Lars Henrik Hansen

The microbiome of New World vultures

Vultures are scavengers that fill a key ecosystem niche, in which they have evolved a remarkable tolerance to bacterial toxins in decaying meat. Here we report the first deep metagenomic analysis of the vulture microbiome. Through face and gut comparisons of 50 vultures representing two species, we demonstrate a remarkably conserved low diversity of gut microbial flora. The gut samples contained an average of 76 operational taxonomic units (OTUs) per specimen, compared with 528 OTUs on the facial skin. Clostridia and Fusobacteria, widely pathogenic to other vertebrates, dominate the vultures gut microbiota. We reveal a likely faecal-oral-gut route for their origin. DNA of prey species detectable on facial swabs was completely degraded in the gut samples from most vultures, suggesting that the gastrointestinal tracts of vultures are extremely selective. Our findings show a strong adaption of vultures and their bacteria to their food source, exemplifying a specialized host-microbial alliance.

Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance

We investigated immediate and long-term effects on bacterial populations of soil amended with cattle manure, sewage sludge or municipal solid waste compost in an ongoing agricultural field trial. Soils were sampled in weeks 0, 3, 9 and 29 after fertilizer application. Pseudomonas isolates were enumerated, and the impact on soil bacterial community structure was investigated using 16S rRNA amplicon pyrosequencing. Bacterial community structure at phylum level remained mostly unaffected. Actinobacteria, Proteobacteria and Chloroflexi were the most prevalent phyla significantly responding to sampling time. Seasonal changes seemed to prevail with decreasing bacterial richness in week 9 followed by a significant increase in week 29 (springtime). The Pseudomonas population richness seemed temporarily affected by fertilizer treatments, especially in sludge- and compost-amended soils. To explain these changes, prevalence of antibiotic- and mercury-resistant pseudomonads was investigated. Fertilizer amendment had a transient impact on the resistance profile of the soil community; abundance of resistant isolates decreased with time after fertilizer application, but persistent strains appeared multiresistant, also in unfertilized soil. Finally, the ability of a P. putida strain to take up resistance genes from indigenous soil bacteria by horizontal gene transfer was present only in week 0, indicating a temporary increase in prevalence of transferable antibiotic resistance genes.

Sequence and comparative analysis of Leuconostoc dairy bacteriophages.

Bacteriophages attacking Leuconostoc species may significantly influence the quality of the final product. There is however limited knowledge of this group of phages in the literature. We have determined the complete genome sequences of nine Leuconostoc bacteriophages virulent to either Leuconostoc mesenteroides or Leuconostoc pseudomesenteroides strains. The phages have dsDNA genomes with sizes ranging from 25.7 to 28.4 kb. Comparative genomics analysis helped classify the 9 phages into two classes, which correlates with the host species. High percentage of similarity within the classes on both nucleotide and protein levels was observed. Genome comparison also revealed very high conservation of the overall genomic organization between the classes. The genes were organized in functional modules responsible for replication, packaging, head and tail morphogenesis, cell lysis and regulation and modification, respectively. No lysogeny modules were detected. To our knowledge this report provides the first comparative genomic work done on Leuconostoc dairy phages.

Smoking Cessation and the Microbiome in Induced Sputum Samples from Cigarette Smoking Asthma Patients.

Asthma is a common disease causing cough, wheezing and shortness of breath. It has been shown that the lung microbiota in asthma patients is different from the lung microbiota in healthy controls suggesting that a connection between asthma and the lung microbiome exists. Individuals with asthma who are also tobacco smokers experience more severe asthma symptoms and smoking cessation is associated with improved asthma control. In the present study we investigated if smoking cessation in asthma patients is associated with a change in the bacterial community in the lungs, examined using induced sputum. We found that while tobacco smokers with asthma have a greater bacterial diversity in the induced sputum compared to non-smoking healthy controls, smoking cessation does not lead to a change in the microbial diversity.

Predictors of neutrophilic airway inflammation in young smokers with asthma.

Abstract Introduction: Asthma is one of the most widespread chronic diseases worldwide. In spite of numerous detrimental effects on asthma, smoking is common among asthma patients. These smoking-induced aggravations of asthma may be attributed to changes in airway inflammation, which is characterized by a higher degree of neutrophilic inflammation than in non-smokers. A state of neutrophilic inflammation may lead to increased steroid resistance and an accelerated loss of lung function owing to tissue destruction. The aim of this study was to elucidate predictors of neutrophilic inflammation in young asthmatic smokers not on steroid treatment, including analysis of tobacco history and bacterial colonization. Methods: In a cross-sectional study, 52 steroid-free, current smokers with asthma were examined with induced sputum, fractional exhaled nitric oxide (FeNO), lung function, ACQ6 score, mannitol and methacholine challenge. A sample from the sputum induction was taken for bacterial analysis using 16S gene PCR technique and sequencing. Results: Using one-way analysis of variance and binary and linear regression models, only age and ACQ6 score were found to be significant predictors for airway neutrophilia. The investigation also included analysis for effect of pack years, current tobacco consumption, body mass index, lung function, FeNO; methacholine and mannitol responsiveness, atopy, gender, asthma history and presence of bacteria. The most common potentially pathogenic bacteria found were Streptococcus spp., Haemophilus spp. and Mycoplasma spp. Conclusion: In this study, no tobacco-related predictors of airway neutrophilia were found, indicating that in the younger years of asthma patients who smoke, the amount of tobacco smoked in life does not influence the degree of neutrophilia. Conversely, for asthmatic smokers, neutrophilia may be induced when a certain threshold of tobacco consumption is reached.

Corrigendum: The microbiome of New World vultures

Nature Communications 5: Article number: 5498 (2014); Published: 25 November 2014; Updated: 21 October 2015. The original version of this Article contained an error in the spelling of the author Thomas Sicheritz-Ponten, which was incorrectly given as Thomas Sicheritz Ponten. This has now been corrected in both the PDF and HTML versions of the Article.