Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

A Regueira‐Iglesias, C Balsa‐Castro… - Molecular Oral …, 2023 - Wiley Online Library
The multi‐batch reanalysis approach of jointly reevaluating gene/genome sequences from
different works has gained particular relevance in the literature in recent years. The large …

[PDF][PDF] Microbiome and allergy: new insights and perspectives

E Zubeldia Varela, TC Barker Tejeda… - … allergology & clinical …, 2022 - jiaci.org
The role of the microbiome in the molecular mechanisms underlying allergy has become
highly relevant in recent years. Studies are increasingly suggesting that altered composition …

Insights into the profile of the human expiratory microbiota and its associations with indoor microbiotas

Y Zhang, F Shen, Y Yang, M Niu, D Chen… - … science & technology, 2022 - ACS Publications
Microorganisms residing in the human respiratory tract can be exhaled, and they constitute a
part of environmental microbiotas. However, the expiratory microbiota community and its …

SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts

MN Hoque, MMH Sarkar, MS Rahman, S Akter… - Scientific reports, 2021 - nature.com
The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against
respiratory infectious diseases. However, scant information is available on interactions of …

Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?

LJ Kerkhof - FEMS microbiology ecology, 2021 - academic.oup.com
This minireview will discuss the improvements in Oxford Nanopore (Oxford; sequencing
technology that make the MinION a viable platform for microbial ecology studies. Specific …

Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model

ME Salliss, JD Maarsingh, C Garza… - npj Biofilms and …, 2021 - nature.com
Bacterial vaginosis (BV) is a gynecologic disorder characterized by a shift in cervicovaginal
microbiota from Lactobacillus spp. dominance to a polymicrobial biofilm composed of …

The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia

AE Pérez-Cobas, C Ginevra, C Rusniok, S Jarraud… - Cell Reports …, 2023 - cell.com
Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-
kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients …

Unraveling the gut-Lung axis: Exploring complex mechanisms in disease interplay

MW Eladham, B Selvakumar, NS Sharif-Askari… - Heliyon, 2024 - cell.com
The link between gut and lung starts as early as during organogenesis. Even though they
are anatomically distinct, essential bidirectional crosstalk via complex mechanisms supports …

Distinctive features of the oropharyngeal microbiome in Inuit of Nunavik and correlations of mild to moderate bronchial obstruction with dysbiosis

M Flahaut, P Leprohon, NP Pham, H Gingras… - Scientific Reports, 2023 - nature.com
Inuit of Nunavik are coping with living conditions that can influence respiratory health. Our
objective was to investigate associations between respiratory health in Inuit communities …

A ribosomal operon database and MegaBLAST settings for strain-level resolution of microbiomes

LJ Kerkhof, PA Roth, SV Deshpande… - FEMS …, 2022 - academic.oup.com
Current methods to characterize microbial communities generally employ sequencing of the
16S rRNA gene (< 500 bp) with high accuracy (∼ 99%) but limited phylogenetic resolution …