Alterations in the gut bacterial microbiome in fungal Keratitis patients

Whole-Genome Sequencing Redefines Shewanella Taxonomy

The genus Shewanella encompasses a diverse group of Gram negative, primarily aquatic bacteria with a remarkable ecological relevance, an outstanding set of metabolic features and an emergent clinical importance. The rapid expansion of the genus over the 2000 s has prompted questions on the real taxonomic position of some isolates and species. Recent work by us and others identified inconsistencies in the existing species classification. In this study we aimed to clarify such issues across the entire genus, making use of the genomic information publicly available worldwide. Phylogenomic analyses, including comparisons based on genome-wide identity indexes (digital DNA-DNA hybridization and Average Nucleotide Identity) combined with core and accessory genome content evaluation suggested that the taxonomic position of 64 of the 131 analyzed strains should be revisited. Based on the genomic information currently available, emended descriptions for some Shewanella species are proposed. Our study establishes for the first time a whole-genome based phylogeny for Shewanella spp. including a classification at the subspecific level.

Anatomic Characterization of the Ocular Surface Microbiome in Children

The microbiome is important in the evolution of the immune system in children; however, information is lacking regarding the composition of the pediatric ocular microbiome and its surrounding structures. A prospective, cross-sectional study of the ocular microbiome was conducted in children <18 years old. Samples from the inferior conjunctival fornix of both eyes, eyelid margin, and periocular skin underwent DNA amplification and 16S sequencing using Illumina MiSeq 250. The microbiome was analyzed using Qiime. Statistical analysis was performed using a two-sided Student’s t-test, diversity indices, and principal coordinate analysis. A total of 15 children were enrolled. The ocular surface microbiome was predominantly composed of Proteobacteria, whereas Bacteroidetes dominated the eyelid margin, and Firmicutes dominated the periocular skin. Despite these variations, no statistically significant compositional differences were found with Bray-Curtis analysis. The conjunctiva had the lowest Shannon diversity index with a value of 2.3, which was significantly lower than those of the eyelid margin (3.4, p = 0.01) and the periocular skin (3.5, p = 0.001). However, the evenness of the species using Faith’s phylogenetic diversity index was similar at all sites. Overall, the ocular surface microbiome is dominated by Proteobacteria in children. The niche is similar to the surrounding structures in terms of composition, but has a lower number and relative abundance of species.

A potential species of next-generation probiotics? The dark and light sides of Bacteroides fragilis in health

Bacteroides fragilis (B. fragilis) is a commensal Gram-negative obligate anaerobe that resides in the mammalian lower gut and can profoundly affect the susceptibility of the host to inflammatory diseases. Previous studies have identified B. fragilis as a common opportunistic pathogen in clinical infections and suggested that it may be responsible for a range of diseases involving a permeable intestinal barrier. However, recent studies of the relationship between nontoxigenic B. fragilis and the immune system have indicated that several B. fragilis strains may be potential probiotic. In the present review, we summarize the factors influencing the intestinal abundance of B. fragilis and discuss the biological interactions between this microbe and the host. Immune system development, age, individual dietary habits, physical condition, drug intake and personal lifestyle habits can all affect the abundance of B. fragilis in the human intestine. Polysaccharide A or outer membrane vesicles from nontoxigenic B. fragilis may mediate beneficial interactions with the host, whereas enterotoxigenic B. fragilis toxin or lipopolysaccharide may stimulate colitis or even systemic inflammation. Generally, this review summarizes the biological characteristics of B. fragilis and describes future application of probiotics.

An Omics Approach to Diagnosing or Investigating Fungal Keratitis

Fungal keratitis (FK) is one of the most severe corneal infectious diseases. FK often leads to poor visual prognosis and thus requires accurate diagnosis. Conventional approaches, including clinical diagnoses, smears, and cultures, often fail to provide reliable diagnostic value. Omics approaches, such as those using genomic, metagenomic, and tear proteomic data sources, provide promising features for improving the diagnosis and monitoring the progression of FK. Genomic approaches are based mainly on detecting amplicons of ribosomal RNA genes, and internal transcribed spacers are gradually gaining popularity in clinical practices. A metagenomic approach based on 16S rRNA genes may help monitor the dynamic change of conjunctival microbiota associated with an FK event, whereas that based on shot-gun and 18S rRNA target enrichment sequencing could have the potential to diagnose FK using clinical samples. A tear proteomic approach may provide comprehensive information about ocular surface defense and injury during FK. Representative up- and down-regulated proteins during FK could also be used as biomarkers to determine the clinical course and develop a treatment strategy in different stages of FK. Consequently, a personalized tear proteomic approach will soon play a key role in FK management.

Fungal-Bacterial Interactions in Health and Disease

Fungi and bacteria encounter each other in various niches of the human body. There, they interact directly with one another or indirectly via the host response. In both cases, interactions can affect host health and disease. In the present review, we summarized current knowledge on fungal-bacterial interactions during their commensal and pathogenic lifestyle. We focus on distinct mucosal niches: the oral cavity, lung, gut, and vagina. In addition, we describe interactions during bloodstream and wound infections and the possible consequences for the human host.

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye

Dysbiosis, or imbalance in the gut microbiome, has been implicated in auto-immune, inflammatory, neurological diseases as well as in cancers. More recently it has also been shown to be associated with ocular diseases. In the present study, the association of gut microbiome dysbiosis with bacterial Keratitis, an inflammatory eye disease which significantly contributes to corneal blindness, was investigated. Bacterial and fungal gut microbiomes were analysed using fecal samples of healthy controls (HC, n = 21) and bacterial Keratitis patients (BK, n = 19). An increase in abundance of several antiinflammatory organisms including Dialister, Megasphaera, Faecalibacterium, Lachnospira, Ruminococcus and Mitsuokella and members of Firmicutes, Veillonellaceae, Ruminococcaceae and Lachnospiraceae was observed in HC compared to BK patients in the bacterial microbiome. In the fungal microbiome, a decrease in the abundance of Mortierella, Rhizopus, Kluyveromyces, Embellisia and Haematonectria and an increase in the abundance of pathogenic fungi Aspergillus and Malassezia were observed in BK patients compared to HC. In addition, heatmaps, PCoA plots and inferred functional profiles also indicated significant variations between the HC and BK microbiomes, which strongly suggest dysbiosis in the gut microbiome of BK patients. This is the first study demonstrating the association of gut microbiome with the pathophysiology of BK and thus supports the gut-eye axis hypothesis. Considering that Keratitis affects about 1 million people annually across the globe, the data could be the basis for developing alternate strategies for treatment like use of probiotics or fecal transplantation to restore the healthy microbiome as a treatment protocol for Keratitis.