On the Road to Strain-Resolved Comparative Metagenomics

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv033 · Cited by 10,133

metaSPAdes: a new versatile metagenomic assembler

Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496

Shotgun metagenomics, from sampling to analysis

Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

Scher, J. U., Sczesnak, A., Longman, R. S., Segata, N., Ubeda, C., Bielski, C., Rostron, T., Cerundolo, V., Pamer, E. G., Abramson, S. B., et al. (2013) · eLife · doi:10.7554/elife.01202 · Cited by 2,047

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) · doi:10.7717/peerj.1165 · Cited by 1,960

Anvi’o: an advanced analysis and visualization platform for ‘omics data

Eren, A. M., Esen, Ö. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., & Delmont, T. O. (2015) · PeerJ · doi:10.7717/peerj.1319 · Cited by 1,869

Infection with Helicobacter pylori strains possessing cagA is associated with an increased risk of developing adenocarcinoma of the stomach.

Blaser, M. J., Perez-Perez, G. I., Kleanthous, H., Cover, T. L., Peek, R. M., Chyou, P.-H., Stemmermann, G. N., & Nomura, A. M. Y. (1995) · PubMed · Cited by 1,608

Epidemic Profile of Shiga-Toxin–Producing Escherichia coli O104:H4 Outbreak in Germany

Frank, C., Werber, D., Cramer, J. P., Askar, M., Faber, M., an der Heiden, M., Bernard, H., Fruth, A., Prager, R., Spode, A., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1106483 · Cited by 1,139

Genomic variation landscape of the human gut microbiome

Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907

OBSOLETE: Bioinformatic Platforms for Metagenomics

Eckenberger, J. (2015) · Elsevier eBooks · doi:10.1016/b978-0-08-100596-5.00009-3

Problèmes d’optimisation combinatoire pour l’étude du métabolisme

Frioux, C., & Siegel, A. (2022) · doi:10.51926/iste.9029.ch2

Metagenomics and Metatranscriptomics

Guyomar, C., & Lemaitre, C. (2022) · doi:10.1002/9781394169641.ch5

An Overview of Genomic Islands’ Main Features and Computational Prediction: The CMNR Group of Bacteria As a Case Study

Rodrigues, T. C. V., Jaiswal, A. K., Aburjaile, F. F., Almeida, C. A., Carvalho, R. D. D. O., de Paula, J. A., Santos, R. P. S., Dominici, F. V., Felice, A. G., Marques, P. H., et al. (2023) · Springer eBooks · doi:10.1007/978-981-19-9342-8_3

Métagénomique et métatranscriptomique

Guyomar, C., & Lemaitre, C. (2023) · doi:10.51926/iste.9066.ch5

Combinatorial Optimization Problems for Studying Metabolism

Frioux, C., & Siegel, A. (2023) · doi:10.1002/9781394229086.ch2

The elite common bean Phaseolus vulgaris cultivar Pinto Saltillo hosts a rich and diverse array of plant-growth promoting bacteria in its rhizospherePreprint

Romo, G. L., Santamaría, R. I., Bustos, P., Echavarría, F. G., Reveles-Torres, L. R., & González, V. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.23.563606

Evaluation of 10 Different Pipelines for Bacterial Single-Nucleotide Variant Detection

Hu, Z.-H., Wang, Y., Yang, L., Cao, Q., Ling, M., Meng, X., Chen, Y., Ni, S., Chen, Z., Liu, C., et al. (2023) · Infectious Microbes & Diseases · doi:10.1097/im9.0000000000000134

Continent-wide assessment of the strain-level diversity of Bradyrhizobium , a dominant soil bacterial genusPreprint

de Mesquita, C. P. B., Olm, M. R., Bissett, A. B., & Fierer, N. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.29.656829

Additional file 1 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

Koo, H., & Morrow, C. D. (2021) · Figshare · doi:10.6084/m9.figshare.16650542

Additional file 7 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

Guerin, E., Shkoporov, A. N., Stockdale, S. R., Colom, J., Khokhlova, E. V., Clooney, A. G., Daly, K. M., Draper, L. A., Stephens, N., Scholz, D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14404004

Additional file 8 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

Guerin, E., Shkoporov, A. N., Stockdale, S. R., Colom, J., Khokhlova, E. V., Clooney, A. G., Daly, K. M., Draper, L. A., Stephens, N., Scholz, D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14404007

Additional file 4 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

Koo, H., & Morrow, C. D. (2021) · Figshare · doi:10.6084/m9.figshare.16650560

Additional file 5 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

Koo, H., & Morrow, C. D. (2021) · Figshare · doi:10.6084/m9.figshare.16650563

Additional file 2 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

Koo, H., & Morrow, C. D. (2021) · Figshare · doi:10.6084/m9.figshare.16650551

Additional file 3 of Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy

Koo, H., & Morrow, C. D. (2021) · Figshare · doi:10.6084/m9.figshare.16650557

Additional file 2 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

Guerin, E., Shkoporov, A. N., Stockdale, S. R., Colom, J., Khokhlova, E. V., Clooney, A. G., Daly, K. M., Draper, L. A., Stephens, N., Scholz, D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14403989

Additional file 3 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

Guerin, E., Shkoporov, A. N., Stockdale, S. R., Colom, J., Khokhlova, E. V., Clooney, A. G., Daly, K. M., Draper, L. A., Stephens, N., Scholz, D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14403992

Additional file 9 of Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

Guerin, E., Shkoporov, A. N., Stockdale, S. R., Colom, J., Khokhlova, E. V., Clooney, A. G., Daly, K. M., Draper, L. A., Stephens, N., Scholz, D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14404010

Additional file 1 of Mora: abundance aware metagenomic read re-assignment for disentangling similar strains

Zheng, A., Shaw, J., & Yu, Y. W. (2024) · Figshare · doi:10.6084/m9.figshare.25670235

Shotgun metagenomics reveals the microbiome and resistome of water harvesting ponds used by Kenyan rural smallholdersPreprint

Gregson, B. H., Bani, A., Steinfield, L., Holt, D., Vamos, E. E., Connell, R., Whitby, C., & Ferguson, R. M. W. (2025) · medRxiv · doi:10.64898/2025.12.05.25341686

Développement et applications d'outils d'analyse métagénomique des communautés microbiennes associées aux insectes

Guyomar, C. (2018) · doi:10.70675/c59f263czbd9fz43edz88d4z1eac5825e1fa

Understanding virulence heterogeneity in Listeria monocytogenes

Hafner, L. (2021) · theses.fr (ABES) · doi:10.70675/46e92af9zd298z42dczbff5zf90528eb75f2

Autochthonous starter culture selection for PGI Salama Piemonte production throug the microbiota analysis

Franciosa, I. (2021) · theses.fr (ABES) · doi:10.70675/82159b0az88c9z48cfz8d5fz801441f06f51

A metagenomic framework for rapid Listeria monocytogenes surveillance in food production environmentsPreprint

Muchaamba, F., Reska, T., Biggel, M., Locken, K. M., Weilguny, L., Corti, S., Kelbert, L., Stephan, R., & Urban, L. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.23.720354

A Conditional Random Field approach for de novo reconstruction of bacterial haplotypes from a de Bruijn graph representationPreprint

Steyaert, A., Hecke, M. V., Kathleen Marchal, D., & Fostier, J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.11.724222

From Multi-Omics to Molecular Causality: A Five-Tier Evidence Framework for the Single-Bacterium–Metabolite Axis in IBD

Song, X., Wang, W., Yang, J., Xinning, L., & Ji, W. (2026) · Microorganisms · doi:10.3390/microorganisms14081744

Matrix-associated spatial structure contributes to compositional stability of a complex multispecies starter culture under microbial perturbation: Insights from kefir grains

Ji, Q.-Y., Qu, H., Chen, D., Li, Q., Zong, L., Liu, Y., Huang, Y., & Gu, R. (2026) · Food Research International · doi:10.1016/j.foodres.2026.120540

Integrating strain‑level metagenomics in human and food microbiomes

Pasolli, E. (2026) · IMAGINE - Repository of the Institute of molecular genetics and genetic engineering (University of Belgrade)

Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges

Park, H., Kim, J. S., Kim, D. J., & Suk, K. T. (2026) · Microorganisms · doi:10.3390/microorganisms14030720 · Cited by 5

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGCPreprint

Smith, B. J., Zhao, C., Dubinkina, V. B., Jin, X., Zahavi, L., Shoer, S., Anderson, J. M., Segal, E., & Pollard, K. S. (2025) · Genome Research · doi:10.1101/gr.279543.124 · Cited by 11

Strain Identification and Quantitative Analysis in Microbial Communities

Ghazi, A. R., Münch, P. C., Chen, D., Jensen, J., & Huttenhower, C. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167582 · Cited by 44

Toward hypothesis-driven, personalized microbiome screening

Sedrani, C., & Wilmes, P. (2022) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100139 · Cited by 5