@article{SchmidtHaywardCoelhoetal.2019, author = {Schmidt, Thomas S. B. and Hayward, Matthew R. and Coelho, Luiis P. and Li, Simone S. and Costea, Paul I. and Voigt, Anita Y. and Wirbel, Jakob and Maistrenko, Oleksandr M. and Alves, Renato J. C. and Bergsten, Emma and de Beaufort, Carine and Sobhani, Iradj and Heintz-Buschart, Anna and Sunagawa, Shinichi and Zeller, Georg and Wilmes, Paul and Bork, Peer}, title = {Extensive transmission of microbes along the gastrointestinal tract}, series = {eLife}, volume = {8}, journal = {eLife}, doi = {10.7554/eLife.42693}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-228954}, pages = {e42693, 1-18}, year = {2019}, abstract = {The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.}, subject = {Barrier}, language = {en} } @article{PimentelElardoGrozdanovProkschetal.2012, author = {Pimentel-Elardo, Sheila Marie and Grozdanov, Lubomir and Proksch, Sebastian and Hentschel, Ute}, title = {Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-75990}, year = {2012}, abstract = {Genomic mining revealed one major nonribosomal peptide synthetase (NRPS) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a Chloroflexi sponge symbiont. Genomic mining studies such as the one presented here for NRPS genes, contribute to on-going efforts to characterize the genomic potential of sponge-associated microbiota for secondary metabolite biosynthesis.}, subject = {Biologie}, language = {en} } @article{NazzalHowariYaslametal.2022, author = {Nazzal, Yousef and Howari, Fares M. and Yaslam, Aya and Iqbal, Jibran and Maloukh, Lina and Ambika, Lakshmi Kesari and Al-Taani, Ahmed A. and Ali, Ijaz and Othman, Eman M. and Jamal, Arshad and Naseem, Muhammad}, title = {A methodological review of tools that assess dust microbiomes, metatranscriptomes and the particulate chemistry of indoor dust}, series = {Atmosphere}, volume = {13}, journal = {Atmosphere}, number = {8}, issn = {2073-4433}, doi = {10.3390/atmos13081276}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-285957}, year = {2022}, abstract = {Indoor house dust is a blend of organic and inorganic materials, upon which diverse microbial communities such as viruses, bacteria and fungi reside. Adequate moisture in the indoor environment helps microbial communities multiply fast. The outdoor air and materials that are brought into the buildings by airflow, sandstorms, animals pets and house occupants endow the indoor dust particles with extra features that impact human health. Assessment of the health effects of indoor dust particles, the type of indoor microbial inoculants and the secreted enzymes by indoor insects as allergens merit detailed investigation. Here, we discuss the applications of next generation sequencing (NGS) technology which is used to assess microbial diversity and abundance of the indoor dust environments. Likewise, the applications of NGS are discussed to monitor the gene expression profiles of indoor human occupants or their surrogate cellular models when exposed to aqueous solution of collected indoor dust samples. We also highlight the detection methods of dust allergens and analytical procedures that quantify the chemical nature of indoor particulate matter with a potential impact on human health. Our review is thus unique in advocating the applications of interdisciplinary approaches that comprehensively assess the health effects due to bad air quality in built environments.}, language = {en} } @article{MaloukhNazzalKumarappanetal.2023, author = {Maloukh, Lina and Nazzal, Yousef and Kumarappan, Alagappan and Howari, Fares and Ambika, Lakshmi Kesari and Yahmadi, Rihab and Sharma, Manish and Iqbal, Jibran and Al-Taani, Ahmed A. and Salem, Imen Ben and Xavier, Cijo M. and Naseem, Muhamad}, title = {Metagenomic analysis of the outdoor dust microbiomes: a case study from Abu Dhabi, UAE}, series = {Atmosphere}, volume = {14}, journal = {Atmosphere}, number = {2}, issn = {2073-4433}, doi = {10.3390/atmos14020327}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-304391}, year = {2023}, abstract = {Outdoor dust covers a shattered range of microbial agents from land over transportation, human microbial flora, which includes pathogen and commensals, and airborne from the environment. Dust aerosols are rich in bacterial communities that have a major impact on human health and living environments. In this study, outdoor samples from roadside barricades, safety walls, and fences (18 samples) were collected from Abu Dhabi, UAE and bacterial diversity was assessed through a 16S rRNA amplicon next generation sequencing approach. Clean data from HiSeq produced 1,099,892 total reads pairs for 18 samples. For all samples, taxonomic classifications were assigned to the OTUs (operational taxonomic units) representative sequence using the Ribosomal Database Project database. Analysis such as alpha diversity, beta diversity, differential species analysis, and species relative abundance were performed in the clustering of samples and a functional profile heat map was obtained from the OTUs by using bioinformatics tools. A total of 2814 OTUs were identified from those samples with a coverage of more than 99\%. In the phylum, all 18 samples had most of the bacterial groups such as Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Twelve samples had Propionibacteria acnes and were mainly found in RD16 and RD3. Major bacteria species such as Propionibacteria acnes, Bacillus persicus, and Staphylococcus captis were found in all samples. Most of the samples had Streptococcus mitis, Staphylococcus capitis. and Nafulsella turpanensis and Enhydrobacter aerosaccus was part of the normal microbes of the skin. Salinimicrobium sp., Bacillus alkalisediminis, and Bacillus persicus are halophilic bacteria found in sediments. The heat map clustered the samples and species in vertical and horizontal classification, which represents the relationship between the samples and bacterial diversity. The heat map for the functional profile had high properties of amino acids, carbohydrate, and cofactor and vitamin metabolisms of all bacterial species from all samples. Taken together, our analyses are very relevant from the perspective of out-door air quality, airborne diseases, and epidemics, with broader implications for health safety and monitoring.}, language = {en} } @article{KrohnMoltAlawiFoerstneretal.2017, author = {Krohn-Molt, Ines and Alawi, Malik and F{\"o}rstner, Konrad U. and Wiegandt, Alena and Burkhardt, Lia and Indenbirken, Daniela and Thieß, Melanie and Grundhoff, Adam and Kehr, Julia and Tholey, Andreas and Streit, Wolfgang R.}, title = {Insights into microalga and bacteria interactions of selected phycosphere biofilms using metagenomic, transcriptomic, and proteomic approaches}, series = {Frontiers in Microbiology}, volume = {2017}, journal = {Frontiers in Microbiology}, number = {8}, doi = {10.3389/fmicb.2017.01941}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173701}, year = {2017}, abstract = {Microalga are of high relevance for the global carbon cycling and it is well-known that they are associated with a microbiota. However, it remains unclear, if the associated microbiota, often found in phycosphere biofilms, is specific for the microalga strains and which role individual bacterial taxa play. Here we provide experimental evidence that \(Chlorella\) \(saccharophila\), \(Scenedesmus\) \(quadricauda\), and \(Micrasterias\) \(crux-melitensis\), maintained in strain collections, are associated with unique and specific microbial populations. Deep metagenome sequencing, binning approaches, secretome analyses in combination with RNA-Seq data implied fundamental differences in the gene expression profiles of the microbiota associated with the different microalga. Our metatranscriptome analyses indicates that the transcriptionally most active bacteria with respect to key genes commonly involved in plant-microbe interactions in the Chlorella (Trebouxiophyceae) and Scenedesmus (Chlorophyceae) strains belong to the phylum of the α-Proteobacteria. In contrast, in the Micrasterias (Zygnematophyceae) phycosphere biofilm bacteria affiliated with the phylum of the Bacteroidetes showed the highest gene expression rates. We furthermore show that effector molecules known from plant-microbe interactions as inducers for the innate immunity are already of relevance at this evolutionary early plant-microbiome level.}, language = {en} } @article{HicklHeintzBuschartTrautweinSchultetal.2019, author = {Hickl, Oskar and Heintz-Buschart, Anna and Trautwein-Schult, Anke and Hercog, Rajna and Bork, Peer and Wilmes, Paul and Becher, D{\"o}rte}, title = {Sample preservation and storage significantly impact taxonomic and functional profiles in metaproteomics studies of the human gut microbiome}, series = {Microorganisms}, volume = {7}, journal = {Microorganisms}, number = {9}, issn = {2076-2607}, doi = {10.3390/microorganisms7090367}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-195976}, year = {2019}, abstract = {With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible about the biological system at the time of sampling. Here, we analyzed human stool samples preserved and stored using different methods, applying metagenomics as well as metaproteomics. Our results demonstrate that sample preservation and storage have a significant effect on the taxonomic composition of identified proteins. The overall identification rates, as well as the proportion of proteins from Actinobacteria were much higher when samples were flash frozen. Preservation in RNAlater overall led to fewer protein identifications and a considerable increase in the share of Bacteroidetes, as well as Proteobacteria. Additionally, a decrease in the share of metabolism-related proteins and an increase of the relative amount of proteins involved in the processing of genetic information was observed for RNAlater-stored samples. This suggests that great care should be taken in choosing methods for the preservation and storage of microbiome samples, as well as in comparing the results of analyses using different sampling and storage methods. Flash freezing and subsequent storage at -80 °C should be chosen wherever possible.}, language = {en} } @article{CosteaCoelhoSunagawaetal.2017, author = {Costea, Paul I. and Coelho, Louis Pedro and Sunagawa, Shinichi and Munch, Robin and Huerta-Cepas, Jaime and Forslund, Kristoffer and Hildebrand, Falk and Kushugulova, Almagul and Zeller, Georg and Bork, Peer}, title = {Subspecies in the global human gut microbiome}, series = {Molecular Systems Biology}, volume = {13}, journal = {Molecular Systems Biology}, number = {12}, doi = {10.15252/msb.20177589}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172674}, year = {2017}, abstract = {Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72\% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.}, language = {en} } @article{CoelhoKultimaCosteaetal.2018, author = {Coelho, Luis Pedro and Kultima, Jens Roat and Costea, Paul Igor and Fournier, Coralie and Pan, Yuanlong and Czarnecki-Maulden, Gail and Hayward, Matthew Robert and Forslund, Sofia K. and Schmidt, Thomas Sebastian Benedikt and Descombes, Patrick and Jackson, Janet R. and Li, Qinghong and Bork, Peer}, title = {Similarity of the dog and human gut microbiomes in gene content and response to diet}, series = {Microbiome}, volume = {6}, journal = {Microbiome}, doi = {10.1186/s40168-018-0450-3}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-223177}, year = {2018}, abstract = {Background Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs. Results We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data). Based on this catalog and taxonomic abundance profiling, we show that the dog microbiome is closer to the human microbiome than the microbiome of either pigs or mice. To investigate this similarity in terms of response to dietary changes, we report on a randomized intervention with two diets (high-protein/low-carbohydrate vs. lower protein/higher carbohydrate). We show that diet has a large and reproducible effect on the dog microbiome, independent of breed or sex. Moreover, the responses were in agreement with those observed in previous human studies. Conclusions We conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.}, language = {en} } @article{CoelhoAlvesMonteiroetal.2019, author = {Coelho, Luis Pedro and Alves, Renato and Monteiro, Paulo and Huerta-Cepas, Jaime and Freitas, Ana Teresa and Bork, Peer}, title = {NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language}, series = {Microbiome}, volume = {7}, journal = {Microbiome}, number = {84}, doi = {10.1186/s40168-019-0684-8}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-223161}, year = {2019}, abstract = {Background Shotgun metagenomes contain a sample of all the genomic material in an environment, allowing for the characterization of a microbial community. In order to understand these communities, bioinformatics methods are crucial. A common first step in processing metagenomes is to compute abundance estimates of different taxonomic or functional groups from the raw sequencing data. Given the breadth of the field, computational solutions need to be flexible and extensible, enabling the combination of different tools into a larger pipeline. Results We present NGLess and NG-meta-profiler. NGLess is a domain specific language for describing next-generation sequence processing pipelines. It was developed with the goal of enabling user-friendly computational reproducibility. It provides built-in support for many common operations on sequencing data and is extensible with external tools with configuration files. Using this framework, we developed NG-meta-profiler, a fast profiler for metagenomes which performs sequence preprocessing, mapping to bundled databases, filtering of the mapping results, and profiling (taxonomic and functional). It is significantly faster than either MOCAT2 or htseq-count and (as it builds on NGLess) its results are perfectly reproducible. Conclusions NG-meta-profiler is a high-performance solution for metagenomics processing built on NGLess. It can be used as-is to execute standard analyses or serve as the starting point for customization in a perfectly reproducible fashion. NGLess and NG-meta-profiler are open source software (under the liberal MIT license) and can be downloaded from https://ngless.embl.de or installed through bioconda.}, language = {en} } @article{CadarJellingerRiedereretal.2021, author = {Cadar, D{\´a}niel and Jellinger, Kurt A. and Riederer, Peter and Strobel, Sabrina and Monoranu, Camelia-Maria and Tappe, Dennis}, title = {No metagenomic evidence of causative viral pathogens in postencephalitic parkinsonism following encephalitis lethargica}, series = {Microorganisms}, volume = {9}, journal = {Microorganisms}, number = {8}, issn = {2076-2607}, doi = {10.3390/microorganisms9081716}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-245074}, year = {2021}, abstract = {Postencephalitic parkinsonism (PEP) is a disease of unknown etiology and pathophysiology following encephalitis lethargica (EL), an acute-onset polioencephalitis of cryptic cause in the 1920s. PEP is a tauopathy with multisystem neuronal loss and gliosis, clinically characterized by bradykinesia, rigidity, rest tremor, and oculogyric crises. Though a viral cause of EL is likely, past polymerase chain reaction-based investigations in the etiology of both PEP and EL were negative. PEP might be caused directly by an unknown viral pathogen or the consequence of a post-infectious immunopathology. The development of metagenomic next-generation sequencing in conjunction with bioinformatic techniques has generated a broad-range tool for the detection of unknown pathogens in the recent past. Retrospective identification and characterization of pathogens responsible for past infectious diseases can be successfully performed with formalin-fixed paraffin-embedded (FFPE) tissue samples. In this study, we analyzed 24 FFPE brain samples from six patients with PEP by unbiased metagenomic next-generation sequencing. Our results show that no evidence for the presence of a specific or putative (novel) viral pathogen was found, suggesting a likely post-infectious immune-mediated etiology of PEP.}, language = {en} }