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Article ; Online: Flavonoid-Modifying Capabilities of the Human Gut Microbiome-An In Silico Study.

Goris, Tobias / Cuadrat, Rafael R C / Braune, Annett

2021 Volume 13, Issue 8

Abstract: Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly ... ...

Abstract	Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in
MeSH term(s)	Bacterial Proteins/metabolism ; Computer Simulation ; Equol/metabolism ; Flavonoids/metabolism ; Gastrointestinal Microbiome/physiology ; Genome, Bacterial ; Humans ; Isoflavones/metabolism ; Metagenome ; Nutritional Physiological Phenomena/physiology ; Peptide Hydrolases/metabolism ; Proteolysis
Chemical Substances	Bacterial Proteins ; Flavonoids ; Isoflavones ; Equol (531-95-3) ; daidzein (6287WC5J2L) ; Peptide Hydrolases (EC 3.4.-)
Language	English
Publishing date	2021-08-03
Publishing country	Switzerland
Document type	Journal Article ; Comment
ZDB-ID	2518386-2
ISSN	2072-6643 ; 2072-6643
ISSN (online)	2072-6643
ISSN	2072-6643
DOI	10.3390/nu13082688
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Goris, Tobias / Cuadrat, Rafael R. C. / Braune, Annett

Nutrients. 2021 Aug. 03, v. 13, no. 8

2021

Abstract	Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.
Keywords	Collinsella ; Roseburia faecis ; Slackia ; computer simulation ; flavones ; gastrointestinal system ; humans ; hydrolases ; intestinal microorganisms ; metagenomics ; oxidoreductases ; polyphenols ; sequence analysis
Language	English
Dates of publication	2021-0803
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2518386-2
ISSN	2072-6643
ISSN	2072-6643
DOI	10.3390/nu13082688
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Ketogenic Diet Has Moderate Effects on the Fecal Microbiota of Wild-Type Mice.

Rohwer, Nadine / El Hage, Racha / Smyl, Christopher / Ocvirk, Soeren / Goris, Tobias / Grune, Tilman / Swidsinski, Alexander / Weylandt, Karsten-H

Nutrients

2023 Volume 15, Issue 21

Abstract: The ketogenic diet (KD) is a high-fat, low-carbohydrate diet that has been reported to have neuroprotective effects. The health effects of KD might be linked to an altered gut microbiome, which plays a major role in host health, leading to ... ...

Abstract	The ketogenic diet (KD) is a high-fat, low-carbohydrate diet that has been reported to have neuroprotective effects. The health effects of KD might be linked to an altered gut microbiome, which plays a major role in host health, leading to neuroprotective effects via the gut-brain axis. However, results from different studies, most often based on the 16S rRNA gene and metagenome sequencing, have been inconsistent. In this study, we assessed the effect of a 4-week KD compared to a western diet (WD) on the colonic microbiome of female C57Bl/6J mice by analyzing fecal samples using fluorescence in situ hybridization. Our results showed distinct changes in the total number of gut bacteria following the 4-week KD, in addition to changes in the composition of the microbiome. KD-fed mice showed higher absolute numbers of
MeSH term(s)	Female ; Mice ; Animals ; Diet, Ketogenic ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; Neuroprotective Agents ; Microbiota ; Diet, High-Fat ; Bacteria/genetics ; Actinobacteria/genetics ; Mice, Inbred C57BL
Chemical Substances	RNA, Ribosomal, 16S ; Neuroprotective Agents
Language	English
Publishing date	2023-10-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2518386-2
ISSN	2072-6643 ; 2072-6643
ISSN (online)	2072-6643
ISSN	2072-6643
DOI	10.3390/nu15214629
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Article ; Online: IncP-type plasmids carrying genes for antibiotic resistance or for aromatic compound degradation are prevalent in sequenced Aromatoleum and Thauera strains.

Lo, Hao-Yu / Martínez-Lavanchy, Paula M / Goris, Tobias / Heider, Johann / Boll, Matthias / Kaster, Anne-Kristin / Müller, Jochen A

Environmental microbiology

2022

Abstract: Self-transferable plasmids of the incompatibility group P-1 (IncP-1) are considered important carriers of genes for antibiotic resistance and other adaptive functions. In the laboratory, these plasmids have a broad host range; however, little is known ... ...

Abstract	Self-transferable plasmids of the incompatibility group P-1 (IncP-1) are considered important carriers of genes for antibiotic resistance and other adaptive functions. In the laboratory, these plasmids have a broad host range; however, little is known about their in situ host profile. In this study, we discovered that Thauera aromatica K172
Language	English
Publishing date	2022-10-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16262
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Association of the human gut microbiota with vascular stiffness.

Cuadrat, Rafael R C / Goris, Tobias / Birukov, Anna / Eichelmann, Fabian / Andrade, Bruno G N / Bang, Corinna / Franke, Andre / Wittenbecher, Clemens / Schulze, Matthias B

Scientific reports

2023 Volume 13, Issue 1, Page(s) 13348

Abstract: Gut microbiota metabolites have been mechanistically linked to inflammatory pathway activation and atherosclerosis, which are major causes of vascular stiffness (VS). Aiming to investigate if the gut microbiome might be involved in VS development, we ... ...

Abstract	Gut microbiota metabolites have been mechanistically linked to inflammatory pathway activation and atherosclerosis, which are major causes of vascular stiffness (VS). Aiming to investigate if the gut microbiome might be involved in VS development, we performed a cross-sectional study (n = 3,087), nested within the population-based European Prospective Investigations into Cancer and Nutrition (EPIC) Potsdam. We investigated the correlation of the gut microbiota (alpha diversity and taxa abundance) with 3 vascular stiffness measures: carotid-femoral (PWV), aortic augmentation index (AIX) and ankle-brachial index (ABI). Shannon index was not significantly associated with VS but the number of observed Amplicon Sequence Variants (ASV) was positively associated with PWV and AIX. We found a total of 19 ASVs significantly associated with at least one VS measure in multivariable-adjusted models. One ASV (classified as Sutterella wadsworthensis) was associated with 2 VS measures, AIX (- 0.11 ± 0.04) and PWV (-0.14 ± 0.03). Other examples of ASVs associated with VS were Collinsella aerofaciens, previously reported to be affected by diet and Bacteroides uniformis, commercially available as probiotics. In conclusion, our study suggests a potential role of individual components of the gut microbiota in the aetiology of VS.
MeSH term(s)	Humans ; Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; Prospective Studies ; Vascular Stiffness ; Cancer Vaccines
Chemical Substances	asunaprevir (S9X0KRJ00S) ; Cancer Vaccines
Language	English
Publishing date	2023-08-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-40178-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples.

Cuadrat, Rafael R C / Sorokina, Maria / Andrade, Bruno G / Goris, Tobias / Dávila, Alberto M R

GigaScience

2020 Volume 9, Issue 5

Abstract: Background: The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of ... ...

Abstract	Background: The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. We used 293 metagenomic samples from the TARA Oceans project to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. Results: After manual curation of ARGs, their abundance and distribution in the global ocean are presented. Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as 1 of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in putative plasmid sequences, suggesting the importance of mobile genetic elements in the dynamics of environmental ARG transmission. Moreover, 4,804 contigs with >=2 putative ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to mobilized colistin resistance genes (mcr) with high abundance on polar biomes. Of these, 5 are assigned to Psychrobacter, a genus including opportunistic human pathogens. Conclusions: This study uncovers the diversity and abundance of ARGs in the global ocean metagenome. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook js avaliable on Github. We also developed a dashboard web application (http://www.resistomedb.com) for data visualization.
MeSH term(s)	Algorithms ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/pharmacology ; Computational Biology/methods ; DNA Barcoding, Taxonomic ; Drug Resistance, Microbial ; Genes, Bacterial ; Humans ; Metagenome ; Metagenomics/methods ; Oceans and Seas ; Plasmids ; Water Microbiology
Chemical Substances	Anti-Bacterial Agents ; Anti-Infective Agents
Language	English
Publishing date	2020-05-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giaa046
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The NiFe Hydrogenases of the Tetrachloroethene-Respiring Epsilonproteobacterium

Kruse, Stefan / Goris, Tobias / Wolf, Maria / Wei, Xi / Diekert, Gabriele

Frontiers in microbiology

2017 Volume 8, Page(s) 444

Abstract: The organohalide-respiring ... ...

Abstract	The organohalide-respiring Epsilonproteobacterium
Language	English
Publishing date	2017-03-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2017.00444
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria.

Kruse, Stefan / Goris, Tobias / Westermann, Martin / Adrian, Lorenz / Diekert, Gabriele

Nature communications

2018 Volume 9, Issue 1, Page(s) 4872

Abstract: Hydrogen-producing bacteria are of environmental importance, since hydrogen is a major electron donor for prokaryotes in anoxic ecosystems. Epsilonproteobacteria are currently considered to be hydrogen-oxidizing bacteria exclusively. Here, we report ... ...

Abstract	Hydrogen-producing bacteria are of environmental importance, since hydrogen is a major electron donor for prokaryotes in anoxic ecosystems. Epsilonproteobacteria are currently considered to be hydrogen-oxidizing bacteria exclusively. Here, we report hydrogen production upon pyruvate fermentation for free-living Epsilonproteobacteria, Sulfurospirillum spp. The amount of hydrogen produced is different in two subgroups of Sulfurospirillum spp., represented by S. cavolei and S. multivorans. The former produces more hydrogen and excretes acetate as sole organic acid, while the latter additionally produces lactate and succinate. Hydrogen production can be assigned by differential proteomics to a hydrogenase (similar to hydrogenase 4 from E. coli) that is more abundant during fermentation. A syntrophic interaction is established between Sulfurospirillum multivorans and Methanococcus voltae when cocultured with lactate as sole substrate, as the former cannot grow fermentatively on lactate alone and the latter relies on hydrogen for growth. This might hint to a yet unrecognized role of Epsilonproteobacteria as hydrogen producers in anoxic microbial communities.
MeSH term(s)	Acetic Acid/metabolism ; Anaerobiosis/drug effects ; Anaerobiosis/physiology ; Campylobacteraceae/drug effects ; Campylobacteraceae/growth & development ; Campylobacteraceae/metabolism ; Coculture Techniques ; Fermentation/drug effects ; Fermentation/physiology ; Fumarates/metabolism ; Fumarates/pharmacology ; Hydrogen/metabolism ; Kinetics ; Lactic Acid/metabolism ; Methanococcus/drug effects ; Methanococcus/growth & development ; Methanococcus/metabolism ; Oxidation-Reduction ; Pyruvic Acid/metabolism ; Pyruvic Acid/pharmacology ; Succinic Acid/metabolism ; Symbiosis/physiology
Chemical Substances	Fumarates ; Lactic Acid (33X04XA5AT) ; Hydrogen (7YNJ3PO35Z) ; Pyruvic Acid (8558G7RUTR) ; fumaric acid (88XHZ13131) ; Succinic Acid (AB6MNQ6J6L) ; Acetic Acid (Q40Q9N063P)
Language	English
Publishing date	2018-11-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-018-07342-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Putative mobilized colistin resistance genes in the human gut microbiome.

Andrade, Bruno G N / Goris, Tobias / Afli, Haithem / Coutinho, Felipe H / Dávila, Alberto M R / Cuadrat, Rafael R C

BMC microbiology

2021 Volume 21, Issue 1, Page(s) 220

Abstract: Background: The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, ... ...

Abstract	Background: The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes. Results: A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings. Conclusion: This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.
MeSH term(s)	Colistin/pharmacology ; Computational Biology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial/genetics ; Genetic Variation ; Humans ; Microbiota/drug effects ; Microbiota/genetics
Chemical Substances	Colistin (Z67X93HJG1)
Language	English
Publishing date	2021-07-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041505-9
ISSN	1471-2180 ; 1471-2180
ISSN (online)	1471-2180
ISSN	1471-2180
DOI	10.1186/s12866-021-02281-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria

Stefan Kruse / Tobias Goris / Martin Westermann / Lorenz Adrian / Gabriele Diekert

Nature Communications, Vol 9, Iss 1, Pp 1-

2018 Volume 13

Abstract: Epsilonproteobacteria, such as Sulfurospirillum, can use molecular hydrogen as an electron donor for respiration. Here, the authors show that Sulfurospirillum can, in addition, release hydrogen during fermentation, allowing metabolic interactions with ... ...

Abstract	Epsilonproteobacteria, such as Sulfurospirillum, can use molecular hydrogen as an electron donor for respiration. Here, the authors show that Sulfurospirillum can, in addition, release hydrogen during fermentation, allowing metabolic interactions with other hydrogen-consuming microorganisms.
Keywords	Science ; Q
Language	English
Publishing date	2018-11-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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