16S rDNA	16S ribosomal deoxyribonucleic acid
16S rRNA	16S ribosomal ribonucleic acid
AECOPD	Acute exacerbation of chronic obstructive pulmonary disease
BAL	Bronchoalveolar lavage
bp	Base pair
C	The number of thermocycles
CF	Cystic fibrosis
COPD	Chronic obstructive pulmonary disease
COVID-19	Coronavirus disease 2019
Ct	Cycle threshold or detection threshold
dATP	Deoxy-adenosine triphosphate
dCTP	Deoxy-cytosine triphosphate
ddNTPs	Di-deoxy-nucleotide triphosphates
dGTP	Deoxy-guanin triphosphate
DNA	Deoxyribonucleic acid
dNTPs	Deoxynucleotide triphosphates
dsDNA	Double-stranded DNA
dTTP	Deoxy-thymine triphosphate
E	The fractional amplification efficiency
FEV1	Forced expiratory volume in one second
GIT	Gastrointestinal tract
HIV	Lung human immunodeficiency virus
HMP	The Human Microbiome Project
ICS	Inhaled corticosteroid
ICU	Intensive care unit
LHMP	The Lung Human Immunodeficiency Virus Microbiome Project
LRT	Lower respiratory tract
LRTIs	Lower respiratory tract infections
N0	The starting number of target molecules
Nc	The number of amplicons
NGS	Next-generation sequencing
NIH	The National Institutes of Health
Nt	The number of amplicons at the defined threshold
OCS	Oral corticosteroid
OTUs	Operational taxonomic units
PCoA	Principal coordinates analysis
PCR	Polymerase chain reaction
qPCR	Quantitative PCR
RDP	Ribosomal Database Project
rRNA-sequence	Ribosomal ribonucleic acid-sequence
RSV	Respiratory syncytial virus
RT-qPCR	Reverse-transcriptase quantitative PCR
SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2
SSU-rRNA	Small subunit ribosomal ribonucleic acid
T-RFLP	Terminal restriction fragment length polymorphism
URT	Upper respiratory tract
USA	The United States of America
WGS	Whole-genome sequencing