Chapter 1. From the gut microbiome to the ocular microbiome: are they associated?

Chapter 2. The cultivable bacteria of the human eye

1. Introduction

2. Commensal microbiome of the ocular surface

2.1. Bacterial load on the ocular surface

2.2. Viable community of bacteria on the ocular surface

2.3. Impact of age on the ocular surface cultivable microbiome

2.5. Impact of geographical location on ocular surface cultivable microbiome

3. Cultivable Microbiome of eye lids and tears

4. Ocular microbiota changes in the diseased eye

4.1 Keratitis

4.2 Conjunctivitis

4.3 Blepharitis

4.5 Orbital cellulitis

4.6 Endopthalmitis

4.7 Uveitis

4.8. Retinitis

4.9. Post-fever Retinitis

4.10. Dacryocystitis

4.11. Meibomian gland dysfunction

4.12. Dry eye disease

4.13. Stevens-Johnson syndrome

4.14. Sjorgen's syndrome

4.15. Lax eyelid syndrome

4.16. Ocular graft-vs host disease

4.17. Prior to cataract surgery

4.18. Diabetes

4.19. Contact lens use

4.20. Alcoholism

4.21. Chronic Limbal Stem Cell Deficiency

5. Treatment of ocular infectious diseases

6. Conclusions

7. References

Chapter 3. The microbiome of the human eye

1. Introduction

2. What is a microbiome?

3. The microbiome approach

3.2 Metagenome sequencing

4. Identification of ocular bacteria by culture-independent methods

4.1 The ocular surface microbiome using amplicon sequencing

4.2 Impact of age on ocular surface microbiome

4.3 Impact of sex on ocular surface microbiome

4.4.Impact of geographical location on ocular surface cultivable microbiome

5. Microbiome of various microhabitats of the eye

6.Effect of Sampling Depth on the ocular surface microbiome

7. Ocular microbiome changes in the diseased eye

7.1 Ocular microbiome of individuals with keratitis

7.2 Ocular microbiome of individuals with Endophthalmitis

7.3 Ocular surface microbiome of individuals with Conjunctivitis

7.4 Ocular surface microbiome of individuals with Blepharitis

7.5 Ocular surface microbiome of individuals with Retinitis

7.7 Ocular surface microbiome of individuals with Dry eye disease

7.8 Ocular surface microbiome of individuals with Stevens-Johnson syndrome

7.9 Ocular surface microbiome of individuals with Sjorgens syndrome

7.10 Ocular surface microbiome of individuals with Ocular Graft Versus Host Disease

7.11 Ocular surface microbiome of individuals with Diabetes Mellitus

7.13 Ocular surface microbiome of individuals with Floppy Eyelid Syndrome

7.14 Ocular surface microbiome of individuals with Trachoma

8. Conclusions

9. References

Chapter 4. Antimicrobial resistance in ocular bacteria

1. Introduction

2. AMR in ocular bacteria

3.Factors driving antibiotic resistance in ocular bacteria

4. What is a biofilm?

5. AMR in ocular bacteria is associated with biofilm formation

6.1. Biofilms