High-throughput microbial culturomics using automation and machine learning

The Sequence Alignment/Map format and SAMtools

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Fast gapped-read alignment with Bowtie 2

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

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MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy096 · Cited by 37,683 · see citing works

BLAST+: architecture and applications

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Search and clustering orders of magnitude faster than BLAST

Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · see citing works

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

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Prokka: rapid prokaryotic genome annotation

Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,512 · see citing works

CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works

QUAST: quality assessment tool for genome assemblies

Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172 · see citing works

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005595 · Cited by 8,728 · see citing works

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S. (2018) · Nature Communications · doi:10.1038/s41467-018-07641-9 · Cited by 5,748 · see citing works

Diversity, stability and resilience of the human gut microbiota

Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533 · see citing works

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz848 · Cited by 5,176 · see citing works

Artificial intelligence in radiology

Hosny, A., Parmar, C., Quackenbush, J., Schwartz, L. H., & Aerts, H. J. W. L. (2018) · Nature Reviews Cancer · doi:10.1038/s41568-018-0016-5 · Cited by 3,803 · see citing works

CARD 2020: Antibiotic Resistome Surveillance with the Comprehensive Antibiotic Resistance Database

Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A.-L. V., Cheng, A. A., Liu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz935 · Cited by 3,202 · see citing works

Gut microbiome structure and metabolic activity in inflammatory bowel disease

Franzosa, E. A., Sirota-Madi, A., Avila-Pacheco, J., Fornelos, N., Haiser, H. J., Reinker, S., Vatanen, T., Hall, A. B., Mallick, H., McIver, L. J., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0306-4 · Cited by 1,995 · see citing works

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works

A new genomic blueprint of the human gut microbiota

Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314 · see citing works

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

Browne, H. P., Forster, S. C., Anonye, B. O., Kumar, N., Neville, B. A., Stares, M. D., Goulding, D., & Lawley, T. D. (2016) · Nature · doi:10.1038/nature17645 · Cited by 1,299 · see citing works

Strains, functions and dynamics in the expanded Human Microbiome Project

Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., et al. (2017) · Nature · doi:10.1038/nature23889 · Cited by 1,267 · see citing works

Ecology drives a global network of gene exchange connecting the human microbiome

Smillie, C. S., Smith, M. B., Friedman, J., Cordero, O. X., David, L. A., & Alm, E. J. (2011) · Nature · doi:10.1038/nature10571 · Cited by 953 · see citing works

Diversity of human colonic butyrate‐producing bacteria revealed by analysis of the butyryl‐CoA:acetate CoA‐transferase gene

Louis, P., Young, P., Holtrop, G., & Flint, H. J. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02066.x · Cited by 783 · see citing works

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

Goodman, A. L., Kallstrom, G., Faith, J. J., Reyes, A., Moore, A. M., Dantas, G. A., & Gordon, J. I. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102938108 · Cited by 779 · see citing works

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

Edgar, R. C. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty113 · Cited by 723 · see citing works

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

Baym, M., Kryazhimskiy, S., Lieberman, T. D., Chung, H., Desai, M. M., & Kishony, R. (2015) · PLOS ONE · doi:10.1371/journal.pone.0128036 · Cited by 685 · see citing works

Deciphering microbial interactions in synthetic human gut microbiome communities

Venturelli, O. S., Carr, A. V., Fisher, G., Hsu, R. H., Lau, R., Bowen, B. P., Hromada, S. E., Northen, T. R., & Arkin, A. P. (2018) · Molecular Systems Biology · doi:10.15252/msb.20178157 · Cited by 539 · see citing works

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

Zou, Y., Xue, W., Luo, G., Deng, Z., Qin, P., Guo, R., Sun, H., Xia, Y., Liang, S., Dai, Y., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0008-8 · Cited by 526 · see citing works

Modifying and reacting to the environmental pH can drive bacterial interactions

Ratzke, C., & Gore, J. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2004248 · Cited by 456 · see citing works

Adaptive Evolution within Gut Microbiomes of Healthy People

Zhao, S., Lieberman, T. D., Poyet, M., Kauffman, K. M., Gibbons, S. M., Groussin, M., Xavier, R. J., & Alm, E. J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.007 · Cited by 434 · see citing works

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing

Liu, B., Chen, S., Rose, A. M. L., Chen, D., Cao, F., Zwinderman, M. R. H., Kiemel, D., Aïssi, M., Dekker, F. J., & Haisma, H. J. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1136 · Cited by 370 · see citing works

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

Poyet, M., Groussin, M., Gibbons, S. M., Ávila-Pacheco, J., Jiang, X., Kearney, S. M., Perrotta, A. R., Berdy, B. M., Zhao, S., Lieberman, T. D., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0559-3 · Cited by 365 · see citing works

The Landscape of Genetic Content in the Gut and Oral Human Microbiome

Tierney, B. T., Yang, Z., Luber, J. M., Beaudin, M., Wibowo, M. C., Baek, C., Mehlenbacher, E., Patel, C. J., & Kostic, A. D. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.07.008 · Cited by 346 · see citing works

The Long-Term Genetic Stability and Individual Specificity of the Human Gut Microbiome

Chen, L., Wang, D., Garmaeva, S., Kurilshikov, A., Vila, A. V., Gaćeša, R., Sinha, T., Study, L. C., Segal, E., Weersma, R. K., et al. (2020) · Cell · doi:10.1016/j.cell.2021.03.024 · Cited by 337 · see citing works

Elevated rates of horizontal gene transfer in the industrialized human microbiome

Groussin, M., Poyet, M., Sistiaga, A., Kearney, S. M., Moniz, K., Noel, M., Hooker, J., Gibbons, S. M., Ségurel, L., Froment, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.052 · Cited by 331 · see citing works

Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence

Juhas, M., Crook, D. W., & Hood, D. W. (2008) · Cellular Microbiology · doi:10.1111/j.1462-5822.2008.01187.x · Cited by 291 · see citing works

Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes

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Metagenomic engineering of the mammalian gut microbiome in situ

Ronda, C., Chen, S. P., Cabral, V., Yaung, S. J., & Wang, H. H. (2019) · Nature Methods · doi:10.1038/s41592-018-0301-y · Cited by 238 · see citing works

Early detection and classification of live bacteria using time-lapse coherent imaging and deep learning

Wang, H., Koydemir, H. C., Qiu, Y., Bai, B., Zhang, Y., Jin, Y., Tok, S., Yılmaz, E. C., Gumustekin, E., Rivenson, Y., et al. (2020) · Light Science & Applications · doi:10.1038/s41377-020-00358-9 · Cited by 214 · see citing works

Application of Machine Learning in Microbiology

Qu, K., Guo, F., Liu, X., Lin, Y., & Zou, Q. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00827 · Cited by 199 · see citing works

EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems

Eichinger, V., Nußbaumer, T., Platzer, A., Jehl, M.-A., Arnold, R. R., & Rattei, T. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1269 · Cited by 184 · see citing works

Characterization of Colony Morphology Variants Isolated fromStreptococcus pneumoniaeBiofilms

Allegrucci, M., & Sauer, K. (2006) · Journal of Bacteriology · doi:10.1128/jb.01369-06 · Cited by 174 · see citing works

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

Rettedal, E. A., Gumpert, H., & Sommer, M. O. A. (2014) · Nature Communications · doi:10.1038/ncomms5714 · Cited by 168 · see citing works

Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

Watterson, W. J., Tanyeri, M., Watson, A. R., Cham, C. M., Shan, Y., Chang, E. B., Eren, A. M., & Tay, S. (2020) · eLife · doi:10.7554/elife.56998 · Cited by 146 · see citing works

A bacterial basic region leucine zipper histidine kinase regulating toluene degradation

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Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation

Woods, L. C., Gorrell, R. J., Taylor, F., Connallon, T., Kwok, T., & McDonald, M. J. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2005331117 · Cited by 130 · see citing works

Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems

Defois, C., Ratel, J., Garrait, G., Denis, S., Goff, O. L., Talvas, J., Mosoni, P., Engel, E., & Peyret, P. (2018) · Scientific Reports · doi:10.1038/s41598-018-29376-9 · Cited by 127 · see citing works

Co-Culture with Bifidobacterium catenulatum Improves the Growth, Gut Colonization, and Butyrate Production of Faecalibacterium prausnitzii: In Vitro and In Vivo Studies

Kim, H., Jeong, Y., Kang, S., You, H. J., & Ji, G. E. (2020) · Microorganisms · doi:10.3390/microorganisms8050788 · Cited by 114 · see citing works

Spatially-resolved metabolic cooperativity within dense bacterial colonies

Cole, J. A., Kohler, L., Hedhli, J., & Luthey-Schulten, Z. A. (2015) · BMC Systems Biology · doi:10.1186/s12918-015-0155-1 · Cited by 106 · see citing works

A practical guide to intelligent image-activated cell sorting

Isozaki, A., Mikami, H., Hiramatsu, K., Sakuma, S., Kasai, Y., Iino, T., Yamano, T., Yasumoto, A., Oguchi, Y., Suzuki, N., et al. (2019) · Nature Protocols · doi:10.1038/s41596-019-0183-1 · Cited by 99 · see citing works

Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides

Lindstad, L. J., Lo, G., Leivers, S., Lu, Z., Michalak, L., Pereira, G. V., Røhr, Å. K., Martens, E. C., McKee, L. S., Louis, P., et al. (2021) · mBio · doi:10.1128/mbio.03628-20 · Cited by 86 · see citing works

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling

Ji, B. W., Sheth, R. U., Dixit, P. D., Huang, Y., Kaufman, A., Wang, H. H., & Vitkup, D. (2019) · Nature Methods · doi:10.1038/s41592-019-0467-y · Cited by 83 · see citing works

Macroecological dynamics of gut microbiota

Ji, B. W., Sheth, R. U., Dixit, P. D., Tchourine, K., & Vitkup, D. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0685-1 · Cited by 81 · see citing works

Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation

Jeong, H., Arif, B., Caetano‐Anollés, G., Kim, K. M., & Nasir, A. (2019) · Scientific Reports · doi:10.1038/s41598-019-42227-5 · Cited by 77 · see citing works

Analysis of intact bacteria using rapid evaporative ionisation mass spectrometry

Strittmatter, N., Jones, E. A., Veselkov, K., Rebec, M., Bundy, J. G., & Takáts, Z. (2013) · Chemical Communications · doi:10.1039/c3cc42015a · Cited by 76 · see citing works

The spatial and metabolic basis of colony size variation

Chacón, J. M., Möbius, W., & Harcombe, W. R. (2018) · The ISME Journal · doi:10.1038/s41396-017-0038-0 · Cited by 71 · see citing works

Emerging mass spectrometry techniques for the direct analysis of microbial colonies

Fang, J., & Dorrestein, P. C. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.06.014 · Cited by 69 · see citing works

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture

Villa, M. M., Bloom, R. J., Silverman, J. D., Durand, H. K., Jiang, S., Wu, A., Dallow, E. P., Huang, S., You, L., & David, L. A. (2020) · mSystems · doi:10.1128/msystems.00864-19 · Cited by 58 · see citing works

Novel neural network application for bacterial colony classification

Huang, L., & Wu, T. (2018) · Theoretical Biology and Medical Modelling · doi:10.1186/s12976-018-0093-x · Cited by 56 · see citing works

Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

Mutalik, V. K., Novichkov, P. S., Price, M. N., Owens, T. K., Callaghan, M., Carim, S., Deutschbauer, A. M., & Arkin, A. P. (2019) · Nature Communications · doi:10.1038/s41467-018-08177-8 · Cited by 49 · see citing works

Colony‐morphology screening uncovers a role for the P seudomonas aeruginosa nitrogen‐related phosphotransferase system in biofilm formation

Cabeen, M. T., Leiman, S. A., & Losick, R. M. (2015) · Molecular Microbiology · doi:10.1111/mmi.13250 · Cited by 45 · see citing works

The Long-Term Genetic Stability and Individual Specificity of the Human Gut MicrobiomePreprint

Chen, L., Wang, D., Garmaeva, S., et al. (2020) · SSRN Electronic Journal · doi:10.2139/ssrn.3653563 · Cited by 32 · see citing works

Use of Colony Morphology To Distinguish Different Enterococcal Strains and Species in Mixed Culture from Clinical Specimens

Qamer, S., Sandoe, J. A. T., & Kerr, K. G. (2003) · Journal of Clinical Microbiology · doi:10.1128/jcm.41.6.2644-2646.2003 · Cited by 16 · see citing works

Regulation of colony morphology and biofilm formation in Shewanella algae

Martín‐Rodríguez, A. J., Villion, K., Yilmaz‐Turan, S., Vilaplana, F., Sjöling, Å., & Römling, U. (2021) · Microbial Biotechnology · doi:10.1111/1751-7915.13788 · Cited by 13 · see citing works

Probiotics, prebiotics, and postbiotics in health and disease

Ji, J., Jin, W., Liu, S., Jiao, Z., & Li, X. (2023) · MedComm · doi:10.1002/mco2.420 · Cited by 416 · see citing works

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic

Porcari, S., Benech, N., Valles-Colomer, M., Segata, N., Gasbarrini, A., Cammarota, G., Sokol, H., & Ianiro, G. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.03.020 · Cited by 331 · see citing works

Soil microbiome engineering for sustainability in a changing environment

Jansson, J. K., McClure, R., & Egbert, R. G. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01932-3 · Cited by 274 · see citing works

AGILE platform: a deep learning powered approach to accelerate LNP development for mRNA delivery

Xu, Y., Ma, S., Cui, H., Chen, J., Xu, S., Gong, F., Golubovic, A., Zhou, M., Wang, K. C., Varley, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50619-z · Cited by 260 · see citing works

Intestinal colonization resistance in the context of environmental, host, and microbial determinants

Woelfel, S., Silva, M. S., & Stecher, B. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.05.002 · Cited by 142 · see citing works

Unraveling plant–microbe interactions: can integrated omics approaches offer concrete answers?

Kimotho, R. N., & Maina, S. (2023) · Journal of Experimental Botany · doi:10.1093/jxb/erad448 · Cited by 133 · see citing works

Harnessing the potential of microalgae-bacteria interaction for eco-friendly wastewater treatment: A review on new strategies involving machine learning and artificial intelligence

Sahu, S., Kaur, A., Singh, G., & Arya, S. K. (2023) · Journal of Environmental Management · doi:10.1016/j.jenvman.2023.119004 · Cited by 125 · see citing works

Community standards and future opportunities for synthetic communities in plant–microbiota research

Northen, T. R., Kleiner, M., Torres, M., Kovács, Á. T., Nicolaisen, M. H., Krzyżanowska, D. M., Sharma, S., Lund, G., Jelsbak, L., Baars, O., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01833-4 · Cited by 125 · see citing works

Unraveling host regulation of gut microbiota through the epigenome–microbiome axis

Pepke, M. L., Hansen, S. B., & Limborg, M. T. (2024) · Trends in Microbiology · doi:10.1016/j.tim.2024.05.006 · Cited by 117 · see citing works

Intestinal microbiota-specific Th17 cells possess regulatory properties and suppress effector T cells via c-MAF and IL-10

Brockmann, L., Tran, A., Huang, Y., Edwards, M., Ronda, C., Wang, H. H., & Ivanov, I. I. (2023) · Immunity · doi:10.1016/j.immuni.2023.11.003 · Cited by 112 · see citing works

Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture

Clagnan, E., Costanzo, M., Visca, A., Gregorio, L. D., Tabacchioni, S., Colantoni, E., Sevi, F., Sbarra, F., Bindo, A., Nolfi, L., et al. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1473666 · Cited by 92 · see citing works

Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis

Li, S., Lian, W., Han, J.-R., Ali, M., Lin, Z., Liu, Y., Li, L., Zhang, D., Jiang, X., Li, W., et al. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00439-8 · Cited by 91 · see citing works

Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules

Ramasamy, K. P., Mahawar, L., Rajasabapathy, R., Rajeshwari, K., Miceli, C., & Pucciarelli, S. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1197797 · Cited by 86 · see citing works

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Ramoneda, J., Jensen, T. B. N., Price, M. N., Casamayor, E. O., & Fierer, N. (2023) · Nature Communications · doi:10.1038/s41467-023-43435-4 · Cited by 83 · see citing works

Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience

Misu, I. J., Kayess, M. O., Siddiqui, M. N., Gupta, D. R., Islam, M. N., & Islam, T. (2025) · Microorganisms · doi:10.3390/microorganisms13020233 · Cited by 79 · see citing works

Gut microbiota-derived fatty acid and sterol metabolites: biotransformation and immunomodulatory functions

Zhang, H., Xie, Y., Cao, F., & Song, X. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2382336 · Cited by 68 · see citing works

Broadening oncological boundaries: the intratumoral microbiota

Lu, Y.-Q., Qiao, H., Tan, X.-R., & Liu, N. (2024) · Trends in Microbiology · doi:10.1016/j.tim.2024.01.007 · Cited by 66 · see citing works

Synergizing artificial intelligence and probiotics: A comprehensive review of emerging applications in health promotion and industrial innovation

Han, X., Liu, Q., Li, Y., Zhang, M., Liu, K., Kwok, L.-Y., Zhang, H., & Zhang, W. (2025) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2025.104938 · Cited by 64 · see citing works

Psychobiotics and the Microbiota–Gut–Brain Axis: Where Do We Go from Here?

Binda, S., Tremblay, A., Iqbal, U., Kassem, O., Barz, M. L., Thomas, V., Bronner, S., Perrot, T. S., Ismail, N., & Parker, J. A. (2024) · Microorganisms · doi:10.3390/microorganisms12040634 · Cited by 57 · see citing works

Modern microbiology: Embracing complexity through integration across scales

Eren, A. M., & Banfield, J. F. (2024) · Cell · doi:10.1016/j.cell.2024.08.028 · Cited by 55 · see citing works

Engineering Microbial Consortia as Living Materials: Advances and Prospectives

Wang, S., Zhan, Y., Jiang, X., & Lai, Y. (2024) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00313 · Cited by 50 · see citing works

Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation

Jiang, X., Peng, Z., & Zhang, J. (2024) · Food Research International · doi:10.1016/j.foodres.2024.114557 · Cited by 48 · see citing works

HiBC: a publicly available collection of bacterial strains isolated from the human gut

Hitch, T. C. A., Masson, J. M., Pauvert, C., Bosch, J., Nüchtern, S., Treichel, N. S., Baloh, M., Razavi, S., Afrizal, A., Kousetzi, N., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59229-9 · Cited by 46 · see citing works

Precise control of process parameters for >23% efficiency perovskite solar cells in ambient air using an automated device acceleration platform

Zhang, J., Wu, J., Barabash, A., Du, T., Qiu, S., Corre, V. M. L., Zhao, Y., Zhang, K., Schmitt, F., Peng, Z., et al. (2024) · Energy & Environmental Science · doi:10.1039/d4ee01432d · Cited by 45 · see citing works

Human microbiome acquisition and transmission

Heidrich, V., Valles‐Colomer, M., & Segata, N. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01166-x · Cited by 45 · see citing works

Isolation and Cultivation of Human Gut Microorganisms: A Review

Wan, X., Yang, Q., Wang, X., Bai, Y., & Liu, Z. (2023) · Microorganisms · doi:10.3390/microorganisms11041080 · Cited by 40 · see citing works

Mining microbial and metabolic dark matter in extreme environments: a roadmap for harnessing the power of multi-omics data

Han, J.-R., Li, S., Li, W., & Dong, L. H. (2024) · Advanced Biotechnology · doi:10.1007/s44307-024-00034-8 · Cited by 40 · see citing works

Pharmacomicrobiomics: The Role of the Gut Microbiome in Immunomodulation and Cancer Therapy

Bolte, L. A., Björk, J. R., Gaćeša, R., & Weersma, R. K. (2025) · Gastroenterology · doi:10.1053/j.gastro.2025.04.025 · Cited by 39 · see citing works

Precise probiotic therapy: Advances, bottlenecks, and the road to microbiome-informed nutrition

Jiang, Y., Jiang, S., Wang, Z., Zhu, P., Zhang, J., Teng, F., & Huang, S. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2623359 · Cited by 39 · see citing works

Data-driven synthetic microbes for sustainable future

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A metagenomic catalogue of the ruminant gut archaeome

Mi, J., Jing, X., Ma, C., Shi, F., Cao, Z., Yang, X., Yang, Y., Kakade, A., Wang, W., & Long, R. (2024) · Nature Communications · doi:10.1038/s41467-024-54025-3 · Cited by 37 · see citing works

Directional long-distance electron transfer from reduced to oxidized zones in the subsurface

Zhang, Y., Tong, M., Lu, Y., Zhao, F., Zhang, P., Wan, Z., Li, P., Yuan, S., Wang, Y., & Kappler, A. A. (2024) · Nature Communications · doi:10.1038/s41467-024-50974-x · Cited by 36 · see citing works

Artificial intelligence in bacterial diagnostics and antimicrobial susceptibility testing: Current advances and future prospects

Lee, S., Park, J. S., Hong, J. H., Woo, H., Lee, C., Yoon, D. S., Lee, K.-B., Chung, S. H., Yoon, D. S., & Lee, J. H. (2025) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2025.117399 · Cited by 36 · see citing works

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases

Gelsinger, D. R., Ronda, C., Ma, J., Kar, O. B., Edwards, M., Huang, Y., Mavros, C. F., Sun, Y., Perdue, T., Vo, P. L. H., et al. (2025) · Science · doi:10.1126/science.adx7604 · Cited by 36 · see citing works

“Trust your gut”: exploring the connection between gut microbiome dysbiosis and the advancement of Metabolic Associated Steatosis Liver Disease (MASLD)/Metabolic Associated Steatohepatitis (MASH): a systematic review of animal and human studies

Bahitham, W., Banoun, Y., Aljahdali, M., Almuaiqly, G., Bahshwan, S. M., Aljahdali, L., Sanai, F. M., Rosado, A. S., & Sergi, C. M. (2025) · Frontiers in Nutrition · doi:10.3389/fnut.2025.1637071 · Cited by 35 · see citing works

Extremozymes: Challenges and opportunities on the road to novel enzymes production

Salas-Bruggink, D. I. J., Martín, J. S.-S., Leiva, G., & Blamey, J. M. (2024) · Process Biochemistry · doi:10.1016/j.procbio.2024.04.035 · Cited by 33 · see citing works

Gut Microbiome Signature in Predisease Phase of Inflammatory Bowel Disease: Prediction to Pathogenesis to Prevention

Turpin, W., Lee, S.-H., & Croitoru, K. (2025) · Gastroenterology · doi:10.1053/j.gastro.2025.01.004 · Cited by 33 · see citing works

Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI

Caminero, A., Tropini, C., Valles‐Colomer, M., Shung, D. L., Gibbons, S. M., Surette, M. G., Sokol, H., Tomeo, N. J., Alenghat, T., Awoniyi, M., et al. (2025) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-025-01100-9 · Cited by 35 · see citing works

Metabolic engineering of human gut microbiome: Recent developments and future perspectives

Li, P., Roos, S., Luo, H., Ji, B., & Nielsen, J. (2023) · Metabolic Engineering · doi:10.1016/j.ymben.2023.06.006 · Cited by 33 · see citing works

Artificial intelligence-powered nanomedicine

Luo, G., 蒋显超, Hu, C., Li, L., Yan, L., Xiao, G., Duo, Y., & Zhang, X. (2026) · Chemical Society Reviews · doi:10.1039/d5cs01406a · Cited by 33 · see citing works

The role of microbiomes in gastrointestinal cancers: new insights

Yarahmadi, A., & Afkhami, H. (2024) · Frontiers in Oncology · doi:10.3389/fonc.2023.1344328 · Cited by 30 · see citing works

Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria

Zheng, M., Wen, L., He, C., Chen, X., Si, L., Li, H., Liang, Y., Zheng, W., & Guo, F. (2024) · Nature Communications · doi:10.1038/s41467-024-53446-4 · Cited by 30 · see citing works

Advances in Culturomics Research on the Human Gut Microbiome: Optimizing Medium Composition and Culture Techniques for Enhanced Microbial Discovery

Song, H. S., Kim, Y. B., Kim, J. Y., Roh, S. W., & Whon, T. W. (2024) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2311.11024 · Cited by 29 · see citing works

Synthetic microbial ecology: engineering habitats for modular consortia

Chen, Y. C., Destouches, L., Cook, A., & Fedorec, A. J. H. (2024) · Journal of Applied Microbiology · doi:10.1093/jambio/lxae158 · Cited by 29 · see citing works

Keystone species in microbial communities: From discovery to soil heavy metal-remediation

Jiang, G., Ruan, Z., Yin, Y., Hu, C., Tian, L., Lu, J., Wang, S., Tang, Y., Qiu, R., & Chao, Y. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.138753 · Cited by 28 · see citing works

Revisiting the current and emerging concepts of postharvest fresh fruit and vegetable pathology for next‐generation antifungal technologies

Ngea, G. L. N., Yang, Q., Xu, M., Ianiri, G., Dhanasekaran, S., Zhang, X., Bi, Y., & Zhang, H. (2024) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.13397 · Cited by 27 · see citing works

Roots of synthetic ecology: microbes that foster plant resilience in the changing climate

Kozaeva, E., Eida, A. A., Gunady, E. F., Dangl, J. L., Conway, J. M., & Brophy, J. A. N. (2024) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2024.103172 · Cited by 27 · see citing works

Gut microbiome evolution from infancy to 8 years of age

Sawhney, S. S., Thänert, R., Thänert, A., Hall-Moore, C. M., Ndao, I. M., Mahmud, B., Warner, B. B., Tarr, P. I., & Dantas, G. A. (2025) · Nature Medicine · doi:10.1038/s41591-025-03610-0 · Cited by 27 · see citing works

Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era

Jiao, J., Abdugheni, R., Zhang, D., Ahmed, I., Ali, M., Chuvochina, M. S., Dedysh, S. N., Dong, X., Göker, M., Hedlund, B. P., et al. (2024) · National Science Review · doi:10.1093/nsr/nwae168 · Cited by 27 · see citing works

Mechanisms of microbial co-aggregation in mixed anaerobic cultures

Doloman, A., & Sousa, D. Z. (2024) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-024-13246-8 · Cited by 26 · see citing works

Microbiota-Focused Dietary Approaches to Support Health: A Systematic Review

Hindle, V., Veasley, N. M., & Holscher, H. D. (2024) · Journal of Nutrition · doi:10.1016/j.tjnut.2024.10.043 · Cited by 26 · see citing works

SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome

Richardson, M., Zhao, S., Lin, L., Sheth, R. U., Qu, Y., Lee, J., Moody, T. U., Ricaurte, D., Huang, Y., Velez‐Cortes, F., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-024-01914-4 · Cited by 26 · see citing works

Globalizing the health-promoting potential of fermented foods: A culturomics pathway to probiotics

Fentie, E. G., Lim, K., Ebabuye, Y., Azizoğlu, U., & Shin, J. (2025) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2025.105119 · Cited by 24 · see citing works

Statistical prediction of microbial metabolic traits from genomes

Li, Z., Selim, A., & Kuehn, S. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011705 · Cited by 24 · see citing works

Emerging chemophysiological diversity of gut microbiota metabolites

Lin, X., He, K., Gu, Z., & Zhao, X. (2024) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2024.07.006 · Cited by 23 · see citing works

The impact of the human gut microbiome on the treatment of autoimmune disease

Nayak, R. R., & Orellana, D. A. (2024) · Immunological Reviews · doi:10.1111/imr.13358 · Cited by 23 · see citing works

Microbiota in tumors: new factor influencing cancer development

Jiang, H., Li, L., Bao, Y., Cao, X., & Ma, L. (2024) · Cancer Gene Therapy · doi:10.1038/s41417-024-00833-0 · Cited by 23 · see citing works

Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes

Qiu, Z. G., Zhu, Y., Zhang, Q., Qiao, X., Mu, R., Xu, Z., Yan, Y., Wang, F., Zhang, T., Zhuang, W., et al. (2023) · Environmental Science and Ecotechnology · doi:10.1016/j.ese.2023.100359 · Cited by 22 · see citing works

A streamlined culturomics case study for the human gut microbiota research

Park, H., Yeo, S., Ryu, C. B., & Huh, C. S. (2024) · Scientific Reports · doi:10.1038/s41598-024-71370-x · Cited by 20 · see citing works

Droplet microfluidics: unveiling the hidden complexity of the human microbiome

Xu, Y., Wang, Z., Li, C., Tian, S., & Du, W. (2025) · Lab on a Chip · doi:10.1039/d4lc00877d · Cited by 20 · see citing works

MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta‐omics and bioinformatics

Bai, D., Ma, C., Xun, J., Luo, H., Yang, H., Lyu, H., Zhu, Z., Gai, A., Yousuf, S., Peng, K., et al. (2025) · iMeta · doi:10.1002/imt2.70002 · Cited by 20 · see citing works

Evaluating agar-plating and dilution-to-extinction isolation methods for generating oak-associated microbial culture collections

Ordonez, A., Hussain, U., Cambon, M. C., Golyshin, P. N., Downie, J., & McDonald, J. E. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf019 · Cited by 19 · see citing works

Synthetic Communities of Gut Microbes for Basic Research and Translational Approaches in Animal Health and Nutrition

Jennings, S. A. V., & Clavel, T. (2023) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-021022-025552 · Cited by 19 · see citing works

Emerging tools and best practices for studying gut microbial community metabolism

Noecker, C. A., & Turnbaugh, P. J. (2024) · Nature Metabolism · doi:10.1038/s42255-024-01074-z · Cited by 19 · see citing works

Strategies in engineering sustainable biochemical synthesis through microbial systems

Song, Y., & Prather, K. L. J. (2024) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2024.102493 · Cited by 19 · see citing works

Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research

Clavel, T., Faber, F., Groussin, M., Haller, D., Overmann, J., Pauvert, C., Poyet, M., Selkrig, J., Stecher, B., Typas, A., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02660-6 · Cited by 18 · see citing works

Emerging technologies and current challenges in intratumoral microbiota research

Wang, Z., Zhang, T., & Liu, Y. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1685862 · Cited by 18 · see citing works

Could the tumor-associated microbiota be the new multi-faceted player in the tumor microenvironment?

Goubet, A. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1185163 · Cited by 18 · see citing works

An optimized culturomics strategy for isolation of human milk microbiota

Wang, F., Yu, L., Ren, Y., Zhang, Q., He, S., Zhao, M., He, Z., Gao, Q., & Chen, J. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1272062 · Cited by 18 · see citing works

Targeting bioinformatics tools to study the dissemination and spread of antibiotic resistant genes in the environment and clinical settings

Singh, C. K., & Sodhi, K. K. (2024) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2024.2429603 · Cited by 18 · see citing works

Human Gut Microbiome Researches Over the Last Decade: Current Challenges and Future Directions

Wu, H., Forslund, S. K., Wang, Z., & Zhao, G. (2023) · Phenomics · doi:10.1007/s43657-023-00131-z · Cited by 18 · see citing works

Engineering microbiomes to enhance macroalgal health, biomass yield, and carbon sequestration

Nair, S., Zhang, Z., Wang, X., Zhang, B., Jiao, N., & Zhang, Y. (2024) · Green Carbon · doi:10.1016/j.greenca.2024.11.001 · Cited by 17 · see citing works

Multi-dimensional metagenomics

Peng, H., Ruiz-Moreno, A. J., & Fu, J. (2025) · Nature Reviews Bioengineering · doi:10.1038/s44222-025-00346-x · Cited by 16 · see citing works

Roles of microbial interactions in determining the establishment and function of synthetic consortium inoculants for soil applications

Xu, Y., Shrestha, S., Sun, Q. H., & Wang, Y. (2025) · The ISME Journal · doi:10.1093/ismejo/wrag050 · Cited by 16 · see citing works

Antimicrobial resistance and biotechnological potential of plastic‐associated bacteria isolated from an urban estuary

Canellas, A. L. B., Abdon, B. B., Diniz, M. N., Alves, G. D. S. O., Lourenço, M. F. D. P., Machado, W., Giambiagi-deMarval, M., de Oliveira, B. F. R., & Laport, M. S. (2023) · Environmental Microbiology · doi:10.1111/1462-2920.16540 · Cited by 16 · see citing works

Impact of cryoprotective agents on human gut microbes and in vitro stabilized artificial gut microbiota communities

Alessandri, G., Rizzo, S. M., Mancabelli, L., Fontana, F., Longhi, G., Turroni, F., van Sinderen, D., & Ventura, M. (2024) · Microbial Biotechnology · doi:10.1111/1751-7915.14509 · Cited by 16 · see citing works

Learning ecosystem-scale dynamics from microbiome data with MDSINE2

Gibson, T. E., Kim, Y., Acharya, S., Kaplan, D. E., DiBenedetto, N., Lavin, R., Berger, B., Allegretti, J. R., Bry, L., & Gerber, G. K. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02112-6 · Cited by 15 · see citing works

Culturomics: A critical approach in studying the roles of human and animal microbiota

Howe, S. M., Liu, Z., Zuo, B., & Zhao, J. (2024) · Animal Nutriomics · doi:10.1017/anr.2024.6 · Cited by 15 · see citing works

Culture-based characterization of gut microbiota in inflammatory bowel disease

Park, H., Yeo, S., Lee, T., Han, Y., Ryu, C. B., & Huh, C. S. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1538620 · Cited by 14 · see citing works

Synthetic biology approaches for restoring gut microbial balance and engineering disease-specific microbiome therapeutics

Mkilima, T. (2025) · Microbial Pathogenesis · doi:10.1016/j.micpath.2025.107931 · Cited by 14 · see citing works

New approaches to secondary metabolite discovery from anaerobic gut microbes

Butkovich, L. V., Vining, O. B., & O'Malley, M. A. (2025) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-024-13393-y · Cited by 14 · see citing works

Clinical microbiology and artificial intelligence: Different applications, challenges, and future prospects

Khalaf, W. S., Morgan, R. N., & Elkhatib, W. F. (2025) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2025.107125 · Cited by 14 · see citing works

Complexity of human death: its physiological, transcriptomic, and microbiological implications

Javan, G. T., Singh, K., Finley, S. J., Green, R. L., & Sen, C. K. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1345633 · Cited by 13 · see citing works

Application Progress of Culturomics in the Isolated Culture of Rhizobacteria: A Review

Ji, C., Guo, J., Ma, Y., Xu, X., Zang, T., Liu, S., An, Z., Yang, M., He, X., & Zheng, W. (2024) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c08885 · Cited by 13 · see citing works

Applications of artificial intelligence and machine learning in microbial diagnostics and identification

Chaturvedi, N., Yadav, M. K., & Sharma, M. (2024) · Methods in microbiology · doi:10.1016/bs.mim.2024.05.013 · Cited by 13 · see citing works

A convenient and versatile culturomics platform to expand the human gut culturome of Lachnospiraceae and Oscillospiraceae

Plomp, N., Liu, L., Walters, L., Bus‐Spoor, C., Khan, M., Sheridan, P. O., Veloo, A. C. M., Walker, A. W., Harmsen, H. J. M., & Tsompanidou, E. (2017) · Beneficial Microbes · doi:10.1163/18762891-bja00042 · Cited by 14 · see citing works

Multi-omic investigation identifies key antifungal biochemistry during fermentation of a Streptomyces biological control agent

Gallart, M., Dow, L., Nowak, V. V., Belt, K., Sabburg, R., Gardiner, D. M., & Thatcher, L. F. (2024) · Microbiological Research · doi:10.1016/j.micres.2024.128032 · Cited by 13 · see citing works

Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems

Darriaut, R., Roose-Amsaleg, C. L., Vanhove, M., & Monard, C. (2025) · Microbiological Research · doi:10.1016/j.micres.2025.128178 · Cited by 12 · see citing works

Improving the odds: Artificial intelligence and the great plate count anomaly

Sipkema, D. (2024) · Microbial Biotechnology · doi:10.1111/1751-7915.70004 · Cited by 12 · see citing works

Sequence based characterization of microbial communities in food: The panacea for smart detection of food microbes or dirty deeds done dirt cheap?

Zhao, Z., & Gänzle, M. G. (2025) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2025.105113 · Cited by 12 · see citing works

EBRC: Enhancing bioeconomy through research and communication

Moon, T. S. (2023) · New Biotechnology · doi:10.1016/j.nbt.2023.10.012 · Cited by 12 · see citing works

Biofilms: from the cradle of life to life support

Baxter, K. J., Sas, E., Clark, K. B., Walsh, M., Pradeep, N., Batool, A., Naney, C., Cruz, M. A. V., Kennerdale, N., Das, K., et al. (2026) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00875-8 · Cited by 11 · see citing works

Understanding Nanoscale Interactions between Minerals and Microbes: Opportunities for Green Remediation of Contaminated Sites

Cao, T., Liu, Y., Gao, C., Yuan, Y., Chen, W., & Zhang, T. (2024) · Environmental Science & Technology · doi:10.1021/acs.est.4c05324 · Cited by 11 · see citing works

Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications

Reuben, R. C., & Torres, C. (2025) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-024-04242-1 · Cited by 11 · see citing works

Comparative analysis of metagenomic next-generation sequencing for pathogenic identification in clinical body fluid samples

Sun, N., Zhang, J., Guo, W., Jin, C., Chen, Y., Gao, D., & Xia, X. (2025) · BMC Microbiology · doi:10.1186/s12866-025-03887-8 · Cited by 11 · see citing works

Rhizosphere endophytes as allies in plant defense against heavy metals and organic pollutants in soil: Advances and applications

Hang, S., Wu, C., Peng, G., Li, F., Ge, F., Gan, J., Li, L., & Li, J. (2025) · Applied Soil Ecology · doi:10.1016/j.apsoil.2025.106119 · Cited by 11 · see citing works

Antibiotics and Antimicrobial Resistance Genes in a Gut Microbiota as a Reservoir—A Review

Dabuo, B., Abubakari, A., Sankah, F. E., & Aryee, H. A. (2025) · Advanced Gut & Microbiome Research · doi:10.1155/agm3/6574751 · Cited by 11 · see citing works

GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities

Engelberts, J. P., Ye, J., Parks, D. H., McMaster, E. S., McInnes, A. S., Woodcroft, B. J., Volmer, J. G., McIlroy, S. J., & Tyson, G. W. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf138 · Cited by 11 · see citing works

A model of early-life interactions between the gut microbiome and adaptive immunity provides insights into the ontogeny of immune tolerance

Tepekule, B., Lim, A. I., & Metcalf, C. J. E. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003263 · Cited by 11 · see citing works

Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it

Bustos-Caparros, E., Viver, T., Gago, J. F., Venter, S. N., Bosch, R., Konstantinidis, K. T., Rodriguez‐R, L. M., & Rossello-Mora, R. A. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf228 · Cited by 11 · see citing works

RAcolony: A Multimodal Platform Integrating Raman Spectroscopy and Automated Imaging for Efficient Construction of Personalized Gut Microbiome BiobanksPreprint

Yan, Y., Jiang, H., Ma, J.-B., Jiang, M.-Z., Chen, C. J., An, Z.-N., Li, X.-Y., Chen, G., Zhu, X., Li, T.-Y., et al. (2026) · Research Square · doi:10.21203/rs.3.rs-9805857/v1

Modular automated high‐throughput isolation and phylogenetic identification of bacteria from complex microbiomes

Chaboy‐Cansado, R., Talavera‐Marcos, S., Gallego, R., Cobeta, P., Roscales, G., Rastrojo, A., & de Cárcer, D. A. (2025) · iMetaOmics. · doi:10.1002/imo2.70037 · Cited by 1 · see citing works

A convenient and versatile culturomics platform to expand the human gut culturome of Lachnospiraceae and Oscillospiraceae

Plomp, N., Liu, L., Walters, L., Bus‐Spoor, C., Khan, M., Sheridan, P. O., Veloo, A. C. M., Walker, A. W., Harmsen, H. J. M., & Tsompanidou, E. (2017) · Beneficial Microbes · doi:10.1163/18762891-bja00042 · Cited by 14 · see citing works

High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategiesPreprint

Watterson, W. J., Tanyeri, M., Watson, A. R., Cham, C. M., Shan, Y., Chang, E. B., Eren, A. M., & Tay, S. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/759969 · Cited by 3 · see citing works

A streamlined culturomics case study for the human gut microbiota research

Park, H., Yeo, S., Ryu, C. B., & Huh, C. S. (2024) · Scientific Reports · doi:10.1038/s41598-024-71370-x · Cited by 20 · see citing works