Abstract:PurposeTo compare the ocular surface and meibum microbial communities of humans with Demodex Blepharitis (DB) and healthy controls.MethodsConjunctival sac and meibum samples from 25 DB patients and 11 healthy controls were analyzed using metagenomic next-generation sequencing (mNGS).ResultsThe alpha-diversity of the conjunctival sac microbiome of the DB group (observed, Chao1, ACE) was lower than that of the control group, whereas all meibum diversity indicators were similar. In conjunctival samples, the relat… Show more
“…Consistent with other studies, the main bacterial phyla present on the OSM are Actinobacteria , Firmicutes and Proteobacteria , while Bacteroidetes seems to be more prevalent in studies employing 16S rRNA gene sequencing ( Zhou et al., 2014 ; Doan et al., 2016 ; Huang et al., 2016 ; Ozkan et al., 2017 ; Ham et al., 2018 ; Dong et al., 2019 ; Li S. et al., 2019 ; Li Z. et al., 2019 ; Yau et al., 2019 ; Andersson et al., 2021 ; Kang et al., 2021 ; Liang et al., 2021 ; Zhang et al., 2021 ; Zysset-Burri et al., 2021 ; Fu et al., 2022 ). The observed overlap of the main constituents of the OSM reinforce the validity of the presented method to characterize the OSM.…”
PurposeThe low microbial abundance on the ocular surface results in challenges in the characterization of its microbiome. The purpose of this study was to reveal factors introducing bias in the pipeline from sample collection to data analysis of low-abundant microbiomes.MethodsLower conjunctiva and lower lid swabs were collected from six participants using either standard cotton or flocked nylon swabs. Microbial DNA was isolated with two different kits (with or without prior host DNA depletion and mechanical lysis), followed by whole-metagenome shotgun sequencing with a high sequencing depth set at 60 million reads per sample. The relative microbial compositions were generated using the two different tools MetaPhlan3 and Kraken2.ResultsThe total amount of extracted DNA was increased by using nylon flocked swabs on the lower conjunctiva. In total, 269 microbial species were detected. The most abundant bacterial phyla were Actinobacteria, Firmicutes and Proteobacteria. Depending on the DNA extraction kit and tool used for profiling, the microbial composition and the relative abundance of viruses varied.ConclusionThe microbial composition on the ocular surface is not dependent on the swab type, but on the DNA extraction method and profiling tool. These factors have to be considered in further studies about the ocular surface microbiome and other sparsely colonized microbiomes in order to improve data reproducibility. Understanding challenges and biases in the characterization of the ocular surface microbiome may set the basis for microbiome-altering interventions for treatment of ocular surface associated diseases.
“…Consistent with other studies, the main bacterial phyla present on the OSM are Actinobacteria , Firmicutes and Proteobacteria , while Bacteroidetes seems to be more prevalent in studies employing 16S rRNA gene sequencing ( Zhou et al., 2014 ; Doan et al., 2016 ; Huang et al., 2016 ; Ozkan et al., 2017 ; Ham et al., 2018 ; Dong et al., 2019 ; Li S. et al., 2019 ; Li Z. et al., 2019 ; Yau et al., 2019 ; Andersson et al., 2021 ; Kang et al., 2021 ; Liang et al., 2021 ; Zhang et al., 2021 ; Zysset-Burri et al., 2021 ; Fu et al., 2022 ). The observed overlap of the main constituents of the OSM reinforce the validity of the presented method to characterize the OSM.…”
PurposeThe low microbial abundance on the ocular surface results in challenges in the characterization of its microbiome. The purpose of this study was to reveal factors introducing bias in the pipeline from sample collection to data analysis of low-abundant microbiomes.MethodsLower conjunctiva and lower lid swabs were collected from six participants using either standard cotton or flocked nylon swabs. Microbial DNA was isolated with two different kits (with or without prior host DNA depletion and mechanical lysis), followed by whole-metagenome shotgun sequencing with a high sequencing depth set at 60 million reads per sample. The relative microbial compositions were generated using the two different tools MetaPhlan3 and Kraken2.ResultsThe total amount of extracted DNA was increased by using nylon flocked swabs on the lower conjunctiva. In total, 269 microbial species were detected. The most abundant bacterial phyla were Actinobacteria, Firmicutes and Proteobacteria. Depending on the DNA extraction kit and tool used for profiling, the microbial composition and the relative abundance of viruses varied.ConclusionThe microbial composition on the ocular surface is not dependent on the swab type, but on the DNA extraction method and profiling tool. These factors have to be considered in further studies about the ocular surface microbiome and other sparsely colonized microbiomes in order to improve data reproducibility. Understanding challenges and biases in the characterization of the ocular surface microbiome may set the basis for microbiome-altering interventions for treatment of ocular surface associated diseases.
“… 52 Figure 1 Relative composition of major kingdoms on human conjunctiva (% of microbial reads), based on 5 studies using the metagenomic shotgun technique, showing an abundant number of bacterial reads (average 91%, median 93%, range [78–98%]), less viral reads (average 5%, median 1%, range [0–20%]), and minimal fungal or other eukaryotic reads (average 4%, median 4%, range [1–7%]). References: Fu et al 2022; 51 Zysset−Burri et al 2021; 39 Kang et al 2021; 49 Deng et al 2020; 48 Wen et al 50 …”
Section: Microbial Flora At the Ocular Surfacementioning
confidence: 99%
“…17 publications featuring 18 cohorts of healthy individuals, including 2 pediatric, met these criteria. 4 , 39 , 49 , 51 , 53–65 Of the available data, relative abundances were reported in at least 2 different cohorts for 20 genera, as shown in Figure 2A . Data from conjunctival samples in one study were provided to us by one of the present co-authors.…”
Section: Bacterial Composition Of the Osmmentioning
confidence: 99%
“…References: Fu et al 2022;. 51 Zysset−Burri et al 2021; 39 Kang et al 2021; 49 Zhang et al 2021; 64 Liang et al 2021; 60 Andersson et al 2021; 53 Dong et al 2019; 55 Li et al 2019 (n= 54); 59 Li et al 2019 (n= 23); 58 Yau et al 2019; 62 Butcher et al 2017; 54 Ham B et al 2018; 56 Ozkan et al 2017; 61 Zhang et al 2017; 63 Doan et al 2016; 4 Huang et al 2016; 57 Zhou et al 2014 (adult and paediatric cohorts). 65 …”
Section: Bacterial Composition Of the Osmmentioning
While pathogens of the eye have been studied for a very long time, the existence of resident microbes on the surface of healthy eyes has gained interest only recently. It appears that commensal microbes are a normal feature of the healthy eye, whose role and properties are currently the subject of extensive research. This review provides an overview of studies that have used 16s rRNA gene sequencing and whole metagenome shotgun sequencing to characterize microbial communities associated with the healthy ocular surface from kingdom to genus level. Bacteria are the primary colonizers of the healthy ocular surface, with three predominant phyla:
Proteobacteria, Actinobacteria
, and
Firmicutes
, regardless of the host, environment, and method used. Refining the microbial classification to the genus level reveals a highly variable distribution from one individual and study to another. Factors accounting for this variability are intriguing - it is currently unknown to what extent this is attributable to the individuals and their environment and how much is artifactual. Clearly, it is technically challenging to accurately describe the microorganisms of the ocular surface because their abundance is relatively low, thus, permitting substantial contaminations. More research is needed, including better experimental standards to prevent biases, and the exploration of the ocular surface microbiome’s role in a spectrum of healthy to pathological states. Outcomes from such research include the opportunity for therapeutic interventions targeting the microbiome.
“…Meibomian gland dysfunction has been shown to alter the complexity of the OSM composition, which varied by disease severity [7]. In Demodex blepharitis, the relative abundance of Proteobacteria has been shown to be higher, with lower abundances of Actinobacteria and Firmicutes in the patients with blepharitis compared to healthy controls [19]. Lower microbiome diversity was also seen in patients with non-Sjogren-associated dry eye compared to normal controls [20].…”
Section: Ocular Surface Dysbiosis and Diseasementioning
Purpose of review
The purpose of this review is to provide an update on emerging literature on the role of the ocular surface microbiome (OSM) in allergic eye diseases.
Recent findings
Findings in the literature suggest that the ocular surface microbiome plays a role in the pathophysiology and course of allergic disease of the ocular surface.
Summary
Knowledge regarding the role of the ocular surface microbiome in allergic disease is important to guide development of targets for future therapeutic interventions.
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