Table 1.

Human research studies conducted on the effect of smoking or nicotine on the microbiome.

Study	Study Purpose	Sample Size	Findings
(146)	To evaluate the effect of electronic cigarettes (EC) or tobacco smoking in oral and gut microbiota.	n = 30 (10 EC users, 10 tobacco users, 10 controls)	Tobacco smokers had higher relative abundance of Prevotella, lowered Bacteroides, and lowered Shannon diversity. No significant differences were found in alpha diversity, beta-diversity, or taxonomic relative abundances between EC users and controls.
(147)	To compare the gut microbiome of smokers versus nonsmokers.	n = 249	Bacterial taxa along the Erysipelotrichi-Catenibacterium lineage and Alphaproteobacteria increased in current smokers. Each taxa exhibited dose-response associations.
(148)	To assess the changes in the intestinal microbiome associated with smoking cessation.	n = 20 (10 subjects in the experimental group; 5 continuing smoker control subjects; 5 non-smoker control subjects)	Increased abundance of Firmicutes and Actinobacteria in smokers. Decreased abundance of Bacteroidetes and Proteobacteria on phylum level in smokers. Microbial diversity increased following smoking cessation.
(149)	To identify the association between human intestinal microbiota (HIM) and smoking habits via data mining analysis.	n = 92	Decision tree was successfully able to identify smokers and non-smokers using operational taxonomic units (OTUs) for analysis. Related OTUs were all found to be uncultured bacteria.
(8)	To assess the relationship between tobacco use and changes in the upper gastrointestinal microbiome.	n = 278 (46.8% current smokers, 12.6% former smokers, 40.6% never smokers)	Subjects were divided into current smokers and never smokers and were characterized by alpha and beta diversity of the gut microbiome. Current smokers had increased alpha (mean 42.3 species) versus never smokers (mean 38.9 species) and exhibited increased beta diversity, Dialister invisus, and Megasphaera micronuciformis.
(9)	To investigate the association of cigarette smoking with the oral microbiome.	n = 1204 (26.3% never smokers, 63.3% former smokers, 10.4% current smokers)	Current smokers had decreased Proteobacteria (4.6%) compared with never smokers (11.7%) at class, genus and OTU levels No difference in Proteobacteria was found between former and never smokers. Reduced genera Capnocytophaga, Peptostreptococcus and Leptotrichia in current smokers compared with never smokers. Functional analysis revealed these genera were related to carbohydrate, energy, and xenobiotic metabolism Increased Atopobium and Streptococcus in current smokers compared with never smokers.
(10)	To evaluate the relation between smoking history and sinonasal microbiome alterations in chronic rhinosinusitis (CRS) and non-CRS subjects.	n = 101 (70 CRS patients and 31 control subjects)	Univariate analysis demonstrated that genus-level compositions of the middle meatus microbiota are significantly associated with smoking (p= 0.04), preoperative antibiotics (p= 0.03), and purulence (p= 0.0002). Multivariable model demonstrated that CRS (p= 0.02), polyposis (p= 0.03), purulence (p= 0.0004), and use of saline rinses (p = 0.5) have significant interactions with smoking. Diverse bacterial taxa varied significantly in composition between never-smokers and current smokers, former smokers and CRS subtypes.
(11)	To examine microbiota found in the lower airway in patients with COPD, smokers without COPD and non-smokers.	n = 37 (18 adults with COPD, 8 smokers with no airways disease, and 11 healthy individuals)	In extended-culture analysis, the total load of aerobic and anaerobic bacteria between the three cohorts were similar. Culture-independent analysis showed increased Pseudomonas, greatest in the lower airways of patients with COPD. There was decreased alpha and beta diversity in the COPD group. Bacteroidetes (Prevotella spp) was increased in the non-COPD comparison groups. Co-occurrence bacterial taxa and putative core were observed within the lower airways.
(12)	To investigate the relation between host genetics and lifestyles with sputum microbiota compositions. Lifestyle factors considered include smoking, alcohol consumption, and physical activity.	n= 257	Providencia and Bacteroides were influenced by host genetic factors. Smoking had the strongest effect on the overall microbial community structure compared to other tested lifestyle factors. Veillonella and Megasphaera were increased in current-smokers, and increased further with the pack-year value and the Fagerstrom Test of Nicotine Dependence (FTND) score. Haemophilus decreased with the pack-year of smoking and the FTND score. Co-occurrence taxa influenced by host genetics were found together.
(13)	To examine the effect of smoking on the composition of the subgingival microbiome and associated risk for disease.	n = 200	Subgingival microbial profiles were different at all taxonomic levels in smokers compared to nonsmokers. Principle coordinate analysis: microbial community clustering performed based on smoking status. Smokers were characterized by a highly diverse, pathogen-rich, commensal-poor, anaerobic microbiome that closely resembles disease-associated communities.
(14)	To investigate the changes in the upper airway microbiome that result from smoking.	n > 4,000 adults.	Approximately 25,000 sequence reads were generated. Samples clustered in the first principal coordinate by whether they were smokers. (19% of variance). Similarly, samples clustered in the second principal coordinate by whether they were never smokers (17% of variance). Former smokers were distributed within and between both these clusters. Specific OTUs increased or decreased with respect to each of the two main clusters.
(150)	To assess the relation between smoking and intestinal microbiota in patients with active Crohn’s disease (CD).	n = 169 (103 subjects with active CD; 66 healthy controls; 29 smokers with CD; 8 smokers in the control group)	Multivariate analysis revealed increased Bacteroides-Prevotella in smokers (38.4%) compared with nonsmokers (28.1%). Healthy controls also exhibited increased Bacteroides-Prevotella (34.8%) compared to nonsmokers (24.1%). Pooled multivariate analysis showed patients with CD had higher bifidobacteria, higher Bacteroides-Prevotella, and lower F. prausnitzii (in comparison to healthy controls.
(151)	To evaluate changes in gut microbiota composition associated in smokers versus nonsmokers with active Crohn’s disease using a metagenomic approach.	n = 42 21 smoking and 21 nonsmoking patients with CD included	Decreased gut microbial gene richness (P=0.01), genus diversity (P<0.01), and species diversity (P=0.01) in smoking patients with CD compared to nonsmoking patients with CD. Decreased relative abundance of the genera Collinsena (P=0.02), Enterohabdus (P=0.02), and Gordonibacter (P=0.02) in smoking patients with CD compared to nonsmoking patients with CD.