Author

H. Smidt

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 10 Cell Biology· 1 Ecology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 9 Research Focus:cell type annotation· 8 Assay:metagenomics· 7 Organism:human· 5 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Research Focus:ecology & biodiversity· 2 Research Focus:host-pathogen & immune response· 2

Frequent Co-Authors

S. Atashgahi· 6 shared T. N. P. Bosma· 3 shared B. Nijsse· 2 shared C. Zhang· 2 shared D. Sipkema· 2 shared P. J. Schaap· 2 shared P. Peng· 2 shared S. A. Shetty· 2 shared

Activity by Year

2017-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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6 shared papersMicrobiology

S. Atashgahi

Mutual co-authors in cluster

Author profile →

12 papers

Recent·Most cited

Metatranscriptomic analysis indicates prebiotic effect of Isomalto/malto-polysaccharides on human colonic microbiota in-vitro

K. Borewicz, B. V. H. Hornung, F. Gu, P. H. van der Zaal, H. A. Schols, P. J. Schaap, H. Smidt

This study uses metatranscriptomics to show that IMMPs with more (1→6) glycosidic linkages increase gene expression in Bacteroides, Lactobacillus, and Bifidobacterium, leading to higher SCFA production in human fecal microbiota.

bioRxiv · Dec 31, 2023 · PreprintMicrobiology

Impact of Donor Individuality, Temporal Variation, and Culture Medium Type on Microbiota Composition and Metabolic Activity in Human Fecal Batch Culture

Z. Liu, J. Gerritsen, H. Smidt, E. G. Zoetendal

This study examines how donor individuality, temporal variation, and culture medium affect microbiota composition and metabolic activity in fecal batch cultures using polydextrose as a carbon source.

bioRxiv · Aug 7, 2023 · PreprintMicrobiology

Organohalide respiration by a Desulforhopalus-dominated community

C. Zhang, S. Atashgahi, T. N. P. Bosma, H. Smidt

The paper isolates a Desulforhopalus-dominated community capable of debromination of 2,6-dibromophenol and identifies RDase genes in multiple bins, revealing their ecological roles and potential for bioremediation.

bioRxiv · Apr 18, 2023 · PreprintMicrobiology

Genome-resolved transcriptomics reveals novel organohalide-respiring bacteria from Aarhus Bay sediments

C. Zhang, T. N. P. Bosma, S. Atashgahi, H. Smidt

This study identifies novel organohalide-respiring bacteria from Aarhus Bay sediments using genome-resolved transcriptomics, revealing new reductive dehalogenase genes and regulatory mechanisms.

bioRxiv · Apr 17, 2023 · PreprintMicrobiology

Unravelling lactate-acetate conversion to butyrate by intestinal Anaerobutyricum and Anaerostipes species

S. A. Shetty, S. Boeren, T. P. Nam Bui, H. Smidt, W. M. De Vos

This study identifies a gene cluster in Anaerobutyricum and Anaerostipes species that enables lactate and acetate conversion to butyrate, highlighting their adaptation for intestinal metabolism.

Environmental Microbiology · Oct 12, 2020Peer-reviewedMicrobiology

Biodiversity and niche partitioning in an anaerobic benzene degrading culture

C. Melkonian, L. Fillinger, S. Atashgahi, U. Nunes da Rocha, E. Kuiper, B. Olivier, M. Braster, W. Gottstein, R. Helmus, J. Parsons, H. Smidt, M. van der Waals, J. Gerritse, B. W. Brandt, D. Molenaar, R. van Spanning

The paper investigates biodiversity and niche partitioning in a 15-year-old anaerobic benzene-degrading bioreactor, showing that species interactions maintain high diversity through trophic levels.

bioRxiv · Jul 17, 2020Ecology

Organohalide-respiring Desulfoluna species isolated from marine environments

P. Peng, T. Goris, Y. Lu, B. Nijsse, A. Burrichter, D. Schleheck, J. J. Koehorst, J. Liu, D. Sipkema, J. S. S. Damste, A. J. M. Stams, M. M. Haggblom, H. Smidt, S. Atashgahi

This paper isolates a third Desulfoluna strain capable of organohalide respiration and characterizes its genetic and metabolic capabilities for dehalogenation.

The ISME Journal · Jan 2, 2020Peer-reviewedMicrobiology

Metagenomic- and cultivation-based exploration of anaerobic chloroform biotransformation in hypersaline sediments as natural source of chloromethanes

P. Peng, Y. Lu, T. N. P. Bosma, I. Nijenhuis, B. Nijsse, S. A. Shetty, A. Ruecker, A. Umanetc, J. Ramiro-Garcia, A. Kappler, D. Sipkema, H. Smidt, S. Atashgahi

The paper investigates chloroform biotransformation in hypersaline sediments using cultivation and metagenomic approaches, finding that Clostridiales likely mediate CF to DCM and CO2 conversion.

bioRxiv · Nov 29, 2019Microbiology

Exploring groundwater microbial communities for natural attenuation potential of micropollutants

A. Aldas-Vargas, E. Hauptfeld, G. Hermes, S. Atashgahi, H. Smidt, H. H. M. Rijnaarts, N. B. Sutton

This study examines groundwater microbial communities in relation to geochemistry and pesticide presence to assess natural attenuation potential of micropollutants.

bioRxiv · Nov 21, 2019 · PreprintMicrobiology

A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle

J. Gerrritsen, B. Hornung, J. Ritari, L. Paulin, G. T. Rijkers, P. J. Schaap, W. M. de Vos, H. Smidt

The paper compares the genomes of three Romboutsia species to understand their metabolic adaptations to intestinal and soil environments.

bioRxiv · Nov 17, 2019 · PreprintMicrobiology

Congruence of location-specific transcriptional programs in intestinal organoids during long-term culture

B. van der Hee, O. Madsen, H. Smidt, J. M. Wells

This study shows intestinal organoids maintain tissue-specific gene expression and location-specific transcriptional programs for at least 17 passages, outperforming a transformed cell line.

bioRxiv · Apr 5, 2019 · PreprintCell Biology

Gut microbiota and resistome dynamics in intensive care patients receiving selective digestive tract decontamination

E. Buelow, T. de Jesus Bello Gonzalez, S. Fuentes, W. A. A. de Steenhuijsen Piters, L. Lahti, J. R. Bayjanov, E. A. M. Majoor, J. C. Braat, M. S. M. van Mourik, E. A. N. Oostdijk, R. J. L. Willems, M. J. M. Bonten, M. W. J. van Passel, H. Smidt, W. van Schaik

This study examines gut microbiota and resistome changes in ICU patients undergoing selective decontamination, finding reduced diversity and specific resistance gene abundance.

bioRxiv · Jan 25, 2017Microbiology