Jens Roat Kultima

European Molecular Biology Laboratory

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Co-Authors

Peer Bork

European Molecular Biology Laboratory

Shinichi Sunagawa

ETH Zurich

Sofia K. Forslund

Charité - Universitätsmedizin Berlin

Paul Igor Costea

BASF (Germany)

Luís Pedro Coelho

Shanghai Center for Brain Science and Brain-Inspired Technology

Patrick Descombes

Nestlé (Switzerland)

Thomas Schmidt

European Molecular Biology Laboratory

Coralie Fournier

Nestlé (Switzerland)

Gail L. Czarnecki-Maulden

University of Illinois System

Manimozhiyan Arumugam

Novo Nordisk Foundation

Cooperative Institutions

Centre National de la Recherche Scientifique

Université Paris-Saclay

Microbiologie de l’alimentation au service de la santé

European Molecular Biology Laboratory

University of Copenhagen

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Harvard University

AgroParisTech

Sorbonne Université

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Tracking Mesenchymal Stem Cells with Iron Oxide Nanoparticle Loaded Poly(lactide-co-glycolide) Microparticles

Nano Letters (2012)

Chenjie Xu David Miranda-Nieves James A. Ankrum Mads Emil Matthiesen Joseph A. Phillips

Monitoring the location, distribution and long-term engraftment of administered cells is critical for demonstrating the success of a cell therapy. Among available imaging-based cell tracking tools, magnetic resonance imaging (MRI) is advantageous due to its noninvasiveness, deep penetration, and high spatial resolution. While tracking cells in preclinical models via internalized MRI contrast agents (iron oxide nanoparticles, IO-NPs) is a widely used method, IO-NPs suffer from low iron content per particle, low uptake in nonphagocytotic cell types (e.g., mesenchymal stem cells, MSCs), weak negative contrast, and decreased MRI signal due to cell proliferation and cellular exocytosis. Herein, we demonstrate that internalization of IO-NP (10 nm) loaded biodegradable poly(lactide-co-glycolide) microparticles (IO/PLGA-MPs, 0.4-3 μm) in MSCs enhances MR parameters such as the r(2) relaxivity (5-fold), residence time inside the cells (3-fold) and R(2) signal (2-fold) compared to IO-NPs alone. Intriguingly, in vitro and in vivo experiments demonstrate that internalization of IO/PLGA-MPs in MSCs does not compromise inherent cell properties such as viability, proliferation, migration and their ability to home to sites of inflammation.

Internalization

PLGA

Iron oxide nanoparticles

10.1021/nl301658q

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Citations (139)

Structure and function of the global ocean microbiome

Science (2015)

Shinichi Sunagawa Luís Pedro Coelho Samuel Chaffron Jens Roat Kultima Karine Labadie

Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

Mesopelagic zone

Biogeochemical Cycle

Prokaryote

Biogeochemistry

10.1126/science.1261359

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Citations (2,540)

Towards standards for human fecal sample processing in metagenomic studies

Nature Biotechnology (2017)

Paul Igor Costea Georg Zeller Shinichi Sunagawa Éric Pelletier Adriana Alberti

Comparability

Transferability

10.1038/nbt.3960

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Citations (677)

Classification and quantification of bacteriophage taxa in human gut metagenomes

The ISME Journal (2014)

Alison S. Waller Takuji Yamada David M. Kristensen Jens Roat Kultima Shinichi Sunagawa

Prophage

Human virome

Lytic cycle

Lysogenic cycle

10.1038/ismej.2014.30

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Citations (149)

Erratum: Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Nature (2017)

Sofia K. Forslund Falk Hildebrand Trine Nielsen Gwen Falony Emmanuelle Le Chatelier

Affect

Clinical phenotype

10.1038/nature22318

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Citations (66)

Dart formation in nematocysts of the sea anemone <i>Metridium senile</i> (Linnaeus, 1761) (Cnidaria: Anthozoa)

Scientia Marina (2010)

Carina Östman Jens Roat Kultima Sau Yu Grace Wong

In examining large acontia b-mastigophore and p-amastigophore nematocysts of the sea anemone Metridium senile (Linnaeus, 1761) darts were observed by interference-contrast light microscopy (LM) and scanning electron microscopy (SEM).The darts consist of closely packed spines detached from the shafts, still in three helical rows.Their spines form a hollow cylinder with a sharp tip and indented base, its width similar to that of an undischarged shaft but varying in length.b-mastigophore darts were more common than those of p-mastigophores and many were longer.

Cnidocyte

Anthozoa

Sea anemone

Nematocyst

Lernaean Hydra

Scyphozoa

Octocorallia

10.3989/scimar.2010.74n3499

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Citations (11)

Additional file 6: of Similarity of the dog and human gut microbiomes in gene content and response to diet

Figshare (2018)

Luís Pedro Coelho Jens Roat Kultima Paul Igor Costea Coralie Fournier Yuanlong Pan

Table S6. Nutritional content of the 3 diets used in this study. Values shown refer to percentage (%) by weight. (XLSX 4Â kb)

Similarity (geometry)

Gut microbiome

Content (measure theory)

10.6084/m9.figshare.6158699

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Citations (0)

An integrated catalog of reference genes in the human gut microbiome

Nature Biotechnology (2014)

Junhua Li Huijue Jia Xianghang Cai Huanzi Zhong Qiang Feng

Gut microbiome

Human Microbiome Project

10.1038/nbt.2942

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Citations (1,839)

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PLoS ONE (2012)

Jens Roat Kultima Shinichi Sunagawa Junhua Li Wei‐Neng Chen Hua Chen

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

Perl

10.1371/journal.pone.0047656

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Citations (193)

Additional file 3 of Similarity of the dog and human gut microbiomes in gene content and response to diet

Figshare (2018)

Luís Pedro Coelho Jens Roat Kultima Paul Igor Costea Coralie Fournier Yuanlong Pan

Table S3. Gene annotation statistics. (XLSX 6Â kb)

Similarity (geometry)

Content (measure theory)

Gut microbiome

10.6084/m9.figshare.6158663

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Citations (0)