Biology subjects

Kirstahler, P.

Publications and source records attributed to Kirstahler, P..

3 recordsLinked to original sources

bioRxiv2022

Detection of Parasites in Microbiomes using Metagenomics

Despite a yearly death toll of up to one million people due to parasite-related infections, parasites are still neglected in genomics research. While there is progress in the detection of bacteria and viruses using metagenomics in the context of infectious diseases, there are still challenges in metagenomics-based detection of parasites. Here, we implement a workflow for the detection of parasites from metagenomics data. We employ stringent cut off criteria to limit false positive detections. We analysed a total of 7.120 metagenomics samples of which 359 originated from gut microbiomes of livestock (pigs and chicken) from nine countries, and 6.761 from gut microbiomes of humans (adults and infants) from 25 countries. Five parasite-related genera were detected in livestock, of which Blastocystis sp. was detected in 71% of all pig herds and Eimeria in 83% of all chicken flocks. Distinct gut bacterial taxa were associated with Blastocystis sp. abundance in pigs. Nine parasite-related genera were detected in humans. Blastocystis sp. subtypes ST1, ST2, and ST3 were detected in all countries, and ST3 was most predominant. A higher overall prevalence of Blastocystis sp. was observed in low-income countries as compared to high-income countries, and a higher diversity of Blastocystis subtypes (ST1, ST2, ST3, ST4, ST6, ST7, ST8) was detected in high-income countries as compared to low-income countries. The prevalence of Blastocystis sp. in infant gut microbiome samples was lower as compared to adults. Overall, metagenomics-based analysis may be a promising tool for parasite detection from complex microbiome samples in clinical and veterinary medicine. Metagenomics could become the preferred method for parasite detection for a wide range of biological samples. Current parasite detection methods often rely on microscopic examination of the sample or using specific PCR. Metagenomics-based analyses may allow for a faster and more convenient way of detecting parasites in humans and animals, as this approach could serve as a one-for-all untargeted approach for pathogen detection, including bacteria, viruses, and parasites.

microbiology↗

bioRxiv2021

A Peek into the Plasmidome of Global Sewage

Plasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions. Plasmid-encoded traits, such as antimicrobial resistance (AMR) or virulence, impact on the ecology and evolution of bacteria and can significantly influence the burden of infectious diseases. Insight about the identity and functions encoded on plasmids on the global scale are largely lacking. Here we investigate the plasmidome of 24 samples (22 countries, 5 continents) from the global sewage surveillance project. We obtained 105 Gbp Oxford Nanopore and 167 Gbp Illumina DNA sequences from plasmid DNA preparations and assembled 165,302 contigs (159,322 circular). Of these, 58,429 encoded for genes with plasmid-related and 11,222 with virus/phage-related proteins. About 90% of the circular DNA elements did not have any similarity to known plasmids. Those that exhibited similarity, had similarity to plasmids whose hosts were previously detected in these sewage samples (e.g. Acinetobacter, Escherichia, Moraxella, Enterobacter, Bacteroides, and Klebsiella). Some AMR classes were detected at a higher abundance in plasmidomes (e.g. macrolide-lincosamide-streptogramin B, macrolide, and quinolone), as compared to the respective complex sewage samples. In addition to AMR genes, a range of functions were encoded on the candidate plasmids, including plasmid replication and maintenance, mobilization, and conjugation. In summary, we describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes. Moreover, the obtained data could provide further valuable insight into the ecology and evolution of microbiomes, knowledge about AMR transmission, and the discovery of novel functions. ImportanceThis is, to the best of our knowledge, the first study to investigate plasmidomes at a global scale using long read sequencing from complex untreated domestic sewage. Previous metagenomic surveys have detected AMR genes in a variety of environments, including sewage. However, it is unknown whether the AMR genes were encoded on the microbial chromosome or are located on extrachromosomal elements, such as plasmids. Using our approach, we recovered a large number of plasmids, of which most appear novel. We identified distinct AMR genes that were preferentially located on plasmids, potentially contributing to their transmissibility. Overall, plasmids are of great importance for the biology of microorganisms in their natural environments (free-living and host-associated), as well as molecular biology, and biotechnology. Plasmidome collections may therefore be valuable resources for the discovery of fundamental biological mechanisms and novel functions useful in a variety of contexts.

microbiology↗

bioRxiv2017

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid

Advances in genomics have the potential to revolutionize clinical diagnostics. Here, we examine the microbiome of vitreous (intraocular body fluid) from patients who developed endophthalmitis following cataract surgery or intravitreal injection. Endophthalmitis is an inflammation of the intraocular cavity and can lead to a permanent loss of vision. As controls, we included vitreous from endophthalmitis-negative patients, balanced salt solution used during vitrectomy, and DNA extraction blanks. We compared two DNA isolation procedures and found that an ultraclean production of reagents appeared to reduce background DNA in these low microbial biomass samples. We created a curated microbial genome database (>5700 genomes) and designed a metagenomics workflow with filtering steps to reduce DNA sequences originating from: i) human hosts, ii) ambiguousness/contaminants in public microbial reference genomes, and iii) the environment. Our metagenomic read classification revealed in nearly all cases the same microorganism than was determined in cultivation- and mass spectrometry-based analyses. For some patients, we identified the sequence type of the microorganism and antibiotic resistance genes through analyses of whole genome sequence (WGS) assemblies of isolates and metagenomic assemblies. Together, we conclude that genomics-based analyses of human ocular body fluid specimens can provide actionable information relevant to infectious disease management.

microbiology↗