35045
2023
eng
1
15
article
1
--
--
--
A primary cell-based in vitro model of the human small intestine reveals host olfactomedin 4 induction in response to Salmonella Typhimurium infection
Infection research largely relies on classical cell culture or mouse models. Despite having delivered invaluable insights into host-pathogen interactions, both have limitations in translating mechanistic principles to human pathologies. Alternatives can be derived from modern Tissue Engineering approaches, allowing the reconstruction of functional tissue models in vitro. Here, we combined a biological extracellular matrix with primary tissue-derived enteroids to establish an in vitro model of the human small intestinal epithelium exhibiting in vivo-like characteristics. Using the foodborne pathogen Salmonella enterica serovar Typhimurium, we demonstrated the applicability of our model to enteric infection research in the human context. Infection assays coupled to spatio-temporal readouts recapitulated the established key steps of epithelial infection by this pathogen in our model. Besides, we detected the upregulation of olfactomedin 4 in infected cells, a hitherto unrecognized aspect of the host response to Salmonella infection. Together, this primary human small intestinal tissue model fills the gap between simplistic cell culture and animal models of infection, and shall prove valuable in uncovering human-specific features of host-pathogen interplay.
Gut Microbes
10.1080/19490976.2023.2186109
urn:nbn:de:bvb:20-opus-350451
@articleDaullary.2023, author = Däullary, Thomas and Imdahl, Fabian and Dietrich, Oliver and Hepp, Laura and Krammer, Tobias and Fey, Christina and Neuhaus, Winfried and Metzger, Marco and Vogel, Jörg and Westermann, Alexander J. and Saliba, Antoine-Emmanuel and Zdzieblo, Daniela, year = 2023, title = A primary cell-based invitro model of the human small intestine reveals host olfactomedin 4 induction in response to Salmonella Typhimurium infection, pages = 2186109, volume = 15, number = 1, journal = Gut microbes, doi = 10.1080/19490976.2023.2186109
md5:b95e97262f4361436df5dc589ef8c15b
2024-02-22T06:45:04+00:00
/tmp/phpXbR7n5
bibtex
65d6ed7099a802.27721416
Gut Microbes (2023) 15:1, 2186109. DOI: 10.1080/19490976.2023.2186109
false
true
CC BY-NC: Creative-Commons-Lizenz: Namensnennung, Nicht kommerziell 4.0 International
Thomas Däullary
Fabian Imdahl
Oliver Dietrich
Laura Hepp
Tobias Krammer
Christina Fey
Winfried Neuhaus
Marco Metzger
Jörg Vogel
Alexander J. Westermann
Antoine-Emmanuel Saliba
Daniela Zdzieblo
eng
uncontrolled
intestinal enteroids
eng
uncontrolled
biological scaffold
eng
uncontrolled
Salmonella Typhimurium
eng
uncontrolled
OLFM4
eng
uncontrolled
NOTCH
eng
uncontrolled
filamentous Salmonella Typhimurium
eng
uncontrolled
bacterial migration
eng
uncontrolled
bacterial virulence
eng
uncontrolled
3D tissue model
eng
uncontrolled
olfactomedin 4
eng
uncontrolled
infection
Medizin und Gesundheit
open_access
Institut für Molekulare Infektionsbiologie
Theodor-Boveri-Institut für Biowissenschaften
Lehrstuhl für Tissue Engineering und Regenerative Medizin
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/35045/Daeullary_Gut_Microbes_2023.pdf
34999
2023
eng
4895-4913
21
article
1
--
--
--
Metadata integrity in bioinformatics: bridging the gap between data and knowledge
In the fast-evolving landscape of biomedical research, the emergence of big data has presented researchers with extraordinary opportunities to explore biological complexities. In biomedical research, big data imply also a big responsibility. This is not only due to genomics data being sensitive information but also due to genomics data being shared and re-analysed among the scientific community. This saves valuable resources and can even help to find new insights in silico. To fully use these opportunities, detailed and correct metadata are imperative. This includes not only the availability of metadata but also their correctness. Metadata integrity serves as a fundamental determinant of research credibility, supporting the reliability and reproducibility of data-driven findings. Ensuring metadata availability, curation, and accuracy are therefore essential for bioinformatic research. Not only must metadata be readily available, but they must also be meticulously curated and ideally error-free. Motivated by an accidental discovery of a critical metadata error in patient data published in two high-impact journals, we aim to raise awareness for the need of correct, complete, and curated metadata. We describe how the metadata error was found, addressed, and present examples for metadata-related challenges in omics research, along with supporting measures, including tools for checking metadata and software to facilitate various steps from data analysis to published research.
Highlights
• Data awareness and data integrity underpins the trustworthiness of results and subsequent further analysis.
• Big data and bioinformatics enable efficient resource use by repurposing publicly available RNA-Sequencing data.
• Manual checks of data quality and integrity are insufficient due to the overwhelming volume and rapidly growing data.
• Automation and artificial intelligence provide cost-effective and efficient solutions for data integrity and quality checks.
• FAIR data management, various software solutions and analysis tools assist metadata maintenance.
Computational and Structural Biotechnology Journal
2001-0370
10.1016/j.csbj.2023.10.006
urn:nbn:de:bvb:20-opus-349990
@articleCaliskan.2023b, author = Caliskan, Aylin and Dangwal, Seema and Dandekar, Thomas, year = 2023, title = Metadata integrity in bioinformatics: Bridging the gap between data and knowledge, pages = 4895–4913, volume = 21, issn = 2001-0370, journal = Computational and structural biotechnology journal, doi = 10.1016/j.csbj.2023.10.006
md5:915737cdcc55a76cbff833848e4574e7
2024-02-21T13:29:23+00:00
/tmp/phpNBmHOh
bibtex
65d5fab31e8564.79548456
Computational and Structural Biotechnology Journal (2023) 21:4895-4913. DOI: 10.1016/j.csbj.2023.10.006
false
true
CC BY-NC-ND: Creative-Commons-Lizenz: Namensnennung, Nicht kommerziell, Keine Bearbeitungen 4.0 International
Aylin Caliskan
Seema Dangwal
Thomas Dandekar
eng
uncontrolled
meta-data
eng
uncontrolled
error
eng
uncontrolled
annotation
eng
uncontrolled
error-transfer
eng
uncontrolled
wrong labelling
eng
uncontrolled
patient data
eng
uncontrolled
control group
eng
uncontrolled
tools overview
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/34999/1-s2.0-S2001037023003616-main.pdf
34998
2023
eng
3293-3314
21
article
1
--
--
--
Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning
Machine learning techniques are excellent to analyze expression data from single cells. These techniques impact all fields ranging from cell annotation and clustering to signature identification. The presented framework evaluates gene selection sets how far they optimally separate defined phenotypes or cell groups. This innovation overcomes the present limitation to objectively and correctly identify a small gene set of high information content regarding separating phenotypes for which corresponding code scripts are provided. The small but meaningful subset of the original genes (or feature space) facilitates human interpretability of the differences of the phenotypes including those found by machine learning results and may even turn correlations between genes and phenotypes into a causal explanation. For the feature selection task, the principal feature analysis is utilized which reduces redundant information while selecting genes that carry the information for separating the phenotypes. In this context, the presented framework shows explainability of unsupervised learning as it reveals cell-type specific signatures. Apart from a Seurat preprocessing tool and the PFA script, the pipeline uses mutual information to balance accuracy and size of the gene set if desired. A validation part to evaluate the gene selection for their information content regarding the separation of the phenotypes is provided as well, binary and multiclass classification of 3 or 4 groups are studied. Results from different single-cell data are presented. In each, only about ten out of more than 30000 genes are identified as carrying the relevant information. The code is provided in a GitHub repository at https://github.com/AC-PHD/Seurat_PFA_pipeline.
Computational and Structural Biotechnology Journal
2001-0370
10.1016/j.csbj.2023.06.002
urn:nbn:de:bvb:20-opus-349989
@articleCaliskan.2023, author = Caliskan, Aylin and Caliskan, Deniz and Rasbach, Lauritz and Yu, Weimeng and Dandekar, Thomas and Breitenbach, Tim, year = 2023, title = Optimized cell type signatures revealed from single-cell data by combining principal feature analysis, mutual information, and machine learning, pages = 3293–3314, volume = 21, issn = 2001-0370, journal = Computational and structural biotechnology journal, doi = 10.1016/j.csbj.2023.06.002
md5:b7d4520c41d2170407387f4382203902
2024-02-21T13:29:23+00:00
/tmp/phpNBmHOh
bibtex
65d5fab31e8564.79548456
Computational and Structural Biotechnology Journal (2023) 21:3293-3314. DOI: 10.1016/j.csbj.2023.06.002
false
true
CC BY-NC-ND: Creative-Commons-Lizenz: Namensnennung, Nicht kommerziell, Keine Bearbeitungen 4.0 International
Aylin Caliskan
Deniz Caliskan
Lauritz Rasbach
Weimeng Yu
Thomas Dandekar
Tim Breitenbach
eng
uncontrolled
single cell analysis
eng
uncontrolled
machine learning
eng
uncontrolled
explainability of machine learning
eng
uncontrolled
principal
eng
uncontrolled
feature analysis
eng
uncontrolled
model reduction
eng
uncontrolled
feature selection
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/34998/1-s2.0-S2001037023002155-main.pdf
35000
2023
eng
12
article
1
--
--
--
Gene editing and scalable functional genomic screening in Leishmania species using the CRISPR/Cas9 cytosine base editor toolbox LeishBASEedit
CRISPR/Cas9 gene editing has revolutionised loss-of-function experiments in Leishmania, the causative agent of leishmaniasis. As Leishmania lack a functional non-homologous DNA end joining pathway however, obtaining null mutants typically requires additional donor DNA, selection of drug resistance-associated edits or time-consuming isolation of clones. Genome-wide loss-of-function screens across different conditions and across multiple Leishmania species are therefore unfeasible at present. Here, we report a CRISPR/Cas9 cytosine base editor (CBE) toolbox that overcomes these limitations. We employed CBEs in Leishmania to introduce STOP codons by converting cytosine into thymine and created http://www.leishbaseedit.net/ for CBE primer design in kinetoplastids. Through reporter assays and by targeting single- and multi-copy genes in L. mexicana, L. major, L. donovani, and L. infantum, we demonstrate how this tool can efficiently generate functional null mutants by expressing just one single-guide RNA, reaching up to 100% editing rate in non-clonal populations. We then generated a Leishmania-optimised CBE and successfully targeted an essential gene in a plasmid library delivered loss-of-function screen in L. mexicana. Since our method does not require DNA double-strand breaks, homologous recombination, donor DNA, or isolation of clones, we believe that this enables for the first time functional genetic screens in Leishmania via delivery of plasmid libraries.
eLife
10.7554/eLife.85605
urn:nbn:de:bvb:20-opus-350002
@articleEngstler.2023, author = Engstler, Markus and Beneke, Tom, year = 2023, title = Gene editing and scalable functional genomic screening in Leishmania species using the CRISPR/Cas9 cytosine base editor toolbox LeishBASEedit, volume = 12, journal = eLife, doi = 10.7554/eLife.85605
md5:d79570f452ed079be943757ce9933390
2024-02-21T13:29:23+00:00
/tmp/phpNBmHOh
bibtex
65d5fab31e8564.79548456
eLife (2023) 12:e85605. DOI: 10.7554/eLife.85605
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Markus Engstler
Tom Beneke
eng
uncontrolled
CRISPR/Cas9
eng
uncontrolled
Leishmania
eng
uncontrolled
cytosine base editor (CBE) toolbox
eng
uncontrolled
gene editing
eng
uncontrolled
scalable functional genomic screening
eng
uncontrolled
LeishBASEedit
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/35000/elife-85605-v1.pdf
35003
2023
eng
2767-2779
21
article
1
--
--
--
PRO-Simat: Protein network simulation and design tool
PRO-Simat is a simulation tool for analysing protein interaction networks, their dynamic change and pathway engineering. It provides GO enrichment, KEGG pathway analyses, and network visualisation from an integrated database of more than 8 million protein-protein interactions across 32 model organisms and the human proteome. We integrated dynamical network simulation using the Jimena framework, which quickly and efficiently simulates Boolean genetic regulatory networks. It enables simulation outputs with in-depth analysis of the type, strength, duration and pathway of the protein interactions on the website. Furthermore, the user can efficiently edit and analyse the effect of network modifications and engineering experiments. In case studies, applications of PRO-Simat are demonstrated: (i) understanding mutually exclusive differentiation pathways in Bacillus subtilis, (ii) making Vaccinia virus oncolytic by switching on its viral replication mainly in cancer cells and triggering cancer cell apoptosis and (iii) optogenetic control of nucleotide processing protein networks to operate DNA storage. Multilevel communication between components is critical for efficient network switching, as demonstrated by a general census on prokaryotic and eukaryotic networks and comparing design with synthetic networks using PRO-Simat. The tool is available at https://prosimat.heinzelab.de/ as a web-based query server.
Computational and Structural Biotechnology Journal
2001-0370
10.1016/j.csbj.2023.04.023
urn:nbn:de:bvb:20-opus-350034
@articleSalihoglu.2023, author = Salihoglu, Rana and Srivastava, Mugdha and Liang, Chunguang and Schilling, Klaus and Szalay, Aladar and Bencurova, Elena and Dandekar, Thomas, year = 2023, title = PRO-Simat: Protein network simulation and design tool, pages = 2767–2779, volume = 21, issn = 2001-0370, journal = Computational and structural biotechnology journal, doi = 10.1016/j.csbj.2023.04.023
md5:16b6d13f3371cd72c64be3747a5d61e7
2024-02-21T13:29:23+00:00
/tmp/phpNBmHOh
bibtex
65d5fab31e8564.79548456
Computational and Structural Biotechnology Journal (2023) 21:2767-2779. DOI: 10.1016/j.csbj.2023.04.023
false
true
CC BY-NC-ND: Creative-Commons-Lizenz: Namensnennung, Nicht kommerziell, Keine Bearbeitungen 4.0 International
Rana Salihoglu
Mugdha Srivastava
Chunguang Liang
Klaus Schilling
Aladar Szalay
Elena Bencurova
Thomas Dandekar
eng
uncontrolled
network simulation
eng
uncontrolled
protein analysis
eng
uncontrolled
signalling pathways
eng
uncontrolled
dynamic protein-protein interactions
eng
uncontrolled
optogenetics
eng
uncontrolled
oncolytic virus
eng
uncontrolled
DNA storage
Biowissenschaften; Biologie
open_access
Institut für Informatik
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/35003/1-s2.0-S2001037023001757-main.pdf
31919
2023
eng
10
13
article
1
--
2023-05-19
--
Immunohistochemical and molecular genetic analysis of canine digital mast cell tumours
Grading, immunohistochemistry and c-kit mutation status are criteria for assessing the prognosis and therapeutic options of canine cutaneous mast cell tumours (MCTs). As a subset, canine digital MCTs have rarely been explored in this context. Therefore, in this retrospective study, 68 paraffin-embedded canine digital MCTs were analysed, and histological grading was assessed according to Patnaik and Kiupel. The immunohistochemical markers KIT and Ki67 were used, as well as polymerase chain reaction (PCR) for mutational screening in c-kit exons 8, 9, 11 and 14. Patnaik grading resulted in 22.1% grade I, 67.6% grade II and 10.3% grade III tumours. Some 86.8% of the digital MCTs were Kiupel low-grade. Aberrant KIT staining patterns II and III were found in 58.8%, and a count of more than 23 Ki67-positive cells in 52.3% of the cases. Both parameters were significantly associated with an internal tandem duplication (ITD) in c-kit exon 11 (12.7%). French Bulldogs, which tend to form well-differentiated cutaneous MCTs, had a higher proportion of digital high-grade MCTs and ITD in c-kit exon 11 compared with mongrels. Due to its retrospective nature, this study did not allow for an analysis of survival data. Nevertheless, it may contribute to the targeted characterisation of digital MCTs.
Animals
2076-2615
10.3390/ani13101694
urn:nbn:de:bvb:20-opus-319199
2023-06-07T08:22:46+00:00
sword
swordwue
attachment; filename=deposit.zip
9e75761e51a7a52d5bbf8364f9f0d74f
Animals (20239 13:10, 1694. https://doi.org/10.3390/ani13101694
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
David Conrad
Alexandra Kehl
Tobias Müller
Robert Klopfleisch
Heike Aupperle-Lellbach
eng
uncontrolled
dog
eng
uncontrolled
digit
eng
uncontrolled
toe
eng
uncontrolled
CD117
eng
uncontrolled
Ki67
eng
uncontrolled
KIT
eng
uncontrolled
grading
eng
uncontrolled
PCR
eng
uncontrolled
sequencing
eng
uncontrolled
c-kit
Landwirtschaft und verwandte Bereiche
open_access
Theodor-Boveri-Institut für Biowissenschaften
Import
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/31919/animals-13-01694-v2.pdf
34996
2023
eng
100417
10
64
article
1
--
--
--
The circadian clock is required for rhythmic lipid transport in Drosophila in interaction with diet and photic condition
Modern lifestyle is often at odds with endogenously driven rhythmicity, which can lead to circadian disruption and metabolic syndrome. One signature for circadian disruption is a reduced or altered metabolite cycling in the circulating tissue reflecting the current metabolic status. Drosophila is a well-established model in chronobiology, but day-time dependent variations of transport metabolites in the fly circulation are poorly characterized. Here, we sampled fly hemolymph throughout the day and analyzed diacylglycerols (DGs), phosphoethanolamines (PEs) and phosphocholines (PCs) using LC-MS. In wild-type flies kept on sugar-only medium under a light-dark cycle, all transport lipid species showed a synchronized bimodal oscillation pattern with maxima at the beginning and end of the light phase which were impaired in period01 clock mutants. In wild-type flies under constant dark conditions, the oscillation became monophasic with a maximum in the middle of the subjective day. In strong support of clock-driven oscillations, levels of the targeted lipids peaked once in the middle of the light phase under time-restricted feeding independent of the time of food intake. When wild-type flies were reared on full standard medium, the rhythmic alterations of hemolymph lipid levels were greatly attenuated. Our data suggest that the circadian clock aligns daily oscillations of DGs, PEs, and PCs in the hemolymph to the anabolic siesta phase, with a strong influence of light on phase and modality.
Journal of Lipid Research
10.1016/j.jlr.2023.100417
urn:nbn:de:bvb:20-opus-349961
@articleAmatobi.2023, author = Amatobi, Kelechi M. and Ozbek-Unal, Ayten Gizem and Schäbler, Stefan and Deppisch, Peter and Helfrich-Förster, Charlotte and Mueller, Martin J. and Wegener, Christian and Fekete, Agnes, year = 2023, title = The circadian clock is required for rhythmic lipid transport in Drosophila in interaction with diet and photic condition, pages = 100417, volume = 64, number = 10, journal = Journal of lipid research, doi = 10.1016/j.jlr.2023.100417
md5:e85aff195db812e21d6e45be958f275e
2024-02-21T13:29:23+00:00
/tmp/phpNBmHOh
bibtex
65d5fab31e8564.79548456
Journal of Lipid Research (2023) 64:10, 100417. DOI: 10.1016/j.jlr.2023.100417
false
true
CC BY-NC-ND: Creative-Commons-Lizenz: Namensnennung, Nicht kommerziell, Keine Bearbeitungen 4.0 International
Kelechi M. Amatobi
Ayten Gizem Ozbek-Unal
Stefan Schäbler
Peter Deppisch
Charlotte Helfrich-Förster
Martin J. Mueller
Christian Wegener
Agnes Fekete
eng
uncontrolled
hemolymph lipids
eng
uncontrolled
lipidomics
eng
uncontrolled
circadian rhythm
eng
uncontrolled
feeding
eng
uncontrolled
locomotor activity
eng
uncontrolled
light-driven metabolism
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Julius-von-Sachs-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/34996/1-s2.0-S0022227523000901-main.pdf
35004
2023
eng
256
article
1
--
--
--
A combination of the frequent fungicides boscalid and dimoxystrobin with the neonicotinoid acetamiprid in field-realistic concentrations does not affect sucrose responsiveness and learning behavior of honeybees
The increasing loss of pollinators over the last decades has become more and more evident. Intensive use of plant protection products is one key factor contributing to this decline. Especially the mixture of different plant protection products can pose an increased risk for pollinators as synergistic effects may occur. In this study we investigated the effect of the fungicide Cantus® Gold (boscalid/dimoxystrobin), the neonicotinoid insecticide Mospilan® (acetamiprid) and their mixture on honeybees. Since both plant protection products are frequently applied sequentially to the same plants (e.g. oilseed rape), their combination is a realistic scenario for honeybees. We investigated the mortality, the sucrose responsiveness and the differential olfactory learning performance of honeybees under controlled conditions in the laboratory to reduce environmental noise. Intact sucrose responsiveness and learning performance are of pivotal importance for the survival of individual honeybees as well as for the functioning of the entire colony. Treatment with two sublethal and field relevant concentrations of each plant protection product did not lead to any significant effects on these behaviors but affected the mortality rate. However, our study cannot exclude possible negative sublethal effects of these substances in higher concentrations. In addition, the honeybee seems to be quite robust when it comes to effects of plant protection products, while wild bees might be more sensitive.
Highlights
• Mix of SBI fungicides and neonicotinoids can lead to synergistic effects for bees.
• Combination of non-SBI fungicide and neonicotinoid in field-realistic doses tested.
• Synergistic effect on mortality of honeybees.
• No effects on sucrose responsiveness and learning performance of honeybees.
• Synergistic effects by other pesticide mixtures or on wild bees cannot be excluded.
Ecotoxicology and Environmental Safety
10.1016/j.ecoenv.2023.114850
urn:nbn:de:bvb:20-opus-350047
@articleSchuhmann.2023, author = Schuhmann, Antonia and Scheiner, Ricarda, year = 2023, title = A combination of the frequent fungicides boscalid and dimoxystrobin with the neonicotinoid acetamiprid in field-realistic concentrations does not affect sucrose responsiveness and learning behavior of honeybees, pages = 114850, volume = 256, journal = Ecotoxicology and environmental safety, doi = 10.1016/j.ecoenv.2023.114850
md5:ed8e72911a988e8cca2afa480199bd2c
2024-02-21T13:29:23+00:00
/tmp/phpNBmHOh
bibtex
65d5fab31e8564.79548456
Ecotoxicology and Environmental Safety (2023) 256:114850. DOI: 10.1016/j.ecoenv.2023.114850
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Antonia Schuhmann
Ricarda Scheiner
eng
uncontrolled
Apis mellifera
eng
uncontrolled
non-SBI fungicide
eng
uncontrolled
insecticide
eng
uncontrolled
pesticide mixture
eng
uncontrolled
synergistic effect
eng
uncontrolled
sublethal effect
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/35004/1-s2.0-S0147651323003548-main.pdf
22316
2019
eng
84
7
article
1
2021-02-05
--
--
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
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.
Microbiome
10.1186/s40168-019-0684-8
urn:nbn:de:bvb:20-opus-223161
publish
Microbiome (2019) 7:84. https://doi.org/10.1186/s40168-019-0684-8
686070
669830
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Luis Pedro Coelho
Renato Alves
Paulo Monteiro
Jaime Huerta-Cepas
Ana Teresa Freitas
Peer Bork
eng
uncontrolled
metagenomics
eng
uncontrolled
next-generation sequencing
eng
uncontrolled
domain-specific language
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
OpenAIRE
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/22316/s40168-019-0684-8.pdf
22317
2018
eng
6
article
1
2021-02-05
--
--
Similarity of the dog and human gut microbiomes in gene content and response to diet
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.
Microbiome
10.1186/s40168-018-0450-3
urn:nbn:de:bvb:20-opus-223177
publish
686070
Microbiome (2018) 6:72. https://doi.org/10.1186/s40168-018-0450-3
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Luis Pedro Coelho
Jens Roat Kultima
Paul Igor Costea
Coralie Fournier
Yuanlong Pan
Gail Czarnecki-Maulden
Matthew Robert Hayward
Sofia K. Forslund
Thomas Sebastian Benedikt Schmidt
Patrick Descombes
Janet R. Jackson
Qinghong Li
Peer Bork
eng
uncontrolled
microbiome
eng
uncontrolled
diet
eng
uncontrolled
metagenomics
eng
uncontrolled
dog microbiome
eng
uncontrolled
human microbiome
eng
uncontrolled
mouse microbiome
eng
uncontrolled
pig microbiome
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
OpenAIRE
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/22317/s40168-018-0450-3.pdf