical clustering using a heatmap showed that the mycobiomes were different. Furthermore, NMDS plots also differentiated the mycobiomes in the three cohorts, implying dysbiosis in the mycobiomes of the conjunctivae and corneal scrapings of bacterial keratitis individuals compared to control individuals. A preponderance of negative interactions in the hub genera in the conjunctival swabs of bacterial keratitis individuals compared to healthy controls further re-emphasized the differences in the mycobiomes. The dysbiotic changes at the genera level in conjunctivae and corneal scrapings of bacterial keratitis individuals are discussed with respect to their possible role in causing or exacerbating ocular surface inflammation. These results demonstrate dysbiosis in the ocular mycobiome in bacterial keratitis patients compared to healthy controls for the first time.
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Affiliation(s)
| | | | | | - Savitri Sharma
- Prof. Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Prashant Garg
- The Cornea Institute, L V Prasad Eye Institute, Hyderabad, India
| | | | - Sisinthy Shivaji
- Prof. Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
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19
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Padakandla SR, Das T, Sai Prashanthi G, Angadi KK, Reddy SS, Reddy GB, Shivaji S. Gut mycobiome dysbiosis in rats showing retinal changes indicative of diabetic retinopathy. PLoS One 2022; 17:e0267080. [PMID: 35439275 PMCID: PMC9017887 DOI: 10.1371/journal.pone.0267080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/03/2022] [Indexed: 11/21/2022] Open
Abstract
The current study compared the gut mycobiomes of diabetic rats generated by a streptozotocin chemical challenge, diabetic rats with retinal changes and normal control rats over a period of 4 months. Sustained increase in blood sugar levels (>150 mg/dL) confirmed the induction of diabetes. Histology and immunohistochemistry were used to identify changes in the retinal tissues in the diabetic rats indicative of the animals progressing into diabetic retinopathy. Gut mycobiomes generated using faecal DNA, indicated dysbiosis at the genus level in both diabetic (DM) and diabetic rats with retinal changes (DRC) when compared with the control rats. In Tables 3–6 the specific genera that were significantly increased/decreased in DM1 and DM2 and in DRC1 and DRC2 respectively compared to the respective controls CT1-CT4 rats are listed. Further, the mycobiomes of the DM and DRC rats separated into distinct clusters following heat-map analysis of the discriminating genera. In addition, β-diversity analysis separated the mycobiomes of DM and DRC rats from that of the control rats, but the mycobiomes of diabetic rats and diabetic rats with retinal changes showed an overlap. Based on the inferred functions of the discriminating genera in the mycobiomes, we speculated that increase in pathogenic fungi might contribute to the inflammatory status both in diabetic rats and rats showing retinal changes.
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Affiliation(s)
- Shalem Raj Padakandla
- Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, India
| | - Taraprasad Das
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L. V. Prasad Eye Institute, Hyderabad, Telangana, India
| | - Gumpili Sai Prashanthi
- Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, India
| | - Kiran Kumar Angadi
- Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad, Telangana, India
| | - S. Sreenivasa Reddy
- Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad, Telangana, India
| | - G. Bhanuprakash Reddy
- Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad, Telangana, India
| | - Sisinthy Shivaji
- Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, Telangana, India
- * E-mail:
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20
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Kaźmierczak-Siedlecka K, Skonieczna-Żydecka K, Hupp T, Duchnowska R, Marek-Trzonkowska N, Połom K. Next-generation probiotics - do they open new therapeutic strategies for cancer patients? Gut Microbes 2022; 14:2035659. [PMID: 35167406 PMCID: PMC8855854 DOI: 10.1080/19490976.2022.2035659] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Gut microbiota and its association with cancer development/treatment has been intensively studied during the past several years. Currently, there is a growing interest toward next-generation probiotics (NGPs) as therapeutic agents that alter gut microbiota and impact on cancer development. In the present review we focus on three emerging NGPs, namely Faecalibacterium prausnitzii, Akkermansia muciniphila, and Bacteroides fragilis as their presence in the digestive tract can have an impact on cancer incidence. These NGPs enhance gastrointestinal immunity, maintain intestinal barrier integrity, produce beneficial metabolites, act against pathogens, improve immunotherapy efficacy, and reduce complications associated with chemotherapy and radiotherapy. Notably, the use of NGPs in cancer patients does not have a long history and, although their safety remains relatively undefined, recently published data has shown that they are non-toxigenic. Notwithstanding, A. muciniphila may promote colitis whereas enterotoxigenic B. fragilis stimulates chronic inflammation and participates in colorectal carcinogenesis. Nevertheless, the majority of B. fragilis strains provide a beneficial effect to the host, are non-toxigenic and considered as the best current NGP candidate. Overall, emerging studies indicate a beneficial role of these NGPs in the prevention of carcinogenesis and open new promising therapeutic options for cancer patients.
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Affiliation(s)
- Karolina Kaźmierczak-Siedlecka
- Department of Surgical Oncology, Medical University of Gdansk, Gdańsk, Poland,CONTACT Karolina Kaźmierczak-Siedlecka Department of Surgical Oncology, Medical University of Gdansk, Ul. Smoluchowskiego 18, 80-214Gdańsk, Poland
| | | | - Theodore Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland,Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland, UK
| | - Renata Duchnowska
- Department of Oncology, Military Institute of Medicine, Warsaw, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science University of Gdańsk, Gdańsk, Poland,Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Połom
- Department of Surgical Oncology, Medical University of Gdansk, Gdańsk, Poland
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21
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Myhill LJ, Stolzenbach S, Mejer H, Krych L, Jakobsen SR, Kot W, Skovgaard K, Canibe N, Nejsum P, Nielsen DS, Thamsborg SM, Williams AR. Parasite-Probiotic Interactions in the Gut: Bacillus sp. and Enterococcus faecium Regulate Type-2 Inflammatory Responses and Modify the Gut Microbiota of Pigs During Helminth Infection. Front Immunol 2022; 12:793260. [PMID: 35069576 PMCID: PMC8766631 DOI: 10.3389/fimmu.2021.793260] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/07/2021] [Indexed: 01/18/2023] Open
Abstract
Dietary probiotics may enhance gut health by directly competing with pathogenic agents and through immunostimulatory effects. These properties are recognized in the context of bacterial and viral pathogens, but less is known about interactions with eukaryotic pathogens such as parasitic worms (helminths). In this study we investigated whether two probiotic mixtures (comprised of Bacillus amyloliquefaciens, B. subtilis, and Enterococcus faecium [BBE], or Lactobacillus rhamnosus LGG and Bifidobacterium animalis subspecies Lactis Bb12 [LB]) could modulate helminth infection kinetics as well as the gut microbiome and intestinal immune responses in pigs infected with the nodular worm Oesophagostomum dentatum. We observed that neither probiotic mixture influenced helminth infection levels. BBE, and to a lesser extent LB, changed the alpha- and beta-diversity indices of the colon and fecal microbiota, notably including an enrichment of fecal Bifidobacterium spp. by BBE. However, these effects were muted by concurrent O. dentatum infection. BBE (but not LB) significantly attenuated the O. dentatum-induced upregulation of genes involved in type-2 inflammation and restored normal lymphocyte ratios in the ileo-caecal lymph nodes that were altered by infection. Moreover, inflammatory cytokine release from blood mononuclear cells and intestinal lymphocytes was diminished by BBE. Collectively, our data suggest that selected probiotic mixtures can play a role in maintaining immune homeostasis during type 2-biased inflammation. In addition, potentially beneficial changes in the microbiome induced by dietary probiotics may be counteracted by helminths, highlighting the complex inter-relationships that potentially exist between probiotic bacteria and intestinal parasites.
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Affiliation(s)
- Laura J Myhill
- Department of Veterinary and Animal Sciences, University of Copenhagen, Faculty of Health and Medical Sciences, Frederiksberg, Denmark
| | - Sophie Stolzenbach
- Department of Veterinary and Animal Sciences, University of Copenhagen, Faculty of Health and Medical Sciences, Frederiksberg, Denmark
| | - Helena Mejer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Faculty of Health and Medical Sciences, Frederiksberg, Denmark
| | - Lukasz Krych
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Simon R Jakobsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Faculty of Health and Medical Sciences, Frederiksberg, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nuria Canibe
- Department of Animal Science - Immunology and Microbiology, Aarhus University, Tjele, Denmark
| | - Peter Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | - Stig M Thamsborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Faculty of Health and Medical Sciences, Frederiksberg, Denmark
| | - Andrew R Williams
- Department of Veterinary and Animal Sciences, University of Copenhagen, Faculty of Health and Medical Sciences, Frederiksberg, Denmark
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22
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Mucosal immunology of the ocular surface. Mucosal Immunol 2022; 15:1143-1157. [PMID: 36002743 PMCID: PMC9400566 DOI: 10.1038/s41385-022-00551-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/26/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023]
Abstract
The eye is a sensory organ exposed to the environment and protected by a mucosal tissue barrier. While it shares a number of features with other mucosal tissues, the ocular mucosal system, composed of the conjunctiva, Meibomian glands, and lacrimal glands, is specialized to address the unique needs of (a) lubrication and (b) host defense of the ocular surface. Not surprisingly, most challenges, physical and immunological, to the homeostasis of the eye fall into those two categories. Dry eye, a dysfunction of the lacrimal glands and/or Meibomian glands, which can both cause, or arise from, sensory defects, including those caused by corneal herpes virus infection, serve as examples of these perturbations and will be discussed ahead. To preserve vision, dense neuronal and immune networks sense various stimuli and orchestrate responses, which must be tightly controlled to provide protection, while simultaneously minimizing collateral damage. All this happens against the backdrop of, and can be modified by, the microorganisms that colonize the ocular mucosa long term, or that are simply transient passengers introduced from the environment. This review will attempt to synthesize the existing knowledge and develop trends in the study of the unique mucosal and immune elements of the ocular surface.
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23
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Raj N, Vanathi M, Ahmed NH, Gupta N, Lomi N, Tandon R. Recent Perspectives in the Management of Fungal Keratitis. J Fungi (Basel) 2021; 7:jof7110907. [PMID: 34829196 PMCID: PMC8621027 DOI: 10.3390/jof7110907] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 12/28/2022] Open
Abstract
Mycotic keratitis is common in warm, humid regions with a varying profile of pathogenic fungi according to geographical origin, socioeconomic status, and climatic condition. Clinical diagnosis can be challenging in difficult cases and those refractory to treatment. Fungal hyphae on microscopic examination and culture isolation have been the gold standard in the laboratory diagnosis of fungal keratitis. A culture isolate of the aetiological fungus is essential to perform antifungal susceptibility testing. As the culture isolation of fungi is time-consuming, causing delays in the initiation of treatment, newer investigative modalities such as in vivo confocal microscopy and molecular diagnostic methods have recently gained popularity. Molecular diagnostic techniques now help to obtain a rapid diagnosis of fungal keratitis. Genomic approaches are based on detecting amplicons of ribosomal RNA genes, with internal transcribed spacers being increasingly adopted. Metagenomic deep sequencing allows for rapid and accurate diagnosis without the need to wait for the fungus to grow. This is also helpful in identifying new emerging strains of fungi causing mycotic keratitis. A custom-tear proteomic approach will probably play an important diagnostic role in future in the management of mycotic keratitis. Positive repeat cultures are being suggested as an important gauge indicative of a poor prognosis. Positive repeat fungal cultures help to modify a treatment regimen by increasing its frequency, providing the addition of another topical and oral antifungal agent along with close follow-up for perforation and identifying need for early therapeutic keratoplasty. The role of collagen crosslinking in the treatment of fungal keratitis is not convincingly established. Rapid detection by multiplex PCR and antifungal susceptibility testing of the pathogenic fungi, adopted into a routine management protocol of fungal keratitis, will help to improve treatment outcome. Early therapy is essential in minimizing damage to the corneal tissue, thereby providing a better outcome. The role of conventional therapy with polyenes, systemic and targeted therapy of antifungal agents, newer azoles and echinocandins in fungal keratitis has been widely studied in recent times. Combination therapy can be more efficacious in comparison to monotherapy. Given the diversity of fungal aetiology, the emergence of new corneal pathogenic fungi with varying drug susceptibilities, increasing the drug resistance to antifungal agents in some genera and species, it is perhaps time to adopt recent molecular methods for precise identification and incorporate antifungal susceptibility testing as a routine.
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Affiliation(s)
- Nimmy Raj
- Cornea, Lens & Refractive Surgery Services—Dr R P Centre for Ophthalmic Sciences, All India Institute for Medical Sciences, New Delhi 110029, India; (N.R.); (N.G.); (N.L.); (R.T.)
| | - Murugesan Vanathi
- Cornea, Lens & Refractive Surgery Services—Dr R P Centre for Ophthalmic Sciences, All India Institute for Medical Sciences, New Delhi 110029, India; (N.R.); (N.G.); (N.L.); (R.T.)
- Correspondence: ; Tel.: +91-11-26593010; Fax: +91-11-26588919
| | - Nishat Hussain Ahmed
- Ocular Microbiology Services—Dr R P Centre for Ophthalmic Sciences, All India Institute for Medical Sciences, New Delhi 110029, India;
| | - Noopur Gupta
- Cornea, Lens & Refractive Surgery Services—Dr R P Centre for Ophthalmic Sciences, All India Institute for Medical Sciences, New Delhi 110029, India; (N.R.); (N.G.); (N.L.); (R.T.)
| | - Neiwete Lomi
- Cornea, Lens & Refractive Surgery Services—Dr R P Centre for Ophthalmic Sciences, All India Institute for Medical Sciences, New Delhi 110029, India; (N.R.); (N.G.); (N.L.); (R.T.)
| | - Radhika Tandon
- Cornea, Lens & Refractive Surgery Services—Dr R P Centre for Ophthalmic Sciences, All India Institute for Medical Sciences, New Delhi 110029, India; (N.R.); (N.G.); (N.L.); (R.T.)
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24
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Mishra K, Bukavina L, Ghannoum M. Symbiosis and Dysbiosis of the Human Mycobiome. Front Microbiol 2021; 12:636131. [PMID: 34630340 PMCID: PMC8493257 DOI: 10.3389/fmicb.2021.636131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 08/04/2021] [Indexed: 12/13/2022] Open
Abstract
The influence of microbiological species has gained increased visibility and traction in the medical domain with major revelations about the role of bacteria on symbiosis and dysbiosis. A large reason for these revelations can be attributed to advances in deep-sequencing technologies. However, the research on the role of fungi has lagged. With the continued utilization of sequencing technologies in conjunction with traditional culture assays, we have the opportunity to shed light on the complex interplay between the bacteriome and the mycobiome as they relate to human health. In this review, we aim to offer a comprehensive overview of the human mycobiome in healthy and diseased states in a systematic way. The authors hope that the reader will utilize this review as a scaffolding to formulate their understanding of the mycobiome and pursue further research.
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Affiliation(s)
- Kirtishri Mishra
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Laura Bukavina
- University Hospitals Cleveland Medical Center, Urology Institute, Cleveland, OH, United States.,Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Mahmoud Ghannoum
- Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Center for Medical Mycology, and Integrated Microbiome Core, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States.,Department of Dermatology, Case Western Reserve University School of Medicine and University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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25
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Katzka W, Dong TS, Luu K, Lagishetty V, Sedighian F, Arias-Jayo N, Jacobs JP, Hsu HY. The Ocular Microbiome Is Altered by Sampling Modality and Age. Transl Vis Sci Technol 2021; 10:24. [PMID: 34661621 PMCID: PMC8525833 DOI: 10.1167/tvst.10.12.24] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background Studies of the ocular microbiome have used a variety of sampling techniques, but no study has directly compared different sampling methods applied to the same eyes to one another or to a reference standard of corneal epithelial biopsy. We addressed this lack by comparing the microbiome from three conjunctival swabs with those of corneal epithelial biopsy. Methods Twelve eyes (11 patients) were swabbed by calcium alginate swab, cotton-tipped applicator, and Weck-Cel cellulose sponge before a corneal epithelial biopsy (48 samples). We then performed 16S rRNA gene sequencing and universal 16S rRNA gene real-time polymerase chain reaction. Negative/blank controls were used to eliminate contaminants. An analysis was performed to examine the concordance of the three swab types to corneal epithelial biopsy. The effect of patient age on the ocular microbiome as determined by epithelial biopsy was also examined. Results The ocular microbiome from corneal epithelial biopsies consisted of 31 genera with a relative abundance of 1% or more, including Weisella, Corynebacterium, and Pseudomonas. Of the three swab types, Weck-Cel differed the most from corneal biopsies based on beta-diversity analysis. Cotton swabs were unable to capture the Bacteroides population seen on epithelial biopsy. Therefore, calcium alginate swabs seemed to be the closest to epithelial biopsies. Older patients (≥65 years old) had higher alpha diversity (P < 0.05) than younger patients. Differential abundance testing showed that there were 18 genera that were differentially abundant between the two age groups, including Streptococcus and eight members of the Proteobacteria phylum. Conclusions We demonstrate that ocular sampling method and patient age can greatly affect the outcome of sequencing-based analysis of the ocular microbiome. Translational Relevance By understanding the impact of different sampling methods on the results obtained from the ocular surface microbiome, future research on the topic will be more reproducible, leading to a better understanding of ocular surface microbiome in health and disease.
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Affiliation(s)
- William Katzka
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Tien S Dong
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, USA.,Department of Medicine, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Kayti Luu
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, USA.,Department of Medicine, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, USA.,Department of Medicine, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Farzaneh Sedighian
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Nerea Arias-Jayo
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Gastroenterology, Hepatology and Parenteral Nutrition, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, USA.,Department of Medicine, Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Hugo Y Hsu
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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26
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Gunardi TH, Susantono DP, Victor AA, Sitompul R. Atopobiosis and Dysbiosis in Ocular Diseases: Is Fecal Microbiota Transplant and Probiotics a Promising Solution? J Ophthalmic Vis Res 2021; 16:631-643. [PMID: 34840686 PMCID: PMC8593547 DOI: 10.18502/jovr.v16i4.9754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To highlight the role of atopobiosis and dysbiosis in the pathomechanism of autoimmune uveitis, therefore supporting fecal microbiota transplant (FMT) and probiotics as potential targeted-treatment for uveitis. METHODS This review synthesized literatures upon the relation between gut microbiota, autoimmune uveitis, FMT, and probiotics, published from January 2001 to March 2021 and indexed in PubMed, Google Scholar, CrossRef. RESULTS The basis of the gut-eye axis revolves around occurrences of molecular mimicry, increase in pro-inflammatory cytokines, gut epithelial barrier disruption, and translocation of microbes to distant sites. In patients with autoimmune uveitis, an increase of gut Fusobacterium and Enterobacterium were found. With current knowledge of aforementioned mechanisms, studies modifying the gut microbiome and restoring the physiologic gut barrier has been the main focus for pathomechanism-based therapy. In mice models, FMT and probiotics targeting repopulation of gut microbiota has shown significant improvement in clinical manifestations of uveitis. Consequently, a better understanding in the homeostasis of gut microbiome along with their role in the gut-eye axis is needed to develop practical targeted treatment. CONCLUSION Current preliminary studies are promising in establishing a causative gut-eye axis relationship and the possibility of conducting FMT and probiotics as targeted treatment to mitigate autoimmune uveitis, to shorten disease duration, and to prevent further complications.
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Affiliation(s)
| | | | - Andi Arus Victor
- Department of Ophthalmology, Dr. Cipto Mangunkusumo National General
Hospital – Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Ratna Sitompul
- Department of Ophthalmology, Dr. Cipto Mangunkusumo National General
Hospital – Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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27
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Padakandla SR, Das T, Sai Prashanthi G, Angadi KK, Reddy SS, Reddy GB, Shivaji S. Dysbiosis in the Gut Microbiome in Streptozotocin-Induced Diabetes Rats and Follow-Up During Retinal Changes. Invest Ophthalmol Vis Sci 2021; 62:31. [PMID: 34431974 PMCID: PMC8399471 DOI: 10.1167/iovs.62.10.31] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Purpose To analyze the gut bacterial microbiome of streptozotocin-induced diabetic rats and rats with retinal changes. Methods Induction of diabetes was confirmed by an increase in blood sugar (>150 mg/dL), and the progression of diabetes with retinal changes was assessed by histology and immunohistochemistry of retinal sections. Microbiomes were generated using fecal DNA, and the V3–V4 amplicons were sequenced and analyzed by QIIME and R. Results Dysbiosis in the gut microbiome of diabetic rats and diabetic rats with retinal changes was observed at the phylum and genus levels compared with the control rats. Heat-map analysis based on the differentially abundant genera indicated that the microbiomes of controls and diabetic rats separated into two distinct clusters. The majority of the microbiomes in diabetic rats with retinal changes also formed a distinct cluster from the control rats. β-diversity analysis separated the microbiome of control rats from the microbiome of diabetic rats and diabetic rats with retinal changes, but the microbiomes of diabetic rats and diabetic rats with retinal changes showed an overlap. Functional analysis indicated that the enhanced inflammation in diabetic rats showing retinal changes could be ascribed to a decrease in anti-inflammatory bacteria and an increase in pathogenic and proinflammatory bacteria. Conclusions This study showed that the gut bacterial microbiome in diabetic rats with retinal changes was different compared with control rats. The results could help develop novel therapeutics for diabetics and diabetic individuals with retinal changes.
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Affiliation(s)
- Shalem Raj Padakandla
- Prof Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, Telangana, India
| | - Taraprasad Das
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L. V. Prasad Eye Institute, Hyderabad, Telangana, India
| | - Gumpili Sai Prashanthi
- Prof Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, Telangana, India
| | - Kiran Kumar Angadi
- Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad, Telangana, India
| | - S Sreenivasa Reddy
- Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad, Telangana, India
| | - G Bhanuprakash Reddy
- Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad, Telangana, India
| | - Sisinthy Shivaji
- Prof Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, Telangana, India
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28
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Wang C, Li S, Hong K, Yu L, Tian F, Zhao J, Zhang H, Chen W, Zhai Q. The roles of different Bacteroides fragilis strains in protecting against DSS-induced ulcerative colitis and related functional genes. Food Funct 2021; 12:8300-8313. [PMID: 34308455 DOI: 10.1039/d1fo00875g] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The role of supplementation with different Bacteroides fragilis (B. fragilis) strains in alleviating ulcerative colitis (UC) is unclear due to the controversial results from animal experiments. In this study, three B. fragilis strains were evaluated for their ability to alleviate dextran sulfate sodium (DSS)-induced UC in C57BL/6J mice. We analyzed the anti-inflammatory effects of different B. fragilis strains and the changes they caused in the intestinal microbiota composition, intestinal epithelial permeability, cytokine concentrations, protein expression of nuclear factor kappa-B (NF-κB) and the underlying specific genes. The results showed that when orally administered, the different B. fragilis strains exerted different effects on the assessed parameters of the mice. The results of real-time quantitative polymerase chain reaction and immunofluorescence staining showed that the supplementation of B. fragilis FSHCM14E1, but not FJSWX11BF, enhanced the expression of the tight-junction proteins ZO-1, occludin and claudin-1. Western blot analysis showed that the anti-inflammatory effects of B. fragilis FSHCM14E1 were related to the NF-κB pathway. Genomic analysis suggested that the anti-inflammatory effects of FSHCM14E1 may be mediated through specific genes associated with defense mechanisms and the secretion of SCFAs. Overall, this study indicates the therapeutic potential of B. fragilis FSHCM14E1 for the prevention of UC.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Sijia Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Kan Hong
- Wuxi People's Hospital Afliated to Nanjing Medical University, Wuxi 214023, Jiangsu, People's Republic of China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China and National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China and Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China and National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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29
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Exploring the signature gut and oral microbiome in individuals of specific Ayurveda prakriti. J Biosci 2021. [DOI: 10.1007/s12038-021-00182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Shivaji S. A systematic review of gut microbiome and ocular inflammatory diseases: Are they associated? Indian J Ophthalmol 2021; 69:535-542. [PMID: 33595467 PMCID: PMC7942081 DOI: 10.4103/ijo.ijo_1362_20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The primary focus of this review was to establish the possible association of dysbiotic changes in the gut bacterial microbiomes with both intestinal and extra-intestinal diseases with emphasis on ocular diseases such as bacterial keratitis, fungal keratitis, uveitis, age-related macular degeneration, and ocular mucosal diseases. For this particular purpose, a systematic search was conducted using PubMed and Google Scholar for publications related to gut microbiome and human health (using the keywords: gut microbiome, ocular disease, dysbiosis, keratitis, uveitis, and AMD). The predictions are that microbiome studies would help to unravel dysbiotic changes in the gut bacterial microbiome at the taxonomic and functional level and thus form the basis to mitigate inflammatory diseases of the eye by using nutritional supplements or fecal microbiota transplantation.
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Affiliation(s)
- Sisinthy Shivaji
- Scientist Emeritus and Distinguished Scientist, Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, Telangana, India
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31
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Pinna NK, Anjana RM, Saxena S, Dutta A, Gnanaprakash V, Rameshkumar G, Aswath S, Raghavan S, Rani CSS, Radha V, Balasubramanyam M, Pant A, Nielsen T, Jørgensen T, Færch K, Kashani A, Silva MCA, Vestergaard H, Hansen TH, Hansen T, Arumugam M, Nair GB, Das B, Pedersen O, Mohan V, Mande SS. Trans-ethnic gut microbial signatures of prediabetic subjects from India and Denmark. Genome Med 2021; 13:36. [PMID: 33658065 PMCID: PMC7931552 DOI: 10.1186/s13073-021-00851-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recent studies have indicated an association of gut microbiota and microbial metabolites with type 2 diabetes mellitus (T2D). However, large-scale investigation of the gut microbiota of "prediabetic" (PD) subjects has not been reported. Identifying robust gut microbiome signatures of prediabetes and characterizing early prediabetic stages is important for the understanding of disease development and could be crucial in early diagnosis and prevention. METHODS The current study performed amplification and sequencing on the variable regions (V1-V5) of the 16S rRNA genes to profile and compare gut microbiota of prediabetic individuals (N = 262) with normoglycemic individuals (N = 275) from two cohorts in India and Denmark. Similarly, fasting serum inflammatory biomarkers were profiled from the study participants. RESULTS After correcting for strong country-specific cohort effect, 16 operational taxonomic units (OTUs) including members from the genera Prevotella9, Phascolarctobacterium, Barnesiella, Flavonifractor, Tyzzerella_4, Bacteroides, Faecalibacterium, and Agathobacter were identified as enriched in normoglycaemic subjects with respect to the subjects with prediabetes using a negative binomial Wald test. We also identified 144 OTUs enriched in the prediabetic subjects, which included members from the genera Megasphaera, Streptococcus, Prevotella9, Alistipes, Mitsuokella, Escherichia/Shigella, Prevotella2, Vibrio, Lactobacillus, Alloprevotella, Rhodococcus, and Klebsiella. Comparative analyses of relative abundance of bacterial taxa revealed that the Streptococcus, Escherichia/Shigella, Prevotella2, Vibrio, and Alloprevotella OTUs exhibited more than fourfold enrichment in the gut microbiota of prediabetic subjects. When considering subjects from the two geographies separately, we were able to identify additional gut microbiome signatures of prediabetes. The study reports a probable association of Megasphaera OTU(s) with impaired glucose tolerance, which is significantly pronounced in Indian subjects. While the overall results confirm a state of proinflammation as early as in prediabetes, the Indian cohort exhibited a characteristic pattern of abundance of inflammatory markers indicating low-grade intestinal inflammation at an overall population level, irrespective of glycemic status. CONCLUSIONS The results present trans-ethnic gut microbiome and inflammation signatures associated with prediabetes, in Indian and Danish populations. The identified associations may be explored further as potential early indicators for individuals at risk of dysglycemia.
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Affiliation(s)
- Nishal Kumar Pinna
- TCS Research, Tata Consultancy Services Limited, 54B Hadapsar Industrial Estate, Pune, 411013, India
| | - Ranjit Mohan Anjana
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Shruti Saxena
- Molecular Genetics Laboratory, Infections and Immunology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, 121001, India
| | - Anirban Dutta
- TCS Research, Tata Consultancy Services Limited, 54B Hadapsar Industrial Estate, Pune, 411013, India
| | - Visvanathan Gnanaprakash
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Gnanavadivel Rameshkumar
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Sukumaran Aswath
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Srividhya Raghavan
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | | | - Venkatesan Radha
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India
| | - Muthuswamy Balasubramanyam
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India.,Present address: SRM Medical College Hospital & Research Centre, SRM Institute of Science & Technology (SRMIST), Kattankulathur, Chennai, India
| | - Archana Pant
- Molecular Genetics Laboratory, Infections and Immunology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, 121001, India
| | - Trine Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Torben Jørgensen
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospitals, University of Copenhagen, Copenhagen, Denmark
| | | | - Alireza Kashani
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark.,Current affiliation: Qbiom, Microbiome Consultancy Service, Copenhagen, Denmark
| | - Maria Camila Alvarez Silva
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Tue Haldor Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark.,Department of Cardiology and Endocrinology, Slagelse Hospital, Slagelse, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark
| | - Gopinath Balakrish Nair
- Molecular Genetics Laboratory, Infections and Immunology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, 121001, India
| | - Bhabatosh Das
- Molecular Genetics Laboratory, Infections and Immunology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad - Gurgaon Expressway, PO box #04, Faridabad, 121001, India.
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Maersk Tower, Building: 07-8-55, DK-2200, Copenhagen N, Denmark.
| | - Viswanathan Mohan
- Madras Diabetes Research Foundation, No. 4, Conran Smith Road, Gopalapuram, Chennai, 600 086, India.
| | - Sharmila Shekhar Mande
- TCS Research, Tata Consultancy Services Limited, 54B Hadapsar Industrial Estate, Pune, 411013, India.
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Szczotka-Flynn LB, Shovlin JP, Schnider CM, Caffery BE, Alfonso EC, Carnt NA, Chalmers RL, Collier S, Jacobs DS, Joslin CE, Kroken AR, Lakkis C, Pearlman E, Schein OD, Stapleton F, Tu E, Willcox MDP. American Academy of Optometry Microbial Keratitis Think Tank. Optom Vis Sci 2021; 98:182-198. [PMID: 33771951 PMCID: PMC8075116 DOI: 10.1097/opx.0000000000001664] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
SIGNIFICANCE Think Tank 2019 affirmed that the rate of infection associated with contact lenses has not changed in several decades. Also, there is a trend toward more serious infections associated with Acanthamoeba and fungi. The growing use of contact lenses in children demands our attention with surveillance and case-control studies. PURPOSE The American Academy of Optometry (AAO) gathered researchers and key opinion leaders from around the world to discuss contact lens-associated microbial keratitis at the 2019 AAO Annual Meeting. METHODS Experts presented within four sessions. Session 1 covered the epidemiology of microbial keratitis, pathogenesis of Pseudomonas aeruginosa, and the role of lens care systems and storage cases in corneal disease. Session 2 covered nonbacterial forms of keratitis in contact lens wearers. Session 3 covered future needs, challenges, and research questions in relation to microbial keratitis in youth and myopia control, microbiome, antimicrobial surfaces, and genetic susceptibility. Session 4 covered compliance and communication imperatives. RESULTS The absolute rate of microbial keratitis has remained very consistent for three decades despite new technologies, and extended wear significantly increases the risk. Improved oxygen delivery afforded by silicone hydrogel lenses has not impacted the rates, and although the introduction of daily disposable lenses has minimized the risk of severe disease, there is no consistent evidence that they have altered the overall rate of microbial keratitis. Overnight orthokeratology lenses may increase the risk of microbial keratitis, especially secondary to Acanthamoeba, in children. Compliance remains a concern and a significant risk factor for disease. New insights into host microbiome and genetic susceptibility may uncover new theories. More studies such as case-control designs suited for rare diseases and registries are needed. CONCLUSIONS The first annual AAO Think Tank acknowledged that the risk of microbial keratitis has not decreased over decades, despite innovation. Important questions and research directions remain.
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Affiliation(s)
| | | | | | | | - Eduardo C Alfonso
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Nicole A Carnt
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Sarah Collier
- U.S. Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Deborah S Jacobs
- Massachusetts Eye and Ear, Cornea Service, Harvard Medical School, Boston, Massachusetts
| | - Charlotte E Joslin
- Department of Ophthalmology and Visual Science, College of Medicine, Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, Illinois
| | - Abby R Kroken
- School of Optometry, University of California, Berkeley, Berkeley, California
| | | | - Eric Pearlman
- Departments of Ophthalmology, and Physiology and Biophysics, University of California, Irvine, Irvine, California
| | - Oliver D Schein
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fiona Stapleton
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Elmer Tu
- University of Illinois Eye and Ear Infirmary, Chicago, Illinois
| | - Mark D P Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, New South Wales, Australia
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Understanding Human Microbiota Offers Novel and Promising Therapeutic Options against Candida Infections. Pathogens 2021; 10:pathogens10020183. [PMID: 33572162 PMCID: PMC7915436 DOI: 10.3390/pathogens10020183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 01/20/2021] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
Human fungal pathogens particularly of Candida species are one of the major causes of hospital acquired infections in immunocompromised patients. The limited arsenal of antifungal drugs to treat Candida infections with concomitant evolution of multidrug resistant strains further complicates the management of these infections. Therefore, deployment of novel strategies to surmount the Candida infections requires immediate attention. The human body is a dynamic ecosystem having microbiota usually involving symbionts that benefit from the host, but in turn may act as commensal organisms or affect positively (mutualism) or negatively (pathogenic) the physiology and nourishment of the host. The composition of human microbiota has garnered a lot of recent attention, and despite the common occurrence of Candida spp. within the microbiota, there is still an incomplete picture of relationships between Candida spp. and other microorganism, as well as how such associations are governed. These relationships could be important to have a more holistic understanding of the human microbiota and its connection to Candida infections. Understanding the mechanisms behind commensalism and pathogenesis is vital for the development of efficient therapeutic strategies for these Candida infections. The concept of host-microbiota crosstalk plays critical roles in human health and microbiota dysbiosis and is responsible for various pathologies. Through this review, we attempted to analyze the types of human microbiota and provide an update on the current understanding in the context of health and Candida infections. The information in this article will help as a resource for development of targeted microbial therapies such as pre-/pro-biotics and microbiota transplant that has gained advantage in recent times over antibiotics and established as novel therapeutic strategy.
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Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy. Sci Rep 2021; 11:2738. [PMID: 33531650 PMCID: PMC7854632 DOI: 10.1038/s41598-021-82538-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 01/21/2021] [Indexed: 02/07/2023] Open
Abstract
Gut bacterial microbiome dysbiosis in type 2 Diabetes Mellitus (T2DM) has been reported, but such an association with Diabetic Retinopathy (DR) is not known. We explored possible link between gut bacterial microbiome dysbiosis and DR. Using fecal samples of healthy controls (HC) and people with T2DM with/without DR, gut bacterial communities were analysed using 16S rRNA gene sequencing and data analysed using QIIME and R software. Dysbiosis in the gut microbiomes, at phyla and genera level, was observed in people with T2DM and DR compared to HC. People with DR exhibited greater discrimination from HC. Microbiomes of people with T2DM and DR were also significantly different. Both DM and DR microbiomes showed a decrease in anti-inflammatory, probiotic and other bacteria that could be pathogenic, compared to HC, and the observed change was more pronounced in people with DR. This is the first report demonstrating dysbiosis in the gut microbiome (alteration in the diversity and abundance at the phyla and genera level) in people with DR compared to HC. Such studies would help in developing novel and targeted therapies to improve treatment of DR.
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Alterations in the conjunctival surface bacterial microbiome in bacterial keratitis patients. Exp Eye Res 2020; 203:108418. [PMID: 33359511 DOI: 10.1016/j.exer.2020.108418] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/17/2020] [Accepted: 12/18/2020] [Indexed: 01/09/2023]
Abstract
Microbial keratitis is an infectious disease of the eye, in which the cornea is inflamed. Under severe conditions, keratitis can lead to significant loss of vision and enucleation of the eye. Ocular trauma is the major risk factor causing keratitis and microorganisms viz., bacteria, fungi, viruses are the causative agents. The current study characterized the conjunctival bacterial microbiomes of healthy individuals and individuals with bacterial keratitis (BK) and assessed whether ocular microbiome dysbiosis is prevalent in BK patients. Ocular bacterial microbiomes were generated from the conjunctival swabs of healthy controls (HC-SW) and conjunctival swabs (BK-SW) and corneal scrapings (BK-CR) of BK patients using V3-V4 amplicon sequencing and data analysed using QIIME and R software. The Alpha diversity indices, diversity and abundance of different phyla and genera, heat map analysis, NMDS plots and inferred functional pathway analysis clearly discriminated the bacterial microbiomes of conjunctival swabs of healthy controls from that of BK patients. Preponderance of negative interactions in the hub genera were observed in BK-CR and BK-SW compared to HC-SW. In addition, a consistent increase in the abundance of pathogenic bacteria, as inferred from published literature, was observed in the conjunctiva of BK patients compared to HC and this may be related to causing or exacerbating ocular surface inflammation. This is the first study demonstrating dysbiosis in the ocular bacterial microbiome of conjunctiva of bacterial keratitis patients compared to the eye of healthy controls. The bacterial microbiome associated with the corneal scrapings of keratitis individuals is also described for the first time.
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Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO, Shin JH. Dynamics of Fecal Microbiota with and without Invasive Cervical Cancer and Its Application in Early Diagnosis. Cancers (Basel) 2020; 12:cancers12123800. [PMID: 33339445 PMCID: PMC7766064 DOI: 10.3390/cancers12123800] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The fecal microbiome has been suggested to be linked to invasive cervical cancer (ICC). Considering that ICC is common in women, it is important to identify bacterial signatures from fecal microbiota that contribute in classifying cervical cancer. Although previous studies have suggested possible biomarkers based on fecal microbiota, limited information exists in terms of the diagnostic ability using gut microbiota-derived signatures for detecting early ICC. The purpose of this study was to investigate the potential association between early ICC and fecal microbiota and to examine whether fecal microbiota-derived markers can be utilized as a non-invasive tool to diagnose early ICC using machine learning (ML) techniques. Further studies to incorporate quantitative and qualitative characterization of identified individual bacterial genus and validate our model in larger cohorts are imperative in terms of causality for the association between cervical cancer and microbes. Abstract The fecal microbiota is being increasingly implicated in the diagnosis of various diseases. However, evidence on changes in the fecal microbiota in invasive cervical cancer (ICC) remains scarce. Here, we aimed to investigate the fecal microbiota of our cohorts, develop a diagnostic model for predicting early ICC, and identify potential fecal microbiota-derived biomarkers using amplicon sequencing data. We obtained fecal samples from 29 healthy women (HC) and 17 women with clinically confirmed early ICC (CAN). Although Shannon’s diversity index was not reached at statistical significance, the Chao1 and Observed operational taxonomic units (OTUs) in fecal microbiota was significantly different between CAN and HC group. Furthermore, there were significant differences in the taxonomic profiles between HC and CAN; Prevotella was significantly more abundant in the CAN group and Clostridium in the HC group. Linear discriminant analysis effect size (LEfSe) analysis was applied to validate the taxonomic differences at the genus level. Furthermore, we identified a set of seven bacterial genera that were used to construct a machine learning (ML)-based classifier model to distinguish CAN from patients with HC. The model had high diagnostic utility (area under the curve [AUC] = 0.913) for predicting early ICC. Our study provides an initial step toward exploring the fecal microbiota and helps clinicians diagnose.
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Affiliation(s)
- Gi-Ung Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
| | - Da-Ryung Jung
- Department of Biomedical Convergence Science & Technology, Kyungpook National University, Daegu 41566, Korea
| | - Yoon Hee Lee
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Daegu 41404, Korea
- Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea
| | - Se Young Jeon
- Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea
| | - Hyung Soo Han
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea
- Department of Physiology, School of Medicine, Kyungpook National University, Daegu 41405, Korea
| | - Gun Oh Chong
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Daegu 41404, Korea
- Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
- Department of Biomedical Convergence Science & Technology, Kyungpook National University, Daegu 41566, Korea
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Gut mycobiomes are altered in people with type 2 Diabetes Mellitus and Diabetic Retinopathy. PLoS One 2020; 15:e0243077. [PMID: 33259537 PMCID: PMC7707496 DOI: 10.1371/journal.pone.0243077] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 11/14/2020] [Indexed: 01/14/2023] Open
Abstract
Studies have documented dysbiosis in the gut mycobiome in people with Type 2 diabetes mellitus (T2DM). However, it is not known whether dysbiosis in the gut mycobiome of T2DM patients would be reflected in people with diabetic retinopathy (DR) and if so, is the observed mycobiome dysbiosis similar in people with T2DM and DR. Gut mycobiomes were generated from healthy controls (HC), people with T2DM and people with DR through Illumina sequencing of ITS2 region. Data were analysed using QIIME and R software. Dysbiotic changes were observed in people with T2DM and DR compared to HC at the phyla and genera level. Mycobiomes of HC, T2DM and DR could be discriminated by heat map analysis, Beta diversity analysis and LEfSE analysis. Spearman correlation of fungal genera indicated more negative correlation in HC compared to T2DM and DR mycobiomes. This study demonstrates dysbiosis in the gut mycobiomes in people with T2DM and DR compared to HC. These differences were significant both at the phyla and genera level between people with T2DM and DR as well. Such studies on mycobiomes may provide new insights and directions to identification of specific fungi associated with T2DM and DR and help developing novel therapies for Diabetes Mellitus and DR.
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Arunasri K, Mahesh M, Sai Prashanthi G, Jayasudha R, Kalyana Chakravarthy S, Tyagi M, Pappuru RR, Shivaji S. Mycobiome changes in the vitreous of post fever retinitis patients. PLoS One 2020; 15:e0242138. [PMID: 33211730 PMCID: PMC7676714 DOI: 10.1371/journal.pone.0242138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
Fungi have been associated with various diseases of the eye like keratitis, uveitis and endophthalmitis. Despite this fact, fungal microbiome (mycobiome) studies compared to the bacterial microbiome studies have remained neglected. In the present study, using metagenomic sequencing, the mycobiomes of the vitreous of healthy control individuals (VC, n = 15) and individuals with post fever retinitis + non-PFR uveitis (PFR+, n = 9) were analysed and compared. The results indicated that Ascomycota was the most predominant phylum in both VC and PFR+ groups. Further, at the genera level it was observed that the abundance of 17 fungal genera were significantly different in post fever retinitis (PFR, n = 6) group compared to control group. Of these 17 genera, it was observed that 14 genera were relatively more abundant in PFR group and the remaining 3 genera in the VC group. Genus Saccharomyces, a commensal of the gut and skin, was predominantly present in the vitreous of both the cohorts, however it was significantly less abundant in PFR group. Further, significant increase in the genera that have a pathogenic interaction with the host were observed in PFR group. On the whole the mycobiome in both the groups differed significantly and formed two distinct clusters in the heatmap and Principal co-ordinate analysis. These results demonstrate significant changes in the mycobiome from the vitreous of post fever retinitis patients compared to healthy controls thus implying that dysbiotic changes in the fungal vitreous microbiome are associated with PFR.
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Affiliation(s)
- Kotakonda Arunasri
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Malleswarapu Mahesh
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Gumpili Sai Prashanthi
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Sama Kalyana Chakravarthy
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Mudit Tyagi
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Rajeev R. Pappuru
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad, India
- * E-mail:
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Tian R, Zou H, Wang L, Liu L, Song M, Zhang H. Analysis of differentially expressed genes in bacterial and fungal keratitis. Indian J Ophthalmol 2020; 68:39-46. [PMID: 31856463 PMCID: PMC6951210 DOI: 10.4103/ijo.ijo_65_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose: This study was aimed at identifying differentially expressed genes (DEGs) in bacterial and fungal keratitis. The candidate genes can be selected and quantified to distinguish between causative agents of infectious keratitis to improve therapeutic outcomes. Methods: The expression profile of bacterial or fungal infection, and normal corneal tissues were downloaded from the Gene Expression Omnibus. The limma package in R was used to screen DEGs in bacterial and fungal keratitis. The Co-Express tool was used to calculate correlation coefficients of co-expressed genes. The “Advanced network merge” function of Cytoscape tool was applied to obtain a fusional co-expression network based on bacterial and fungal keratitis DEGs. Finally, functional enrichment analysis by DAVID software and KEGG analysis by KOBAS of DEGs in fusion network were performed. Results: In total, 451 DEGs in bacterial keratitis and 353 DEGs in fungal keratitis were screened, among which 148 DEGs were found only in bacterial keratitis and 50 DEGs only in fungal keratitis. Besides, 117 co-expressed gene pairs were identified among bacterial keratitis DEGs and 87 pairs among fungal keratitis DEGs. In total, nine biological pathways and seven KEGG pathways were screened by analyzing DEGs in the fusional co-expression network. Conclusion: TLR4 is the representative DEG specific to bacterial keratitis, and SOD2 is the representative DEG specific to fungal keratitis, both of which are promising candidate genes to distinguish between bacterial and fungal keratitis.
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Affiliation(s)
- Rui Tian
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - He Zou
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Lufei Wang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Lu Liu
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Meijiao Song
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Hui Zhang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, Jilin Province, China
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Peng L, Zhong J, Xiao Y, Wang B, Li S, Deng Y, He D, Yuan J. Therapeutic effects of an anti-IL-6 antibody in fungal keratitis: Macrophage inhibition and T cell subset regulation. Int Immunopharmacol 2020; 85:106649. [DOI: 10.1016/j.intimp.2020.106649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 12/24/2022]
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Ma C, Huo D, You Z, Peng Q, Jiang S, Chang H, Zhang J, Zhang H. Differential pattern of indigenous microbiome responses to probiotic Bifidobacterium lactis V9 consumption across subjects. Food Res Int 2020; 136:109496. [PMID: 32846577 DOI: 10.1016/j.foodres.2020.109496] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 01/13/2023]
Abstract
Various factors, including those associated with the host and environment, should be considered to further explore the health-promoting effects of probiotics. However, it is important to consider persistence as a basic but crucial factor in the function of probiotics in the gut. To date, few studies have investigated the factors that influence probiotic persistence. To address these challenges, we designed a cohort experiment that included 49 subjects and used the probiotic Bifidobacterium lactis V9 to identify intestinal microbiota related to probiotic persistence based on high-throughput amplicon sequencing. All of the subjects were divided into three groups (Persisters, Temporary and Non-Persisters) according to the detected amount of viable Bifidobacterium lactis V9 in their faeces. Accordingly, the intestinal microbiota fluctuations in the Persisters group were significant and persistent, whereas those observed in the Non-Persisters group were limited. At the genus level, up to seven genera changed significantly in Persisters group, whereas only the genus Anaerobacterium changed significantly in Non-Persisters group throughout the experiment. At baseline, we observed highly distinct microbial alpha diversity and taxonomic features between the Persisters and Non-Persisters groups. A total of 12 genera were associated with probiotic persistence, with Bifidobacterium and eight other genera negatively associated with probiotic persistence and Anaerobacterium, Paraprevotella and Erysipelatoclostridium positively associated with probiotic persistence. Based on these potential biomarkers, an "Anti-Engraftment Index" (AEI) was derived to classify and predict probiotic persistence in test and validation cohorts with high accuracy. However, we also observed that the AEI did not work in other probiotic consumption experiments, indicating that the AEI was strain-specific.
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Affiliation(s)
- Chenchen Ma
- College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Dongxue Huo
- College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Zhengkai You
- College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Qiannan Peng
- College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Shuaiming Jiang
- College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Haibo Chang
- College of Food Science and Technology, Hainan University, Haikou 570228, PR China
| | - Jiachao Zhang
- College of Food Science and Technology, Hainan University, Haikou 570228, PR China; Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Produce Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010018, PR China.
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Produce Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010018, PR China.
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Liu CZ, Chen W, Wang MX, Wang Y, Chen LQ, Zhao F, Shi Y, Liu HJ, Dou XB, Liu C, Chen H. Dendrobium officinale Kimura et Migo and American ginseng mixture: A Chinese herbal formulation for gut microbiota modulation. Chin J Nat Med 2020; 18:446-459. [PMID: 32503736 DOI: 10.1016/s1875-5364(20)30052-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Indexed: 02/07/2023]
Abstract
Dendrobium officinale Kimura et Migo (D. officinale) is a famous traditional Chinese medicine (TCM). A mixture of D. officinale and American ginseng has been shown to enhance cell-mediated immunity, humoral immunity, and monocyte/macrophage functions in mice. Here, the effects of a D. officinale and American ginseng mixture on the structure of gut microbial community in dogs were examined using high-throughput 16S rRNA gene amplicon sequencing. The data revealed that while the mixture did not change the diversity of gut microbial community significantly, differences among individuals were significantly reduced. Furthermore, the mixture-responsive operational taxonomic units (OTUs) exhibited a phase-dependent expression pattern. Fifty-five OTUs were found to exhibit a mixture-induced expression pattern, among which one third were short-chain fatty acid (SCFA)-producing genera and the others were probiotic genera included Lactobacillus spp., Sutterella, Alistipes, Anaerovorax, Bilophila, Coprococcus, Gordonibacter, Oscillibacter, among others. By contrast, 36% of the OTUs exhibiting a mixture-repressed expression pattern were disease-associated microorganisms, and six genera, namely Actinomyces, Escherichia/Shigella, Fusobacterium, Slackia, Streptococcus and Solobacterium, were associated with cancer. In addition, five genera were closely associated with diabetes, namely Collinsella, Rothia, Howardella, Slackia and Intestinibacter. Our results indicate that this D. officinale and American ginseng mixture may be used as a prebiotic agent to enhance SCFA-producing genera and prevent gut dysbiosis.
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Affiliation(s)
- Cheng-Zhi Liu
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Wei Chen
- Hangzhou Huqing yu tang Traditional Chinese Medicine Mordernize Institute, Hangzhou 311100, China
| | - Mei-Xia Wang
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Ying Wang
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Li-Qing Chen
- Hangzhou Huqing yu tang Traditional Chinese Medicine Mordernize Institute, Hangzhou 311100, China
| | - Feng Zhao
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China; College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Ya Shi
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Hui-Jun Liu
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China
| | - Xiao-Bing Dou
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Chao Liu
- Department of Orthopaedics, Sir Sun Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China.
| | - Huan Chen
- Key laboratory of Microbial technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou 310012, China; NMPA Key laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute of Microbiology, Hangzhou 310012, China.
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Arunasri K, Mahesh M, Sai Prashanthi G, Jayasudha R, Kalyana Chakravarthy S, Tyagi M, Pappuru RR, Shivaji S. Comparison of the Vitreous Fluid Bacterial Microbiomes between Individuals with Post Fever Retinitis and Healthy Controls. Microorganisms 2020; 8:E751. [PMID: 32429503 PMCID: PMC7285296 DOI: 10.3390/microorganisms8050751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/23/2020] [Accepted: 05/04/2020] [Indexed: 12/21/2022] Open
Abstract
Ocular microbiome research has gained momentum in the recent past and has provided new insights into health and disease conditions. However, studies on sight threatening intraocular inflammatory diseases have remained untouched. In the present study, we attempted to identify the bacterial microbiome associated with post fever retinitis using a metagenomic sequencing approach. For this purpose, bacterial ocular microbiomes were generated from vitreous samples collected from control individuals (VC, n = 19) and individuals with post fever retinitis (PFR, n = 9), and analysed. The results revealed 18 discriminative genera in the microbiomes of the two cohorts out of which 16 genera were enriched in VC and the remaining two in PFR group. These discriminative genera were inferred to have antimicrobial, anti-inflammatory, and probiotic function. Only two pathogenic bacteria were differentially abundant in 20% of the PFR samples. PCoA and heatmap analysis showed that the vitreous microbiomes of VC and PFR formed two distinct clusters indicating dysbiosis in the vitreous bacterial microbiomes. Functional assignments and network analysis also revealed that the vitreous bacterial microbiomes in the control group exhibited more evenness in the bacterial diversity and several bacteria had antimicrobial function compared to the PFR group.
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Affiliation(s)
- Kotakonda Arunasri
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Malleswarapu Mahesh
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Gumpili Sai Prashanthi
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Sama Kalyana Chakravarthy
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
| | - Mudit Tyagi
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (M.T.); (R.R.P.)
| | - Rajeev R. Pappuru
- Smt. Kanuri Santhamma Centre for Vitreo Retinal Diseases, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (M.T.); (R.R.P.)
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, L V Prasad Marg, Banjara Hills, Hyderabad 500034, India; (K.A.); (M.M.); (G.S.P.); (R.J.); (S.K.C.)
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Shivaji S. Connect between gut microbiome and diseases of the human eye. J Biosci 2019; 44:110. [PMID: 31719219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Implicating dysbiosis of gut microbiome in digestive tract diseases/diet-related diseases (obesity, inflammatory bowel disease, enterocolitis, diabetes, etc.) may be expected. However, when gut microbiome dysbiosis is implicated in extraintestinal diseases like cancers, muscular dystrophy, mental disorders, vaginosis, etc., it is all the more challenging. An additional challenge would be to ascertain the role of gut microbiome in ocular diseases, which are as remote as the brain. The present review highlights studies that establish the connect between gut microbiome dysbiosis and inflammatory ocular diseases such as uveitis, bacterial keratitis, fungal keratitis, etc.
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Affiliation(s)
- S Shivaji
- Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500 034, India,
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Senapati T, Kothidar A, Banerjee SK, DAS B. Insights into the gastrointestinal tract microbiomes of Indian population. J Biosci 2019; 44:113. [PMID: 31719222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Trillions of microbes living in the gastrointestinal tract (GIT) of the human body finely tune homeostatic equilibrium in the GIT ecosystem and encode key functionalities that play crucial role in host metabolic functions, synthesis of macro- and micronutrients, xenobiotics metabolisms, development of innate and adaptive immune systems, tissue and organ developments and resistance against invasion of enteric pathogens. The microbial diversity and richness of GIT ecosystem varies greatly between individuals and over time. Extent of taxonomic and functional variations in GIT ecosystem is linked with dietary habit, pharmaceuticals usages, age, sex, body mass index, ethnicity, geography, altitude and civilization. Understanding a holistic picture of GIT microbiome of healthy people living across geography and identifying population specific 'keystone' taxa is of immense importance for identifying microbial species that may provide protection against chronic and metabolic diseases. Knowledge on geographic or ethnicity specific microbial signatures may also help us to understand the varied efficacy of different drugs and vaccines in different population. India is the home of more than 1.36 billion people belonging to 2000 human communities residing in well distinct geography. In the present review, we discuss the microbial signatures in health and diseases of the rural and urban Indians living in sea level and high altitude areas.
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Affiliation(s)
- Tarosi Senapati
- Molecular Genetics Laboratory, Centre for Human Microbial Ecology, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121 001, India
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Jayasudha R, Kalyana Chakravarthy S, Sai Prashanthi G, Sharma S, Tyagi M, Shivaji S. Implicating Dysbiosis of the Gut Fungal Microbiome in Uveitis, an Inflammatory Disease of the Eye. Invest Ophthalmol Vis Sci 2019; 60:1384-1393. [PMID: 30938773 DOI: 10.1167/iovs.18-26426] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose In this study, the gut fungal microbiome of uveitis (UVT) patients was generated and compared with healthy controls (HC) to identify dysbiosis in UVT patients and ascertain the role of gut fungal microbiome in disease pathology. Methods In the present study, gut fungal microbiomes were analyzed in the fecal samples of HC (n = 24) and UVT patients (n = 14) using high-throughput Illumina sequencing of ITS2 region of the fungal ribosomal RNA. QIIME and R software were used for data analysis. Results The gut fungal richness and diversity were significantly decreased in UVT patients compared to HC. Our analyses showed enrichment of several pathogenic fungi including Malassezia restricta, Candida albicans, Candida glabrata, and Aspergillus gracilis in UVT patients. Heatmap and discriminatory OTUs further confirmed the disparities between UVT and HC microbiomes. Conclusions This is the first study demonstrating dysbiosis in the gut fungal communities of UVT patients indicating the importance of fungal microbiome in the disease pathology. These initial findings might warrant further investigation into the fungal microbiome, especially interactions between fungal and bacterial that then might give further insight into how probiotics or fecal transplants might benefit.
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Affiliation(s)
- Rajagopalaboopathi Jayasudha
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, India
| | - Sama Kalyana Chakravarthy
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, India
| | - Gumpili Sai Prashanthi
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, India
| | - Savitri Sharma
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, India
| | - Mudit Tyagi
- Smt. Kanuri Santhamma Centre for Vitreoretinal Diseases, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, India
| | - Sisinthy Shivaji
- Jhaveri Microbiology Centre, Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy Campus, Hyderabad, India
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Senapati T, Kothidar A, Banerjee SK, Das B. Insights into the gastrointestinal tract microbiomes of Indian population. J Biosci 2019. [DOI: 10.1007/s12038-019-9927-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Alterations in the Ocular Surface Fungal Microbiome in Fungal Keratitis Patients. Microorganisms 2019; 7:microorganisms7090309. [PMID: 31480776 PMCID: PMC6780152 DOI: 10.3390/microorganisms7090309] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/28/2019] [Accepted: 08/31/2019] [Indexed: 12/17/2022] Open
Abstract
Keratitis, an inflammatory disease of the eye, when neglected could lead to sight-threatening complications and ultimately blindness. Globally, over a million people are affected by keratitis annually. Keratitis has a microbial etiology and is caused by bacteria, fungi, viruses, etc. The present study compared the ocular surface fungal microbiome of healthy individuals and individuals with fungal keratitis. Fungal microbiomes from the conjunctival swabs of healthy individuals and from conjunctival swabs and corneal scrapings of individuals with fungal keratitis were generated using ITS2 region amplicons. Microbiomes were sequenced using Illumina MiSeq 2 × 250 base pair chemistry with a paired-end protocol. Based on Alpha diversity indices, phylum and genera level diversity, abundance differences, and heat map analysis, the fungal microbiomes of conjunctival swabs and corneal scrapings of individuals with fungal keratitis exhibited dysbiosis (alterations in the diversity and abundance) compared to the ocular surface microbiome of the healthy control individuals. This is the first report indicating dysbiosis in the fungal microbiome of conjunctival swabs and corneal scrapings in individuals with fungal keratitis. A total of 11 genera present in the majority of the eyes constituted the variable core ocular microbiome.
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