Functional metagenomic profile of the lacrimal sac microbial communities in primary acquired nasolacrimal duct obstruction: The Lacriome paper 2

Abstract

Purpose To study the functional metagenomic profile of the microbes isolated from the lacrimal sac of patients with primary acquired nasolacrimal duct obstruction. Methods A prospective study was performed on 10 consecutive lacrimal sac samples obtained for the metagenomic analysis from patients with primary acquired nasolacrimal duct obstruction ( who underwent endoscopic dacryocystorhinostomy at a tertiary care Dacryology service. The samples were collected intraoperatively soon after a full-length lacrimal sac marsupialization and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina NOVASEQ 6000TM platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMetaTM pipeline and functional analysis using the MG-RASTTM pipeline. Results The microbial gene mapping and protein prediction demonstrated proteins with known functions to range from 66.41% to 84.03% across the samples. The functional category distribution of Kyoto Encyclopedia of Genes and Genomes ortholog (level 1 data) showed metabolism to be the most commonly involved function followed by environmental information processes, genetic information processes and cellular processes. The functional subsystem profiling demonstrated genes associated with carbohydrate, protein and RNA metabolism, Amino acids and their derivatives, cofactors and prosthetic groups and factors involved in cell structure regulation and cell cycle control. Conclusion This is the first functional metagenomic profile of the lacrimal sac microbiota from patients with primary acquired nasolacrimal duct obstruction. Functional analysis has provided newer insights into the ecosystem dynamics and strategies of microbial communities inhabiting the lacrimal sac. Further Lacriome studies may provide clues for better understanding of the disease etiopathogenesis.

Metagenomics of infective canaliculitis: The Lacriome paper 3

“…15 The functional profiling of microbial communities in PANDO has demonstrated their involvement in a wide range of metabolic processes, environmental information processes, genetic information processes, cell cycle regulation, dormancy, and sporulation. 16 In comparison, the metagenomic profile of infectious canaliculitis is quite distinct from that of PANDO, as demonstrated in the present study.…”

Clinical characteristics and cytological changes in mucinous obstruction diagnosed by dacryoendoscopy

“…To comprehend the fundamental etiopathogenesis of PANDO, the concept of the ‘lacriome’ was recently introduced, defining it as the collective microenvironments of the lacrimal drainage system. 18 – 21 Metagenomic profiling of organisms isolated from PANDO patients commonly reveals the presence of bacteria, followed by viruses and archaea. 22 In this study, we observed bacterial colonies in 22.6% of mucinous obstruction cases, but none in membranous obstruction, with a significant difference between the two groups.…”

Microbial Metagenomics of the Extubated Lacrimal Stents Following Dacryocystorhinostomy: The Lacriome Paper 4

“…Functional metagenomics of the microbial isolates from lacrimal stents was mostly similar to those isolated from the lacrimal sac in patients with primary acquired nasolacrimal duct obstruction. 21 The stent microbial communities were involved in several metabolic, environmental, and genetic information processes. The Kyoto Encyclopedia of Genes and Genomes and Cluster of Orthologous Genes annotation profiles showed high expression of exodeoxyribonuclease, iron complex transport system permease, methyl-accepting chemotaxis proteins, valine-glycine repeat G proteins, 3-oxacyl reductase fabG protein, and regulatory subunits of transposase, bacterial NADPH-aldehyde dehydrogenase, and multidrug efflux pumps (Fig.…”

“…The whole shotgun metagenome sequencing technique was similar to the one published earlier. 20,21 In brief, following the DNA extraction and quality assessment, the Qubit 4.0 fluorometer and DNA HS assay kit (Thermo Fischer Scientific, MA, U.S.A.) were used to quantify the final libraries. Insert size of the library was identified using the highly sensitive D1000 screentapes on Tapestation 4150 (Agilent, CA, U.S.A.).…”