Velma Aho

The microbiome of the human lower airways: a next generation sequencing perspective

For a long time, the human lower airways were considered a sterile environment where the presence of microorganisms, typically revealed by culturing, was interpreted as an abnormal health state. More recently, high-throughput sequencing-based studies have led to a shift in this perception towards the notion that even in healthy conditions the lower airways show either transient presence or even permanent colonization by microorganisms. However, challenges related to low biomass and contamination in samples still remain, and the composition, structure and dynamics of such putative microbial communities are unclear. Here, we review the evidence for the presence of microbial communities in the human lower airways, in healthy subjects and within the context of medical conditions of interest. We also provide an overview of the methodology pertinent to high-throughput sequencing studies, specifically those based on amplicon sequencing, including a discussion of good practices and common pitfalls.

More than constipation – bowel symptoms in Parkinson's disease and their connection to gut microbiota

The majority of Parkinsons disease (PD) patients suffer from gastrointestinal symptoms of which constipation is considered the most prominent. Recently, in addition to constipation, a diagnosis of irritable bowel syndrome (IBS) was also found to be associated with increased PD risk. Gut microbiota alterations have been reported in IBS and recently also in PD. IBS‐like bowel symptoms in PD and their possible connection to other non‐motor symptoms and faecal microbiota were assessed.

Gut microbiome in gestational diabetes: a cross‐sectional study of mothers and offspring 5 years postpartum

An altered gut microbiome composition is shown to be associated with various diseases and health outcomes. We compare the gut microbiota of women who developed gestational diabetes mellitus (GDM) with that of those who did not, and the gut microbiota of their offspring, to determine any differences in the composition and diversity of their gut microbiota, which may be correlated with their GDM state.

Bile microbiota in primary sclerosing cholangitis: Impact on disease progression and development of biliary dysplasia

Objective The etiopathogenesis and risk for development of biliary neoplasia in primary sclerosing cholangitis (PSC) are largely unknown. Microbes or their metabolites have been suggested to play a role. To explore this potential microbial involvement, we evaluated the differences in biliary microbiota in PSC patients at an early disease stage without previous endoscopic retrograde cholangiography (ERC) examinations, advanced disease stage, and with biliary dysplasia or cholangiocarcinoma. Design Bile samples from the common bile duct were collected from 46 controls and 80 patients with PSC during ERC (37 with early disease, 32 with advanced disease, and 11 with biliary dysplasia). DNA isolation, amplification, and Illumina MiSeq sequencing were performed for the V1-V3 regions of the bacterial 16S rRNA gene. Results The most common phyla found were Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria, and Actinobacteria. The most common families were Prevotellaceae, Streptococcaceae, Veillonellaceae, Fusobacteriaceae, and Pasteurellaceae, and the most common genera were Prevotella, Streptococcus, Veillonella, Fusobacterium, and Haemophilus. The bacterial communities of non-PSC subjects and early stage PSC patients were similar. Alpha diversity was lower in patients with biliary dysplasia/cholangiocarcinoma than in other groups. An increase in Streptococcus abundance was positively correlated with the number of ERC examinations. Streptococcus abundance was also positively correlated with an increase in disease severity, even after controlling for the number of ERC examinations. Conclusions Our findings suggest that the aetiology of PSC is not associated with changes in bile microbial communities, but the genus Streptococcus may play a pathogenic role in the progression of the disease.

Isotretinoin and lymecycline treatments modify the skin microbiota in acne

Oral retinoids and tetracyclines have a major role in acne treatment. Here, we report for the first time the effect of isotretinoin and lymecycline therapy on the skin microbiota in cheek, back and armpit swab samples of acne vulgaris patients using 16S ribosomal RNA (16S rRNA) gene amplicon sequencing. Propionibacterium acnes was the most common in sebaceous areas of healthy and untreated acne skin and more abundant in back than cheek samples. Five taxa, including a Streptococcus taxon, differed significantly between the cheek samples of healthy controls and acne patients, and acne severity was positively correlated with the abundance of Propionibacterium. Both treatments reduced clinical acne grades and the abundance of Propionibacterium, while the abundance of several other taxa was significantly higher in treated cheek samples compared with untreated ones. Less variation was observed in back samples and none in armpit samples. There were no differences in alpha diversity between control and acne patients in any of the sampled skin areas, but the diversity of the microbiota on the cheek and the back was significantly increased after acne treatments. This study provides insight into the skin microbiota in acne and how it is modulated by systemic acne treatment.

Loss of cutaneous microbial diversity during first 3 weeks of life in very low birthweight infants

Neonatal sepsis (NS) is a frequent problem in neonatal intensive care, especially in preterm and very low birthweight (VLBW) infants. The objective of the study was to characterize the cutaneous bacterial microbiome in VLBW infants treated in the neonatal intensive care unit (NICU). Non‐invasive skin microbiome specimens were taken repeatedly from 12 VLBW infants during treatment in NICU starting on the first day of life. All infants received benzylpenicillin and netilmicin during the first 1‐5 postnatal days. Samples were also collected from incubators. High cutaneous microbial diversity was present at birth in 11 of 12 of the infants, but the diversity decreased substantially after the first weeks of life in all infants regardless of their infection status. After the loss of diversity, one Staphylococcus operational taxonomic unit dominated the skin microbiome. Recovery of microbial diversity was seen in six of 12 neonates. The microbiome of incubators showed typical environmental bacterial genera. Maternal antibiotic treatment, the aetiology of the preterm birth or being born by C‐section did not appear to affect the diversity of skin microbiota at birth, and no correlation was found between cutaneous microbiome and NS.

Skin microbiome in melanomas and melanocytic nevi

BackgroundHigh-throughput DNA sequencing has shown that the cutaneous microbiome varies due to different exogenous and endogenous factors.ObjectivesTo characterize the microbiome of cutaneous melanomas and melanocytic nevi.Material and MethodsNon-invasive swab specimens were taken from 15 cutaneous melanomas and 17 benign melanocytic nevi. Partial sequencing of the 16S ribosomal RNA gene was carried out on the 454 GS-FLX Titanium platform and the resulting sequence data was analysed by bioinformatics and statistical methods.Results95% of the OTUs (Operational Taxonomic Units) belonged to four phyla: Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes. The genus Propionibacterium was overall the mostcommongenus, followed by Staphylococcus and Corynebacterium. Statistical analysis showed no significant differences in the relative abundances of bacterial genera or bacterial diversity between the patient groups. Melanoma samples showed a marginally decreased cutaneous microbial diversity.ConclusionOur data suggests that the skin microbiome may not be a useful diagnostic tool for melanoma and melanocytic nevi.