Table 1.
Summary table of the studies included in the review
| Source First author, year [ref] | Disease | Study design No. of patients | Sample collection methods | Analysis | Key findings | Weaknesses | Level evidence |
|---|---|---|---|---|---|---|---|
| Paulino et al . 2006 18 | PV |
Case control 3 PV/5 HV |
Sterile swabs Lesional and nonlesional skin Multiple sampling in one PV and 2 HV |
18S rRNA 5.8S rDNA | ▪ Malassezia mycobiota substantially different PV vs. HV | ▪ Small cohort | Low |
| Amaya et al . 2007 19 | PV |
Case control 22 PV/36 AD/30 HV |
OpSite® transparent adhesive dressings Lesional and nonlesional skin |
5.8S rDNA | ▪ Malassezia species detected in overall sites higher in PV and AD compared to HV |
▪ Small cohort ▪ PV patients on treatment ▪ Limited analysis ▪ Different skin site collection PV vs. AD and HV |
Low |
| Paulino et al . 2008 20 | PV |
Case control 1 PV/1 HV |
Sterile swabs Lesional and nonlesional skin Multiple time points |
5.8S rDNA |
▪ Mycobiota relatively stable over time. ▪ No significant dichotomy between PV and HV. |
▪ Small cohort ▪ Limited analysis |
Low |
| Gao et al . 2008 21 | PV |
Case control 6 PV/6 HV |
Sterile swabs Lesional and nonlesional skin |
16S rRNA V1‐V9 |
▪ Firmucutes more abundant in lesional skin PV vs. nonlesional skin and HV. ▪ Actinobacteria less abundant in lesional skin PV vs. nonlesional skin and HV. |
▪ Small cohort ▪ No serial sampling |
Low |
| Fahlen et al . 2011 22 | PV |
Case control 10 PV/12 HV |
2‐mm skin punch biopsies | 16S rRNA V3‐V4 |
▪ Most common phyla in PV and HV: Firmicutis, Proteobacteria, Actinobacteria. ▪ Staphylococci and Propionibacteria were less common in psoriatic lesions |
▪ Small cohort ▪ No serial sampling ▪ Variation in skin sample sites |
Low |
| Alekseyenko et al . 2013 23 | PV |
Case control & Prospective longitudinal cohort study CC: 54 PV/37 HV PC: 17 PV/15 HV |
Sterile swabs Lesional and nonlesional skin HV matched sites Multiple sampling |
16S rRNA V1‐V3 |
▪ Most common phyla in PV and HV: Firmicutis, Proteobacteria, Actinobacteria. ▪ Combined relative abundance of Corynebacterium, Streptococcus and Staphylococcus was increased in psoriatic skin, compared to unaffected skin and healthy control skin |
▪ Some patients on active treatment ▪ Mainly severe patients |
Low to moderate |
| Statnikov et al . 2013 24 | PV |
Case control 54 PV/37 HV |
Sterile swabs Lesional and nonlesional skin HV matched sites |
16S rRNA V1‐V3 and V3‐V5 | ▪ Microbiome signatures could be used to diagnose psoriasis | ▪ No serial sampling | Low to moderate |
| Takemoto et al . 2015 25 | PV |
Case control 12 PV/12 HV |
PV: psoriatic scales by tweezer HV: OpSite® transparent adhesive dressings |
26S rRNA D1 – D2 |
▪ Psoriatic lesions exhibited significantly greater diversity compared to HV ▪ Malassezia restricta levels were significantly higher in psoriatic lesions, compared to healthy controls |
▪ Small cohort ▪ No serial sampling ▪ Only male patients ▪ Different sample method PV and HV |
Low |
| Salava et al . 2017 26 | PV |
Case control 13 PV |
Sterile swabs Lesional and nonlesional skin |
16S rRNA V1‐V3 | ▪ No significant differences microbial diversity between lesional and nonlesional skin |
▪ Small cohort ▪ No serial sampling ▪ Variation in skin sample sites |
Low |
| Tett et al . 2017 27 | PV |
Case control 28 PV |
Sterile swabs Lesional and nonlesional skin |
WMS sequencing |
▪ Plaques at the ear had a significant decrease in microbial diversity, and increase in Staphylococcus abundance ▪ At species level, no differences between lesional and nonlesional skin were observed |
▪ Small cohort ▪ No serial sampling ▪ Some patients on active treatment |
Low |
| Ring et al . 2017 28 | HS |
Case control 30 HS 24 HV |
Biopsies Lesional and nonlesional skin |
16S rRNA V3‐V4 18S rDNA V3‐V4 |
▪ Microbiome in HS significantly different from HV in lesional and nonlesional skin ▪ Five microbiome types identified ▪ Lesional skin consisted predominantly of Corynebacterium species (type I) and Peptoniphilus species (type IV) ▪ Propionibacterium showed a significant higher abundance in HV |
▪ Small cohort ▪ No serial sampling |
Low |
| Guet‐Revillet et al . 2017 29 | HS |
Prospective cohort 65 HS |
Sterile swabs Lesional and nonlesional skin |
16S rRNA V1‐V2 |
▪ Lesional skin consisted predominantly of anaerobes (Porphyromonas and Prevotella species) ▪ Clinical severity significantly associated with variations in lesional microbiota ▪ Fusobacterium associated with severe HS |
▪ Small cohort | Low |
| Dowd et al . 2008 30 | UC |
Prospective cohort 10 VLU/10 DFU/ 10 PU |
Debridement samples | 16S rRNA V4 |
▪ Major populations include of all wound include: Staphylococcus, Pseudomonas, Peptoniphilus, Enterobacter, Strenotrophomonas, Finegoldia and Serratia species ▪ Each wound type different profile, dependent on oxygen tolerance of the bacterial population |
▪ Small study ▪ No serial sampling |
Low |
| Price et al . 2009 31 | UC |
Prospective cohort 7 DFU/7 NU/3 VLU/3 PSU/4 OTH |
Wound base curette Multiple time points |
16S rRNA V3 |
▪ Fastidious anaerobic bacteria of the Clostridiales family XI were the most prevalent bacteria in wounds ▪ Wound microbiota from antibiotic treated patients were significantly different from untreated patients ▪ In diabetic patients, Streptococcus was more abundant |
▪ Small study ▪ Sampling time point variable ▪ Patients on wide variety of treatments |
Low |
| Price et al . 2011 32 | UC |
Cross‐sectional 4 DFU/3 NU/3 VLU/2 OTH |
Wound base curette Multiple samples taken |
16S rRNA V3‐V4 |
▪ The 10 most common genera included Staphylococcus, Pseudomonas, Streptococcus, Anaerococcus, Ralstonia, Morganella, Porphyromonas, Peptoniphilus, Janthinobacterium and Corynebacterium
▪ Samples from different sites within individual wounds shared similarities in bacterial community compositions ▪ Samples taken from different wounds were less similar than those taken from different sites within the same wound |
▪ Small cohort ▪ Patients on active treatment ▪ No serial sampling |
Low |
| Rhoads et al . 2012 33 | UC |
Cross‐sectional 4 DFU/3 NU/3 VLU/2 OTH |
Wound base curette | 16S rRNA V1‐V3 |
▪ The ten most common genera included Staphylococcus, Pseudomonas, Streptococcus, Anaerococcus, Ralstonia, Morganella, Porphyromonas, Peptoniphilus, Janthinobacterium and Corynebacterium
▪ Samples from different sites within individual wounds shared similarities in bacterial community compositions ▪ Samples taken from different wounds were less similar than those taken from different sites within the same wound |
▪ Small cohort ▪ Patients on active treatment ▪ No serial sampling |
Low |
| Gjodsbol et al . 2012 34 | UC |
Comparative 46 VLU |
Filter paper pad & punch biopsies | 16S rRNA V1‐V3 |
▪ Staphylococcus aureus most found species ▪ Multiple sampling over time lead to identification of additional species ▪ No difference in outcomes different sample techniques |
▪ No controls | Low |
| Gardner et al . 2013 35 | UC |
Cross‐sectional 52 DFU |
Sterile swabs | 16S rRNA V1‐V3 |
▪ The most abundant OTU was Staphylococcus, with S. aureus the most common species ▪ Ulcer closing was positively correlated with number of species level OTUs, higher microbial diversity, relative abundance of Proteobacteria, and negatively correlated with relative abundance of Staphylococcus ▪ Ulcer depth was negatively associated with Staphylococcus abundance and positively associated with anaerobic bacteria relative abundance |
▪ No serial sampling ▪ No controls |
Low |
| Wolcott et al . 2016 37 | UC |
Cohort 2963 910 DFU/916 VLU/676 DU/370 PSU |
Sharp debridement at surface wound bed | 16S rRNA V1‐V3 |
▪ Neither patient demographics (age, gender, race, diabetes status) nor wound type influenced the bacterial composition of the chronic wound microbiome ▪ Staphylococcus and Pseudomonas comprise the most prevalent genera present in the microbiota of chronic wounds, with S. aureus and S. epidermidis the most predominant species ▪ Chronic wounds are frequently colonized by communalistic and anaerobic bacteria, including coagulation‐negative Staphylococcus, Corynebacterium, and Propionibacterium species |
▪ Unclear whether patients were on treatment | Low to moderate |
| Smith et al . 2016 36 | UC |
Cohort 20 DFU |
Sterile swabs | 16S rRNA V4 |
▪ The most commonly detected bacteria in all ulcers were Peptoniphilus, Anaerococcus and Corynebacterium species ▪ In new ulcers, the most commonly detected bacteria were the above and Staphylococcus species ▪ The majority of OTUs residing in both new and recurrent ulcers (>67%) were mostly Gram‐positive cocci (Staphylococcus, Streptococcus, Anaerococcus, Peptoniphilus and Finegoldia ▪ Lower HbA1c values and shorter duration of diabetes correlated with higher diversity within the ulcer |
▪ Small cohort ▪ No serial sampling ▪ No controls |
Low |
| Kalan et al . 2016 38 | UC |
Prospective longitudinal cohort 100 DFU |
Sterile swabs Multiple time point sampling |
ITS1 rRNA |
▪ Fungal microbiome was highly heterogeneous over time and between subjects ▪ Fungal diversity increased with antibiotic administration ▪ The proportion of the phylum Ascomycota were significantly greater at the beginning of the study in wounds that took >8 weeks to heal |
▪ No controls ▪ Most patients on active treatment |
Low to moderate |
| Loesche et al . 2017 39 | UC |
Prospective longitudinal cohort 100 DFU |
Sterile swabs Multiple time point sampling |
16S rRNA V1‐V3 |
▪ The most abundant genus identified was Staphylococcus, followed by Streptococcus, Corynebacterium and Anaerococcus
▪ The major OTU attributed to Staphylococcus was S. aureus ▪ Ulcer microbiota was highly dynamic, with community type transitions occurring approximately every 3.52 weeks ▪ Microbiota community instability was associated with faster healing and improved outcomes ▪ Exposure to systemic antibiotics destabilize wound microbiota, rather than altering overall diversity or relative abundance of specific taxa |
▪ No controls ▪ Most patients on active treatment |
Low to moderate |
| Kuk Park et al . 2012 40 | SD/PC |
Case control 4 PC 3 HV |
Sterile swabs | 26S rRNA D1‐D2 |
▪ P. meleagrinum and P. chrusogenum detected on dandruff scalp ▪ Malassezia spp. 2 times more abundant on dandruff scalp |
▪ Small cohort ▪ No serial sampling |
Low |
| Clavaud et al . 2013. 41 | SD/PC |
Case–control 29 PC 20 HV |
Sterile swabs In 20 PC patients lesional and nonlesional sampling |
16S 28S‐ITS |
▪ M. restricta major fungal species on scalp PC and HV ▪ M. restricta and s. epidermidis significantly more abundant on PC scalp ▪ Propionibacterium acnes significantly less abundant on PC scalp ▪ M. restricta/P. acnes ratio significantly higher in PC scalp |
▪ Small cohort ▪ No serial sampling |
Low |
| Soares et al . 2015 42 | SD/PC |
Case control 9 SD (5 mild, 4 severe) 5 HV |
Sterile swabs Scalp, forehead chin, shoulder and interface samples |
5.8S/ITS2 rDNA |
▪ In general, no association between Malassezia mycobiota and SD was found ▪ Higher m. globosa abundance was found in nonscalp lesions of severe SD patients |
▪ Small cohort ▪ No serial sampling |
Low |
| Park et al . 2017 43 | SD/PC |
Case control 29 SD 28 PC 45 HV |
Sterile swabs Scalp samples |
16 s rRNA V4‐V5 ITS1 rDNA |
▪ Higher abundance of Staphylococcus sp. and m. restricta, and lower abundance of Propionibacterium associated with scalp disease | ▪ No serial sampling | Low |
| Bek‐Thomsen et al . 2008 44 | AV |
Case control 5 AV/3 HV |
Cyanoacrylate biopsy AV acne lesion face HV nose area |
16S rRNA V1‐V9 | ▪ Acne skin higher diversity, P. acnes and S. epidermidis most common species |
▪ Small cohort ▪ Only moderate to severe patients ▪ No serial sampling ▪ No nonlesional patient sampling |
Low |
| Fitz‐Gibbon et al . 2013 45 | AV |
Case control 49 AV/52 HV |
Bioré® Deep Cleansing Pore strips Nose area |
16S rRNA V1‐V9 |
▪ No difference relative abundance P. acnes AV in HV. ▪ Association specific P. acnes strain and acne. |
▪ Some patients on active treatment ▪ No serial sampling ▪ No nonlesional patient sampling |
Low |
| Barnard et al . 2016 46 | AV |
Case control 38 AV/34 HV |
Bioré® Deep Cleansing Pore strips Nose area |
WMS sequencing | ▪ Association specific P. acnes strain and acne. |
▪ Some patients on active treatment ▪ No serial sampling ▪ No nonlesional patient sampling |
Low |
| Dreno et al . 2017 47 | AV |
Single‐center, randomized‐controlled, double‐blind Erythromycin 4% OR Dermatocosmetic 26 AV |
Sterile swabs Lesional and nonlesional skin Multiple time points |
16S rRNA V4 |
▪ Different microbiota profiles on different sites. ▪ Erythromycin treatment reduced the number of Actinobacteria, and dermocosmetic reduced Actinobacteria and Staphylococcus spp. |
▪ Small cohort ▪ Multiple samples excluded due to insufficient bacterial material |
Moderate |
| Kelhala et al . 2017 48 | AV |
Single‐centre, controlled study isotretinoin 0.4–0.6 mg kg–1 or lymecycline 300 mg twice daily 17 isotretinoin 11 lymecycline 16 HV |
Sterile swabs Predose and after 6 weeks Cheek, back and armpit |
16S rRNA V1‐V3 |
▪ Positive correlation Propionibacterium abundance and acne severity grade ▪ Both treatments reduced clinical acne grades ▪ Propionibacterium decreased in cheek samples after both treatments ▪ Propionibacterium decreased in back samples after lymecycline, but not isotretinoin treatment ▪ Diversity increased after treatment |
▪ Small cohort ▪ No nonlesional patient sampling |
Moderate |
| Sugita et al . 2004 58 | AD |
Case control 13 AD/12 HV |
OpSite® transparent adhesive dressings Lesional skin HV matched sites |
26S and 5S rRNA intergenic spacer region 1 | ▪ M. restricta colonizes both AD and HV |
▪ Small cohort ▪ No serial sampling ▪ Limited analysis ▪ Patients on active treatment |
Low |
| Dekio et al . 2007 49 | AD |
Case control 13 AD/10 HV |
Sterile swabs Forehead skin |
16S rRNA |
▪ In both AD and HV there was a high rate of Streptococcus species ▪ In AD Strenotrophomonas maltophilia was significantly more common |
▪ Small cohort ▪ No serial sampling ▪ Patients on active treatment |
Low |
| Kaga et al. 2009 50 | AD |
Case control 56 AD/32 HV |
OpSite® transparent adhesive dressings Lesional skin AD Face HV |
26S and 5S rRNA intergenic spacer region 1 |
▪ In mild and moderate AD, M. restricta was predominant over M. globose
▪ In patients with severe AD, proportions of M. restricta and M. globose were almost identical |
▪ Limited analysis ▪ No serial sampling ▪ Variation in skin sample sites ▪ Patients possibly on active treatment |
Low to moderate |
| Yim et al . 2010 51 | AD |
Prospective cohort 60 |
Sterile swabs 5 body sites |
26S | ▪ There were no significant differences between positive Malassezia culture, Malassezia species, and severity of AD |
▪ Limited analysis ▪ Patients on emollient treatment |
Low to moderate |
| Akaza et al . 2010 52 | AD |
Case control 67 |
Sterile swabs Lesional and nonlesional skin Face and trunk |
26S | ▪ For the total number of Malassezia species, there were no significant differences between lesional and nonlesional areas |
▪ No serial sampling ▪ Patients on active treatment |
Low to moderate |
| Kong et al . 2012 60 | AD |
Prospective cohort 12 AD/11 HV |
Sterile swabs Multiple time points Baseline, flare, post‐flare |
16S rRNA V1‐V9 |
▪ Flare ups were associated with an increased proportion of Staphylococcus sequences, particularly S. aureus, and correlated with disease severity ▪ Increases in Streptococcus, Propionbacterium, and Corynebacterium species were observed following therapy |
▪ Small cohort ▪ Only moderate to severe patients ▪ Different treatments regimens during flare |
Low to moderate |
| Seite et al . 2014 54 | AD |
Prospective cohort Emolliens treatment 46 |
Sterile swabs Lesional and nonlesional skin Multiple time points |
16S rRNA V1‐V2 |
▪ Affected skin harboured a greater relative abundance of Staphylococcus, and in particular S. epidermis, compared to healthy skin ▪ Responders had increased microbial diversity and decrease in Staphylococcus species |
▪ Large time between first and second sample ▪ Only moderate patients |
Low to moderate |
| Chng et al . 2016 55 | AD |
Case control 19 medical history AD/15 HV/5 positive skin prick |
Tape stripping anti‐cubital fossa |
16S rRNA V3‐V6 WMS |
▪ Nonflare, baseline skin microbiome signatures enriched for Streptococcus and Gemella in AD prone skin versus normal skin ▪ Increased percentage of S. aureus carriers noted in AD cohort over control subjects |
▪ Small cohort ▪ No serial sampling ▪ No lesional samples |
Low |
| Gonzalez et al . 2016 56 | AD |
Randomized, placebo‐controlled, single‐blinded Topical steroid or Topical steroid + dilute bleach bath 21 AD/14 HV |
Sterile swabs Lesional and nonlesional skin Multiple time points |
16S rRNA V4 |
▪ Affected skin harboured a greater relative abundance of S. aureus
▪ Microbial diversity at all lesional sites inversely correlated with overall EASI Index score ▪ Taxonomic normalization occurred on lesional following treatments ▪ Bacterial communities on lesional skin resemble nonlesional skin but remain distinct from healthy control skin |
▪ Small study | Moderate |
| Seite et al . 2017 57 | AD |
Double‐blind, Randomized, comparative Emollient A or Emollient B 53 |
Sterile swabs Lesional and nonlesional skin Multiple time points |
16S rRNA V1‐V2 |
▪ Significant increased levels of Xanthomonas genus in patients treated with emollient A ▪ Levels of Staphylococcus genus increased between Day 1 and Day 28 in patients treated with emollient B |
▪ Only moderate patients ▪ No wash‐out other treatments |
Moderate |
| Kim et al . 2017 59 | AD |
Prospective cohort Wet dressings Topical steroids Antihistamines Antibiotics 27 AD 6 HV |
Saline soaked gauzes | 16S rRNA V1‐V3 |
▪ Proportion of Staphylococcus significantly decreased after treatment ▪ Diversity (Shannon Index) significantly increased after treatment |
▪ Small study ▪ Patients on wide variety of treatments ▪ No nonlesional skin analysis |
Low to moderate |
AD, atopic dermatitis; AV, acne vulgaris; DFU, diabetic foot ulcer; HS, hidradenitis suppurativa; NU, neuropathic ulcer; OTH, other; OTU, operational taxonomic unit; PSU, post‐surgical ulcer; PU, pressure ulcer; PV, psoriasis vulgaris; SD/PC, seborrhoeic dermatitis/pityriasis capitis; UC, ulcus cruris; VLU, venous leg ulcer