Biology subjects

Hansen, L. H.

Publications and source records attributed to Hansen, L. H..

3 recordsLinked to original sources

bioRxiv2018

The Genome of BAM-degrading Aminobacter sp. MSH1 with Several Low Copy Plasmids

As one of the only described degraders of the recalcitrant metabolite 2,6-dichlorobenzamide (BAM) of the pesticide dichlobenil, Aminobacter sp. MSH1 has been intensively studied for its characteristics with regards to physiology and its use in bioremediation. Two plasmid sequences from strain MSH1 have previously been published, while the remaining genome sequence has been left uninvestigated. We here present the complete genome sequence of this important strain, which consists of a chromosome, two megaplasmids and five smaller plasmids. Intriguingly, the plasmid copy numbers are mostly below one per bacterial chromosome, indicating that plasmids in strain MSH1 are under very unstable conservation. The results of this report improve our understanding of the genomic dynamics of Aminobacter sp. MSH1.

microbiology↗

bioRxiv2017

Protective role of the vulture facial and gut microbiomes aid adaptation to scavenging

BackgroundVultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial and gut microbiomes from the black and turkey vultures. We characterized i) the functional potential and taxonomic diversity of their microbiomes, ii) the potential pathogenic challenges they face, and iii) elements in the microbiome that could play a protective role to the vultures face and gut.\n\nResultsWe found elements involved in diseases, such as periodontitis and pneumonia (more abundant in the face), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing health beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasites and antiinsectisides in the face. Based on the identified phages, we suggest that phages aid in the control, and possibly elimination as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we also identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role though biofilm formation played by Fusobacteria and Clostridia in the gut.\n\nConclusionsOur results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.

bioinformatics↗

bioRxiv2017

Plasmids, Viruses, And Other Circular Elements In Rat Gut

Circular DNA such as plasmids and some viruses is the major source of genetic variation in bacteria and thus has the same important evolutionary function as sexual reproduction in eukaryotic species: It allows dissemination of advantageous traits through bacterial populations. Here, we present the largest collection of novel complete extrachromosomal genetic elements to date, and compare the diversity, distribution, and content of circular sequences from 12 rat cecum samples from the pristine Falkland Islands and Danish hospital sewers, two environments with contrasting anthropogenic impact. Using a validated pipeline, we find 1,869 complete, circular, non-redundant sequences, of which only 114 are previously described. While sequences of similar size from the two environments share general features, the size distribution of the elements between environments differs significantly, with hospital sewer samples hosting larger circular elements than Falkland Island samples, a possible consequence of the massive anthropogenic influence in the hospital sewer environment. Several antibiotic resistance genes have been identified with a notably larger diversity in hospital sewer samples than in Falkland Islands samples in concordance with expectations. Our findings suggest that even though sequences of similar length carry similar traits, the mobilome of rat gut bacteria are affected by human activities in that sewer rats have larger elements and more diverse large elements than pristine island rats. More than 1000 novel and not classified small sequences was identified and hint the existence of a biological unit not previously described on a community level.\n\nList of figures O_LISampling sites and Rat gut anatomy\nC_LIO_LIRarefaction curves of circular elements\nC_LIO_LIElements shared between environments\nC_LIO_LISize distribution plots of rep, mob, stab, capsid carrying elements.\nC_LIO_LIGraphical representation of representative elements\nC_LIO_LIReplication genes content, diversity\nC_LIO_LIRep_2 plasmid replication gene phylogeny\nC_LIO_LITable Resfams findings\nC_LI\n\nList of appendices O_LIbasic statistics table\nC_LIO_LIPhylogeny of plasmid replication genes\nC_LIO_LIList of known plasmids and circular sequences found in 1869 elements\nC_LIO_LIAutomatic identification of identical circular elements with different breaking points\nC_LIO_LITest of separation of plasmids and viruses based on predicted, annotated genes\nC_LIO_LINo false positive circular sequences from MG1655 genomic sequencing.\nC_LI

microbiology↗