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Rauer, L.

Publications and source records attributed to Rauer, L..

3 recordsLinked to original sources

Association between movement patterns, microbiome diversity, and potential pathogen presence in free-ranging feral pigeons foraging in dairy farms.

The feedback between host behavior and disease transmission is well acknowledged, but empirical studies demonstrating associations between individuals pathogens or microbiota composition and their movement are rare. We investigated these associations in feral pigeons (Columba livia domestica), a synanthrope species known to host a plethora of zoonotic pathogens. We captured pigeons in three dairy farms along an urbanization gradient in central Israel. We combined GPS-tracking with Next Generation Sequencing to characterize pigeons movement and microbiota, respectively. We found that pigeons roosted primarily in human settlements, with frequent visits to dairy farms and other agricultural sites. Microbiota diversity and composition varied between sites and the individuals within them, and several pathogens relevant to poultry, cattle, and human-health were frequently detected. Pigeons in the urban site covered shorter distances and carried a greater diversity of bacteria compared to those in rural sites. Intriguingly, beyond these among-site differences, exploratory individuals (measured by the number of unique locations they visited) had more diverse microbiota. We conclude that pigeons can potentially serve as transmission vectors among wildlife, livestock, and humans . Further, the associations between host behavior and microbiota diversity emphasize the relevance of wildlife movement analyses for disease ecology and One Health.

zoology↗

Bioinformatic correction of bacterial morphology-based extraction bias and chimeras in microbiome sequencing data

IntroductionMicrobiome amplicon sequencing data are distorted by multiple protocol-dependent biases, originating from bacterial DNA extraction, contamination, sequence errors, and chimeras. In particular, extraction bias is a major confounder in sequencing-based microbiome analyses, with no correction method available to date. Here, we suggest using mock community controls to bioinformatically correct extraction bias based on morphological properties. MethodsWe compared dilution series of 3 mock communities with an even or staggered composition. DNA was extracted with 8 different extraction protocols (2 buffers, 2 extraction kits, 2 lysis conditions). Extracted DNA was sequenced (V1-V3 16S rRNA gene) together with corresponding DNA mocks. Sequences were denoised using DADA2, and annotated by matching against mock reference genomes. ResultsMicrobiome composition was significantly different between extraction kits and lysis conditions, but not between buffers. Independent of the extraction protocol, chimera formation increased with high input cell number. Contaminants originated mostly from buffers, and considerable cross-contamination was observed in low-input samples. Comparison of microbiome composition of the cell mocks to corresponding DNA mocks revealed taxon-specific protocol-dependent extraction bias. Strikingly, this extraction bias per species was predictable by bacterial cell morphology. Morphology-based bioinformatic correction of extraction bias significantly improved sample compositions when applied to different samples, even with different taxa. ConclusionsOur results indicate that higher DNA density increases chimera formation during PCR amplification. Furthermore, we show that bioinformatic correction of extraction bias is feasible based on bacterial cell morphology.

microbiology↗

Microbial fingerprints reveal interaction between museum objects, curators and visitors

Microbiomes populate the border between humans and their environment. Whether the microbiome can be leveraged to gain information on human interaction with museum objects is unclear. To answer this question, museum objects varying in material and size from two museums, the Museum fur Naturkunde and the Pergamonmuseum in Berlin, Germany, which forms part of UNESCO World Heritage since 1999, were defined. In total 126 samples of natural and cultural heritage objects were taken with sterile nylon flocked swabs and subsequently subjected to 16S rRNA amplicon sequencing. By comparing the microbial composition of touched and untouched mollusc and fossil natural heritage objects we derived a robust microbial touch signature characterized by increased abundance of microbes known to be present in human skin. Application of this touch signature to cultural heritage objects from the Pergamonmuseum revealed areas of differential exposure to human contact on the Ishtar gate and Samal gate lions. Moreover, we were able to distinguish museum objects and personal office items touched by two different individuals with high sensitivity. Our results demonstrate that the microbial composition of museum objects gives insight into the degree of exposure to human contact, which is an important parameter for conservation and heritage science, and possibly provenance research.

microbiology↗