The Gut Microbiome: Connecting Spatial Organization to Function

Diversity of the Human Intestinal Microbial Flora

Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K. C., Santee, C. A., Lynch, S. V., et al. (2009) · Cell · doi:10.1016/j.cell.2009.09.033 · Cited by 4,554

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000322 · Cited by 3,058 · cited 1×

Periodontitis: from microbial immune subversion to systemic inflammation

Hajishengallis, G. (2015) · Nature Reviews Immunology · doi:10.1038/nri3785 · Cited by 3,046

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

Desai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., Pudlo, N. A., Kitamoto, S., Terrapon, N., Muller, A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.043 · Cited by 2,805

Gut biogeography of the bacterial microbiota

Donaldson, G. P., Lee, S. M., & Mazmanian, S. K. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro3552 · Cited by 2,535

The Domain-specific Probe EUB338 is Insufficient for the Detection of all Bacteria: Development and Evaluation of a more Comprehensive Probe Set

Daims, H., Brühl, A., Amann, R., SCHLEIFER, K. H., & Wagner, M. (1999) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(99)80053-8 · Cited by 2,273

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

Johansson, M. E. V., Phillipson, M., Petersson, J., Velcich, A., Holm, L., & Hansson, G. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803124105 · Cited by 2,200

The Long-Term Stability of the Human Gut Microbiota

Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058

An impedance-based chemiresistor for the real-time detection of gut microbiota-generated short-chain fatty acidsPreprint

Yavarinasab, A., Flibotte, S., Liu, S., & Tropini, C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.11.507374 · Cited by 2

Colonic spermidine promotes proliferation and migration of intestinal epithelial cellsPreprint

Flory, M., Gao, A. Y., Morrow, M., & Alam, A. M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.26.559404 · Cited by 2

Altered microbiome and metabolome profiling in companion dogs, diagnosed with phobia: an exploratory studyPreprint

Sacchettino, L., Costanzo, M., Veneruso, I., D’Argenio, V., Mayer, M., Avallone, L., Napolitano, F., & d’Angelo, D. (2024) · Research Square · doi:10.21203/rs.3.rs-4413150/v1 · Cited by 2

Sex Differences in Colonic Mucosal Microbiome of Irritable Bowel Syndrome Patients Compared to Healthy ControlsPreprint

Mahurkar‐Joshi, S., Shera, S., Labus, J. S., Dong, T. S., Jacobs, J. P., & Chang, L. (2024) · medRxiv · doi:10.1101/2024.07.31.24311317 · Cited by 2

Expanding the chicken gut virome: Uncovering viral diversity, host interactions, and regional variations across the intestinal tractPreprint

Zhao, J.-X., Ni, H.-B., Nan, F., Yan, Q., Li, S., Su, J., Cai, Y., Meng, J., Yu, H., Shang, K.-M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.15.647674 · Cited by 2

Visualizing phenotypic heterogeneity and single-cell morphology in situ during gut infectionPreprint

DiBenedetto, N., Donnelly-Morell, M. L., Kumamoto, C. A., & Shen, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.30.651596 · Cited by 2

Pro-restitutive Bacteroides thetaiotaomicron reprograms the transcriptome of intestinal epithelial cells by modulating the expression of genes essential for proliferation and migrationPreprint

Gao, A., Newhart, V., Flory, M., & Alam, A. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.30.679439 · Cited by 2

Community coalescence reveals strong selection and coexistence within species in complex microbial communitiesPreprint

Walton, S. J., Xu, Q., Sharma, R., Gellert, H. R., Yeh, C.-F., Cremer, J., Xue, K. S., Petrov, D. A., & Good, B. H. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.06.687011 · Cited by 2

Visualization of Respiratory Commensal Bacteria in Context of Their Natural Host Environment

Bonifacio, J. P. P., & Schmolke, M. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.678389 · Cited by 1

The Emerging Role of the Microbiota and Antibiotics in Diverticulitis Treatment

Troester, A. M., Weaver, L., & Jahansouz, C. (2024) · Clinics in Colon and Rectal Surgery · doi:10.1055/s-0044-1791521 · Cited by 1

Three-Dimensional Imaging of Native Microbiota in Intact Colon

Du, Y., Zhou, Y., Lin, H., Yang, C. J., & Wang, W. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.4c06059 · Cited by 1

Intestinal bacteria translocation promotes β-cell dysfunction in DIO mice

Yu, X.-F., Gurung, C., Yu, Z., Xiao, W., Kerem, G., Teng, B., Zhang, J. V., Su, Z., Zhou, Y. J., & Ren, P. (2025) · Scientific Reports · doi:10.1038/s41598-025-15244-w · Cited by 1

Transkingdom network analysis reveals the dominant role of ileal microbiota in host metabolism over colonic microbiota in diet-induced obesity

Chen, P., Li, X., Yang, S., Liu, H., & Li, Z. (2025) · mSystems · doi:10.1128/msystems.01199-25 · Cited by 1

Tequila bats (Phyllostomidae: Leptonycteris yerbabuenae ) and their associated bat flies: disentangling the effects of physical proximity and organism source as predictors of microbiota dissimilarities

Víquez‐R, L., Speer, K. A., Wilhelm, K., Perkins, S. L., Simmons, N. B., Medellín, R. A., Sommer, S., & Tschapka, M. (2025) · Journal of Mammalogy · doi:10.1093/jmammal/gyaf080 · Cited by 1

Multi-omics reveals the involvement of endophytes in the growth of Moso bamboo (Phyllostachys edulis) shoots

Zhao, A., Huang, M., Cheng, Y., Li, Q., Cai, H., Bi, Y., Wang, A., Du, X., & Ding, X. (2026) · Communications Biology · doi:10.1038/s42003-025-09436-3 · Cited by 1

Characterization of dysbiosis patterns in gut microbiota of digestive system cancers: an umbrella review

Wang, J., Liu, Y., Yan, Y. J., Chen, X., Chen, G., Chen, Y., Chen, X., & Liu, S. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1782471 · Cited by 2

Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri

Mouali, Y. E., Tawk, C., Huang, K. D., Sivapornnukul, P., Mengoni, C., Segata, N., & Strowig, T. (2026) · Cell Host & Microbe · doi:10.1016/j.chom.2026.04.006 · Cited by 3

Geometric ordering in bacterial communities

Gorgi, M., Kasallis, S. J., Trinh, C., de Ora, L. O., Wiles, T. J., & Siryaporn, A. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2526643123 · Cited by 1

Animal gut microbes and microbiomes in the 21st century and beyond

Zhang, Z., Jiang, F., Li, Z. Y., Lin, L., Qi, B., Han, D., Ran, C., Mao, S., Wang, J., Zhou, Z., et al. (2026) · Science China Life Sciences · doi:10.1007/s11427-026-3312-5 · Cited by 1

The protease code of the bacterial gut microbiota: ecological regulation, barrier disruption, and rewiring host defense and signaling

Eckhard, U., Ramírez-Larrota, J. S., Estevan-Morió, E., & Gomis‐Rüth, F. X. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2687149 · Cited by 1

The gut microbiome and colorectal cancer

Dietz, M. A., Subramanian, S., & Staley, C. M. (2026) · Clinical Microbiology Reviews · doi:10.1128/cmr.00332-25 · Cited by 1

Getting to know our microbial friends by dropping into their neighbourhood

Ruby, E. G. (2020) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12895 · Cited by 1

Abdominelle Distension und Blähungen

Misselwitz, B., & Wiest, R. (2021) · Schweizer Gastroenterologie · doi:10.1007/s43472-021-00048-w · Cited by 1

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

Ng, K. M., & Tropini, C. (2021) · Journal of Visualized Experiments · doi:10.3791/62646-v · Cited by 1

CDEMI: Characterizing differences in microbial composition and function in microbiome data

Wang, L., Xiao, L., Chen, H., Cao, L., Liu, L., Zhu, F., Ding, Y., Tang, J., & Xie, Y. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.03.044 · Cited by 1

The “normal” gut microbiome and human health

Xia, Y., & Sun, J. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-98338-9.00001-3 · Cited by 1

The past, present and future of polymicrobial infection research: Modelling, eavesdropping, terraforming and other stories

Bényei, É. B., Nazeer, R. R., Askenasy, I., Mancini, L., Ho, P.-M., Sivarajan, G. A. C., Swain, J. E. V., & Welch, M. (2024) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/bs.ampbs.2024.04.002 · Cited by 1

Positive-Charge-Based Small Molecule Dyes for Gut Microbiota Fluorescent Imaging

Liu, Y., Wang, Z., Li, K., Song, R., Xu, Z., Yu, T., Wang, J., Feng, X., & Chen, H. (2024) · ACS Omega · doi:10.1021/acsomega.4c03727 · Cited by 1

Techniques for Studying the Microbiome

Zain, M., Saba, S., Hussain, A., Khalid, J., Janiad, S., Mahmood, S., & Cheema, M. T. (2024) · Springer eBooks · doi:10.1007/978-981-97-3790-1_3 · Cited by 1

Hydrodynamic confinement of bacteria within intestinal folds

Yang, J., Omori, T., Kikuchi, K., & Ishikawa, T. (2025) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2024.3068 · Cited by 1

An engineered bacterial symbiont maps micron-scale sugar gradients in the honeybee gut

Chhun, A., Quinn, A., Pérez‐Lorente, A. I., Steiner, T., Zoppi, F., Nguyen, T. T. T., Engel, P., & Schaerli, Y. (2026) · PLoS Biology · doi:10.1371/journal.pbio.3003997 · Cited by 1

Microbial Eukaryotic Diversity and Function Within the Human Gut Microbiota

Cevasco, M. E. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-819265-8.00096-6 · Cited by 1

Mikrobiota jelitowa a leki. Interakcje wpływające na skuteczność i bezpieczeństwo farmakoterapii

Nycz, J., & Zajdel, A. (2021) · Postępy Higieny i Medycyny Doświadczalnej · doi:10.2478/ahem-2021-0009 · Cited by 1

“The invisible enemy: Gut microbiota and their role in anastomotic leak”

Lam, A., Keskey, R. C., & Alverdy, J. C. (2022) · Seminars in Colon and Rectal Surgery · doi:10.1016/j.scrs.2022.100880 · Cited by 1

Gut bacteria go on record

Crits‐Christoph, A., & Suez, J. (2022) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-022-00653-3 · Cited by 1

Elucidating the mechanisms of anastomotic leakage: a new point of view

van Praagh, J. (2020) · doi:10.33612/diss.119066366 · Cited by 1

Spatial profiling of microbial communities by sequential FISH with error-robust encodingPreprint

Dai, L., Cao, Z., Zuo, W., Wang, L., Chen, J., Qu, Z., & Jin, F. (2021) · Research Square · doi:10.21203/rs.3.rs-601828/v1 · Cited by 1

A High-Fish Oil Diet Can Significantly Reshape The Gut Microbiota In MicePreprint

Sun, H., Chen, D., Yang, Y., Tan, B., Huang, C., Li, Y., & Qian, J. (2021) · Research Square · doi:10.21203/rs.3.rs-525477/v1 · Cited by 1

Dissecting the intestinal mucosal niche with the pathobiont Allobaculum mucolyticum

van Muijlwijk, G. H. (2022) · Utrecht University Repository (Utrecht University) · doi:10.33540/1173 · Cited by 1

Engineering synthetic spatial patterns in microbial populations and communitiesPreprint

Barbier, I., Kusumawardhani, H., & Schaerli, Y. (2022) · doi:10.31219/osf.io/yxwkt · Cited by 1

Promoting diversity in ecological systems through toxin productionPreprint

Lui, G. C., & Goyal, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.06.531399 · Cited by 1

Hypogonadal (Gnrh1 hpg ) mice reveal niche-specific influence of reproductive axis and sex on intestinal microbial communitiesPreprint

Sisk-Hackworth, L., Brown, J., Sau, L., Levine, A. A., Tam, L. Y. I., Ramesh, A., Shah, R. S., Kelley-Thackray, E. T., Wang, S., Nguyen, A., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.20.545808 · Cited by 1

Bioinformatic correction of bacterial morphology-based extraction bias and chimeras in microbiome sequencing dataPreprint

Rauer, L., Tomassi, A. D., Müller, C. L., Hülpüsch, C., Traidl‐Hoffmann, C., Reiger, M., & Neumann, A. U. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.06.547990 · Cited by 1

Antibiotics for UTIs Cause Distinct Alterations in Gut Microbiota and Host Health Compared to Enteritis TreatmentPreprint

Liu, F., Sun, Y., Xu, Z., Lin, H., Tang, Y., Xia, Q., Wei, S., Hu, J., Sheng, J., Hu, L., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-3353463/v1 · Cited by 1

Antibiotics for UTIs Cause Distinct Alterations in Gut Microbiome and Host Health Compared to Enteritis TreatmentPreprint

Xu, Z., Xu, J., Jiang, P., Wei, S., Gu, C., Gu, Y., Wei, Q., Guo, H., Wang, S., Li, Z., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-5550411/v1 · Cited by 1

Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community within alveoli-like geometriesPreprint

Mancini, L., Saliekh, L., Claydon, R., Kotar, J., Bényei, É. B., Munro, C. A., Shendruk, T. N., Brown, A. T., Welch, M., & Cicuta, P. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.22.644766 · Cited by 1

Multiscale Spatial Mapping of Microbial Communities for Biotherapeutic DevelopmentPreprint

Sehgal, P., Shaw, A. G., Cutler, K., Letson, B., Booth, G. T., Scuderi, G. J., Doshi, A., Diebold, P. J., Bronson, H., Trisolini, M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.31.646377 · Cited by 1

An RNA regulates iron homeostasis and host mucus colonization in Bacteroides thetaiotaomicronPreprint

Prezza, G., Fansler, R. T., Guest, T., Mädler, G., Schlauch, H., Zhu, W., & Westermann, A. J. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.08.672848 · Cited by 1

Micro-scale spatial metagenomics: revealing high-resolution spatial biogeography of gut microbiomesPreprint

Pietroni, C., Wang, B. Z., Bogri, A., Langa, J., Odriozola, I., Horisberger, Z., Contreras‐Serrano, M., Lauritsen, J. G., Gaun, N., Toffano, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.30.679663 · Cited by 1

Use of lung microbiota strains to shape local immunity at steady state and during Mycobacterium tuberculosis infection in the mouse model

Bernard, L. (2020) · theses.fr (ABES) · doi:10.70675/589a776dz18d9z4813z9d6fzd73632aa4df7 · Cited by 1

Gut Microbes in Liver Diseases

Arunima, A., Das, J. K., & Suar, M. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-814468-8.00010-7

Identificación de componentes de la microbiota intestinal potencialmente beneficiosos frente a la obesidad

Villanueva, E. M. G. D. P. (2018) · RiuNet (Universitat Politècnica de València) · doi:10.4995/thesis/10251/114770

Molecular characterization of the microbiota in patients with ulcerative colitis in the Kingdom of Saudi Arabia

Abdelfattah, D., Al-Quait, A., Al-Yamani, E., Ibrahim, A. S., & Al-Salamah, A. (2019) · Egyptian Pharmaceutical Journal · doi:10.4103/epj.epj_9_19

Next Generation Sequencing Methods: Pushing the Boundaries

Finnegan, L. A., Crispie, F., Claesson, M. J., Cotter, P. D., & Kenny, J. G. (2020) · Elsevier eBooks · doi:10.1016/b978-0-08-100596-5.22688-7

Oxygen-independent chemogenetic protein tags for live-cell fluorescence microscopyPreprint

Iyer, A., Baranov, M., Foster, A. J., Chordia, S., Roelfes, G., van den Bogaart, G., & Poolman, B. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.03.234815

Fluorescent Antibody Multiplexing with Oligo-Based Combinatorial LabelingPreprint

McCarthy, M. E., Anglin, C. M., Peer, H. A., Boleman, S., Klaubert, S. R., & Birtwistle, M. R. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.06.371906

Bacterial species singled out from a diverse crowd

Nguyen, J., & Tropini, C. (2020) · Nature · doi:10.1038/d41586-020-03315-z

Invasion of Oral Microbiota into the Gut

Li, B., Yang, G., Cheng, L., Zeng, B., Yu, J., Peng, X., Zhao, J., Li, W., Ren, B., Li, M., et al. (2020) · Springer eBooks · doi:10.1007/978-981-15-7899-1_8

Understanding mucus selective permeability across length scales

Samad, T. S. (2019) · DSpace@MIT (Massachusetts Institute of Technology)

Probiotic Bacteria and Their Encapsulation Evaluated in Advanced Co-culture Models

Yuan, L. (2021) · doi:10.33612/diss.160691131

Fish Oil Can Significantly Reshape Diet-Based Gut Microbiota in MicePreprint

Sun, H., Chen, D., Yang, Y., Tan, B., Huang, C., Li, Y., & Qian, J. (2020) · Research Square · doi:10.21203/rs.3.rs-52260/v1

Niche-Specialist And Age-Related Microbial Ecosystem: Correlation Analysis With Immune Cells In Oral HomeostasisPreprint

Lin, D., Yang, L. Y., Hu, Q., Wang, D., Dai, W., Xiao, Y., Lu, H., Fang, J., & Wang, Z. (2021) · Research Square · doi:10.21203/rs.3.rs-829179/v1

2-5 液晶テレビの好ましい視距離(2) : 画面サイズと表示輝度の影響(第2部門 ディスプレイ)

小林, 雄., 小野, 石., 窪田, 悟., 岸本, 和., 山根, 康., 五十嵐, 陽., 芳賀, 秀., & 中枝, 武. (2008) · doi:10.11485/itewac.2008.0__2-5-1_

Descifrando las funciones de la microbiota intestinal en la obesidad.

López‐Almela, I. (2021) · RiuNet (Universitat Politècnica de València) · doi:10.4995/thesis/10251/174897

Modulating Residence Time and Biogeography of Engineered Probiotics

Said, R., Mays, Z. J. S., & Nair, N. U. (2022) · Wiley eBooks · doi:10.1002/9783527825462.ch4

Faculty Opinions recommendation of Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation.

van der Meer, J. R., & Carraro, N. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.737594052.793576386

Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivoPreprint

Burckhardt, J. C., Chong, D. H. Y., Pett, N., & Tropini, C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.09.511496

Pectin methyl-ester distribution; analysis, modification and biofunctionality

Jermendi, É. (2022) · doi:10.18174/577333

Spatial structure, chemotaxis and quorum sensing shape biomass accumulation in complex systemsPreprint

Scheidweiler, D., Bordoloi, A., Sentchilo, V., Bollani, M., Engel, P., & de Anna, P. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.28.534616

The microenvironment: how it impacts enterococcus faecalis wound pathogenesis

Tan, C. A. Z. (2023) · DR-NTU (Nanyang Technological University) · doi:10.32657/10356/165582

A PILLAR OF CARDIOVASCULAR DISEASES: INFLAMMAGING

Kutsal, A. (2023) · The Turkish Journal of Geriatrics · doi:10.29400/tjgeri.2023.350

Emergent Antibiotic Persistence in Cross-Feeding Bacteria in Structured HabitatsPreprint

Xiong, X., Othmer, H. G., & Harcombe, W. R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.09.561574

Additional file 6 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens

Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lü, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779894

Additional file 1 of Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle

Zhen, L. I., Cui, R., Wang, Y., Luo, Y.-B., Xue, P.-X., Tang, Q., & Fang, M. (2023) · Figshare · doi:10.6084/m9.figshare.24522618

Additional file 9 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens

Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lü, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779903

Additional file 7 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens

Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lü, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779897

Additional file 10 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens

Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lü, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779876

Additional file 2 of Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation

Li, N., Zuo, B., Huang, S., Zeng, B., Han, D., Li, T., Liu, T., Wu, Z., Wei, H., Zhao, J., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13257810

Additional file 8 of Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens

Gan, M., Wu, B., Yan, G., Li, G., Sun, L., Lü, G., & Zhou, W. (2021) · Figshare · doi:10.6084/m9.figshare.16779900

CÂNCER COLORRETAL: UM DESAFIO DESDE SUAS BASES MOLECULARES ATÉ A PRÁTICA DO NUTRICIONISTA

Freitas, B. C., Paiva, A. D., Braga, C. B. M., & Simon, C. R. (2023) · Acta Biologica Brasiliensia. · doi:10.18554/acbiobras.v6i1.7245

Quantifying the intra- and inter-species community interaction in a microbiome by dynamic covariance mappingPreprint

Serohijos, A. W. R., Gencel, M., Hui, C., Sahaf, Z., Gauthier, L., Matta, C., Gagné-Leroux, D., Tsang, D., Philpott, D. J., Ramathan, S., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4355889/v1

Die Bedeutung des Darmes und der Mikrobiota bei viralen Krankheiten und Epidemien

Fegerl, S. P. (2024) · Springer eBooks · doi:10.1007/978-3-662-67508-3_8

General Characteristics and Properties of Organic Life

Knoflacher, M. (2024) · Springer eBooks · doi:10.1007/978-3-662-69423-7_5

Acute Colonic Pseudo-Obstruction (ACPO)

Patel, M., Collier, J., Bohl, J. L., Carucci, L. R., & Zuelzer, W. A. (2024) · Springer eBooks · doi:10.1007/978-3-031-58946-1_9

Bowel preparation-induced changes in the gut environment facilitate pathogen and pathobiont colonizationPreprint

Clayton, C. A., McCallum, G., Ng, K. M., Srini, A., Sie, C., Tertigas, D., Porter, I., Pepin, D. M., Fardeen, T., Sinha, S. R., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4940942/v1

Missing the forest for the trees: Time to address stool microbial load and everything else that realistically matters in microbiome studies

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Zhang, H., Zhou, Y., Jiang, Y.-H., Hu, W.-P., Huang, L., Lin, H.-X., Zuo, Z., Du, J., & Lou, Y. (2025) · World Journal of Gastroenterology · doi:10.3748/wjg.v31.i13.105248

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Heldt-Döpel, R., Schütz, L., & Berling, N. (2025) · Ernährung & Medizin · doi:10.1055/a-2439-5831

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Wanyama, J. W., Okyere, L., Duan, L., & Gaulke, C. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.08.652836

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Greter, G., Hummel, S., Künzli, D., Duenki, N., Ruoho, N., Burkhardt, P., Ganguillet, S., Radiom, M., Moresi, C., Laganenka, L., et al. (2026) · PLoS Biology · doi:10.1371/journal.pbio.3003772

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Haffner, J. J., Ahn, S. H., & Qiu, T. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.01.657309

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Jasper, R. J., Kapopoulou, A., Peischl, S., Yılmaz, B., Becker, J., & Bank, C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.06.658271

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