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Illuminating Functional Networks and Keystone Species in the Gut


Conversion of Rutin, a Prevalent Dietary Flavonol, by the Human Gut Microbiota

Author(s): Alessandra Riva, Ditta Kolimár, Andreas Spittler, Lukas Wisgrill, Craig W. Herbold, László Abrankó, David Berry
Published in: Frontiers in Microbiology, Issue 11, 2020, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2020.585428

Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms

Author(s): Kriti Sharma, Márton Palatinszky, Georgi Nikolov, David Berry, Elizabeth A Shank
Published in: eLife, Issue 9, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.56275

Targeting Gut Bacteria Using Inulin-Conjugated Mesoporous Silica Nanoparticles

Author(s): von Baeckmann C, Riva A, Guggenberger P, Kählig H, Han SW, Inan D, Del Favero G, Berry D, Kleitz F
Published in: Advanced Materials Interfaces, Issue 21967350, 2022, ISSN 2196-7350
Publisher: Wiley
DOI: 10.1002/admi.202102558

Crypt residing bacteria and proximal colonic carcinogenesis in a mouse model of Lynch syndrome

Author(s): Michaela Lang, Maximilian Baumgartner, Aleksandra Rożalska, Adrian Frick, Alessandra Riva, Michael Jarek, David Berry, Christoph Gasche
Published in: International Journal of Cancer, Issue 147/8, 2020, Page(s) 2316-2326, ISSN 0020-7136
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/ijc.33028

Lipid synthesis at the trophic base as the source for energy management to build complex structures

Author(s): Schnorr SL, Berry D
Published in: Current Opinion in Biotechnology, Issue 09581669, 2022, Page(s) 364-373, ISSN 0958-1669
Publisher: Elsevier BV
DOI: 10.1016/j.copbio.2021.09.014

Aberrant gut-microbiota-immune-brain axis development in premature neonates with brain damage

Author(s): David Seki, Margareta Mayer, Bela Hausmann, Petra Pjevac, Vito Giordano, Katharina Goeral, Lukas Unterasinger, Katrin Klebermaß-Schrehof, Kim De Paepe, Tom Van de Wiele, Andreas Spittler, Gregor Kasprian, Benedikt Warth, Angelika Berger, David Berry, Lukas Wisgrill
Published in: Cell Host & Microbe, Issue 29/10, 2021, Page(s) 1558-1572.e6, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2021.08.004

Persistence of the antagonistic effects of a natural mixture of Alternaria mycotoxins on the estrogen-like activity of human feces after anaerobic incubation

Author(s): Crudo F, Aichinger G, Dellafiora L, Kiss E, Mihajlovic J, Del Favero G, Berry D, Dall'Asta C, Marko D
Published in: Toxicology Letters, Issue 03784274, 2022, Page(s) 88-99, ISSN 0378-4274
Publisher: Elsevier BV
DOI: 10.1016/j.toxlet.2022.01.015

Individuality of the Extremely Premature Infant Gut Microbiota Is Driven by Ecological Drift

Author(s): Seki D, Schauberger C, Hausmann B, Berger A, Wisgrill L, Berry D
Published in: mSystems, Issue 23795077, 2022, ISSN 2379-5077
Publisher: American Society for Microbiology
DOI: 10.1128/msystems.00163-22

Single-cell stable isotope probing in microbial ecology

Author(s): Alcolombri U, Pioli R, Stocker R, Berry D
Published in: ISME Communications, Issue 27306151, 2022, ISSN 2730-6151
Publisher: Springer Nature
DOI: 10.1038/s43705-022-00142-3

Mucosal Biofilms Are an Endoscopic Feature of Irritable Bowel Syndrome and Ulcerative Colitis

Author(s): Maximilian Baumgartner, Michaela Lang, Hunter Holley, Daniel Crepaz, Bela Hausmann, Petra Pjevac, Doris Moser, Felix Haller, Fabian Hof, Andrea Beer, Elisabeth Orgler, Adrian Frick, Vineeta Khare, Rayko Evstatiev, Susanne Strohmaier, Christian Primas, Werner Dolak, Thomas Köcher, Kristaps Klavins, Timo Rath, Markus F. Neurath, David Berry, Athanasios Makristathis, Markus Muttenthaler, Christoph G
Published in: Gastroenterology, Issue 161/4, 2021, Page(s) 1245-1256.e20, ISSN 0016-5085
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1053/j.gastro.2021.06.024

Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes

Author(s): Richard R. Rodrigues, Manoj Gurung, Zhipeng Li, Manuel García-Jaramillo, Renee Greer, Christopher Gaulke, Franziska Bauchinger, Hyekyoung You, Jacob W. Pederson, Stephany Vasquez-Perez, Kimberly D. White, Briana Frink, Benjamin Philmus, Donald B. Jump, Giorgio Trinchieri, David Berry, Thomas J. Sharpton, Amiran Dzutsev, Andrey Morgun, Natalia Shulzhenko
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-20313-x

Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization

Author(s): Fátima C. Pereira, Kenneth Wasmund, Iva Cobankovic, Nico Jehmlich, Craig W. Herbold, Kang Soo Lee, Barbara Sziranyi, Cornelia Vesely, Thomas Decker, Roman Stocker, Benedikt Warth, Martin von Bergen, Michael Wagner, David Berry
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-18928-1

Impaired Mucosal Homeostasis in Short-Term Fiber Deprivation Is Due to Reduced Mucus Production Rather Than Overgrowth of Mucus-Degrading Bacteria

Author(s): Overbeeke A, Lang M, Hausmann B, Watzka M, Nikolov G, Schwarz J, Kohl G, De Paepe K, Eislmayr K, Decker T, Richter A, Berry D
Published in: Nutrients, Issue 20726643, 2022, Page(s) 3802, ISSN 2072-6643
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu14183802

Next-generation biomonitoring of the early-lifechemical exposome in neonatal and infantdevelopment

Author(s): Jamnik T, Flasch M, Braun D, Fareed Y, Wasinger D, Seki D, Berry D, Berger A, Wisgrill L, Warth B
Published in: Nature Communications, Issue 20411723, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-30204-y

A look beyond dietary (poly)phenols: The low molecular weight phenolic metabolites and their concentrations in human circulation

Author(s): Carregosa D, Pinto C, Ávila-Gálvez MÁ, Bastos P, Berry D, Santos CN
Published in: Comprehensive Reviews in Food Science and Food Safety, Issue 15414337, 2022, Page(s) 3931-3962, ISSN 1541-4337
Publisher: International Life Sciences Institute
DOI: 10.1111/1541-4337.13006

Microbial nitrogen limitation in the mammalian large intestine

Author(s): Aspen T. Reese, Fátima C. Pereira, Arno Schintlmeister, David Berry, Michael Wagner, Laura P. Hale, Anchi Wu, Sharon Jiang, Heather K. Durand, Xiyou Zhou, Richard T. Premont, Anna Mae Diehl, Thomas M. O’Connell, Susan C. Alberts, Tyler R. Kartzinel, Robert M. Pringle, Robert R. Dunn, Justin P. Wright, Lawrence A. David
Published in: Nature Microbiology, 2018, ISSN 2058-5276
Publisher: Nature Publishing Group
DOI: 10.1038/s41564-018-0267-7

Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples

Author(s): Jesse P. Harrison, David Berry
Published in: Frontiers in Microbiology, Issue 8, 2017, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2017.00675

Long-distance electron transport in individual, living cable bacteria

Author(s): Jesper T. Bjerg, Henricus T. S. Boschker, Steffen Larsen, David Berry, Markus Schmid, Diego Millo, Paula Tataru, Filip J. R. Meysman, Michael Wagner, Lars Peter Nielsen, Andreas Schramm
Published in: Proceedings of the National Academy of Sciences, Issue 115/22, 2018, Page(s) 5786-5791, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1800367115

An automated Raman-based platform for the sorting of live cells by functional properties

Author(s): Kang Soo Lee, Márton Palatinszky, Fátima C. Pereira, Jen Nguyen, Vicente I. Fernandez, Anna J. Mueller, Filippo Menolascina, Holger Daims, David Berry, Michael Wagner, Roman Stocker
Published in: Nature Microbiology, Issue 4/6, 2019, Page(s) 1035-1048, ISSN 2058-5276
Publisher: Nature Publishing Grouip
DOI: 10.1038/s41564-019-0394-9

Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis

Author(s): Simone Herp, Sandrine Brugiroux, Debora Garzetti, Diana Ring, Lara M. Jochum, Markus Beutler, Claudia Eberl, Saib Hussain, Steffi Walter, Roman G. Gerlach, Hans J. Ruscheweyh, Daniel Huson, Mikael E. Sellin, Emma Slack, Buck Hanson, Alexander Loy, John F. Baines, Philipp Rausch, Marijana Basic, André Bleich, David Berry, Bärbel Stecher
Published in: Cell Host & Microbe, Issue 25/5, 2019, Page(s) 681-694.e8, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2019.03.004

Berry-Enriched Diet in Salt-Sensitive Hypertensive Rats: Metabolic Fate of (Poly)Phenols and the Role of Gut Microbiota

Author(s): Gomes, Oudot, Macià, Foito, Carregosa, Stewart, Van de Wiele, Berry, Motilva, Brenner, dos Santos
Published in: Nutrients, Issue 11/11, 2019, Page(s) 2634, ISSN 2072-6643
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu11112634

A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome

Author(s): Alessandra Riva, Orest Kuzyk, Erica Forsberg, Gary Siuzdak, Carina Pfann, Craig Herbold, Holger Daims, Alexander Loy, Benedikt Warth, David Berry
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-12413-0

Stable-Isotope Probing of Human and Animal Microbiome Function

Author(s): David Berry, Alexander Loy
Published in: Trends in Microbiology, Issue 26/12, 2018, Page(s) 999-1007, ISSN 0966-842X
Publisher: Elsevier BV
DOI: 10.1016/j.tim.2018.06.004

Elucidating the role of the gut microbiota in the physiological effects of dietary fiber

Author(s): Deehan EC, Zhang Z, Riva A, Armet AM, Perez-Muñoz ME, Nguyen NK, Krysa JA, Seethaler B, Zhao YY, Cole J, Li F, Hausmann B, Spittler A, Nazare JA, Delzenne NM, Curtis JM, Wismer WV, Proctor SD, Bakal JA, Bischoff SC, Knights D, Field CJ, Berry D, Prado CM, Walter J
Published in: Microbiome, Issue 20492618, 2022, Page(s) 77, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-022-01248-5

Gut microbiota and undigested food constituents modify toxin composition and suppress the genotoxicity of a naturally occurring mixture of Alternaria toxins in vitro

Author(s): Francesco Crudo, Georg Aichinger, Jovana Mihajlovic, Luca Dellafiora, Elisabeth Varga, Hannes Puntscher, Benedikt Warth, Chiara Dall’Asta, David Berry, Doris Marko
Published in: Archives of Toxicology, Issue 94/10, 2020, Page(s) 3541-3552, ISSN 0340-5761
Publisher: Springer Verlag
DOI: 10.1007/s00204-020-02831-1

Early-life chemical exposome and gut microbiome development: African research perspectives within a global environmental health context

Author(s): Ayeni KI, Berry D, Wisgrill L, Warth B, Ezekiel CN
Published in: Trends in Microbiology, Issue 18784380, 2022, Page(s) 1084-1100, ISSN 1878-4380
Publisher: Cell Press
DOI: 10.1016/j.tim.2022.05.008

Ecological Processes Shaping Microbiomes of Extremely Low Birthweight Infants

Author(s): Zioutis C, Seki D, Bauchinger F, Herbold C, Berger A, Wisgrill L, Berry D
Published in: Front. Microbiol., Issue 1664302X, 2022, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.812136

In vitro interactions of Alternaria mycotoxins, an emerging class of food contaminants, with the gut microbiota: a bidirectional relationship

Author(s): Francesco Crudo, Georg Aichinger, Jovana Mihajlovic, Elisabeth Varga, Luca Dellafiora, Benedikt Warth, Chiara Dall’Asta, David Berry, Doris Marko
Published in: Archives of Toxicology, Issue 95/7, 2021, Page(s) 2533-2549, ISSN 0340-5761
Publisher: Springer Verlag
DOI: 10.1007/s00204-021-03043-x

Combined hormonal contraceptives are associated with minor changes in composition and diversity in gut microbiota of healthy women

Author(s): Jovana Mihajlovic, Michael Leutner, Bela Hausmann, Gudrun Kohl, Jasmin Schwarz, Hannah Röver, Nina Stimakovits, Peter Wolf, Katharina Maruszczak, Magdalena Bastian, Alexandra Kautzky‐Willer, David Berry
Published in: Environmental Microbiology, Issue 23/6, 2021, Page(s) 3037-3047, ISSN 1462-2912
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/1462-2920.15517

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