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 6000^TM platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMeta^TM pipeline and functional analysis using the MG-RAST^TM 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.

Keywords

Lacrimal microbiome metagenome primary acquired nasolacrimal duct obstruction functional Lacriome

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References

Ali

Paulsen

. Etiopathogenesis of primary acquired nasolacrimal duct obstruction: what We know and what We need to know. Ophthalmic Plast Reconstr Surg 2019; 35: 426–433.

Mills

Bodman

Meyer

, et al. . The microbiologic spectrum of dacryocystitis: a national study of acute versus chronic infection. Ophthalmic Plast Reconstr Surg. 2007; 23: 302–306.

Ali

. Metagenomics of the lacrimal sac in primary acquired nasolacrimal duct obstruction: the lacriome paper 1. Br J Ophthalmol 2021 (Epub).

Ali

. Introducing the concept of “lacriome”. Graefes Arch Clin Exp Ophthalmol 2021;259(5)1087-1088.

Chung

Rafailov

Turbin

, et al. The microbiologic profile of dacryocystitis. Orbit 2019; 38: 72–78.

Ali

Motukupally

Joshi

, et al. The microbiological profile of lacrimal abscess: two decades of experience from a tertiary eye care center. J Ophthalmic Inflamm Infect 2013; 3(1):57.

Ali

Joshi

Naik

, et al. Clinical profile and management outcome of acute dacryocystitis: two decades of experience in a tertiary eye care center. Semin Ophthalmol 2015; 30: 118–123.

Lynch

Pedersen

. The human intestinal microbiome in health and disease. N Engl J Med 2016; 375: 2369–2379.

Lloyd

Marsland

. Lung homeostasis: influence of age, microbes, and the immune system. Immunity 2017; 46: 549–561.

10.

Bassiouni

Paramasivan

Shiffer

, et al. Microbiotyping the sinonasal microbiome. Front Cell Infect Microbiol 2020;10:137.

11.

De Filippo

Ramazzotti

Fontana

, et al. Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. Brief Bioinform 2012; 13: 696–710.

12.

Schirawski

Unden

. Menaquinone-dependent succinate dehydrogenase of bacteria catalyzes reversed electron transport driven by the proton potential. Eur J Biochem 1998; 257: 210–215.

13.

Castillo Villamizar

Nacke

Boehning

, et al. Functional metagenomics reveals an overlooked diversity and novel features of soil-derived bacterial phosphatases and phytases. mBio 2019; 10: e01966–18.