Shotgun metagenomics, from sampling to analysis

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Metagenomic biomarker discovery and explanation

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Structure, function and diversity of the healthy human microbiome

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A human gut microbial gene catalogue established by metagenomic sequencing

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

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A metagenome-wide association study of gut microbiota in type 2 diabetes

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Fecal microbiota relationships with childhood obesity: A scoping comprehensive review

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Indoor Microbiome and Airborne Pathogens

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Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights

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Metagenomic analysis and antibacterial activity of kefir microorganisms

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Diet and gut microbial associations in irritable bowel syndrome according to disease subtype

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Revealing the influence of exogenously inoculated Bacillus spp. on the microbiota and metabolic potential of medium-temperature Daqu: A meta-omics analysis

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Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization

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Roles of gut microbiome-associated metabolites in pulmonary fibrosis by integrated analysis

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Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases

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Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements

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Periodontitis: Microbial Dysbiosis, Non‐Resolving Inflammation, or Both?

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Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism

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Appropriate Use and Future Directions of Molecular Diagnostic Testing

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Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

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Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers

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Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease

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A lab in the field: applications of real-time, in situ metagenomic sequencing

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On the triad of air PM pollution, pathogenic bioaerosols, and lower respiratory infection

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A Metagenomics Investigation of Intergenerational Effects of Non-nutritive Sweeteners on Gut Microbiome

Wang, W., Nettleton, J. E., Gänzle, M. G., & Reimer, R. A. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2021.795848 · Cited by 29

Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice

Peeb, A., Dang, N. P., Truu, M., Nõlvak, H., Petrich, C., & Truu, J. (2022) · Microorganisms · doi:10.3390/microorganisms10020328 · Cited by 29

Marine Microbial-Derived Resource Exploration: Uncovering the Hidden Potential of Marine Carotenoids

Steven, R., Humaira, Z., Natanael, Y., Dwivany, F. M., Trinugroho, J. P., Dwijayanti, A., Kristianti, T., Tallei, T. E., Emran, T. B., Jeon, H. H., et al. (2022) · Marine Drugs · doi:10.3390/md20060352 · Cited by 31

Shotgun metagenomic sequencing of bulk tank milk filters reveals the role of Moraxellaceae and Enterobacteriaceae as carriers of antimicrobial resistance genes

Rubiola, S., Macori, G., Chiesa, F., Panebianco, F., Moretti, R., Fanning, S., & Civera, T. (2022) · Food Research International · doi:10.1016/j.foodres.2022.111579 · Cited by 30

Chronic effects of benzalkonium chlorides on short chain fatty acids and methane production in semi-continuous anaerobic digestion of waste activated sludge

Yang, C., He, Z.-W., Liu, W., Wang, A., Wang, L., Liu, J., Liu, B., Ren, N.-Q., Yu, S., & Guo, Z. (2022) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2022.157619 · Cited by 29

Characterization of metagenome-assembled genomes from the International Space Station

Singh, N. K., Wood, J. M., Patané, J. S. L., Moura, L. M. S., Lombardino, J., Setúbal, J. C., & Venkateswaran, K. (2023) · Microbiome · doi:10.1186/s40168-023-01545-7 · Cited by 29

Metaphor—A workflow for streamlined assembly and binning of metagenomes

Salazar, V. W., Shaban, B., Quiroga, M. D. M., Turnbull, R., Tescari, E., Marcelino, V. R., Verbruggen, H., & Cao, K. L. (2022) · GigaScience · doi:10.1093/gigascience/giad055 · Cited by 24

Unveiling Plant-Beneficial Function as Seen in Bacteria Genes from Termite Mound Soil

Enagbonma, B. J., & Babalola, O. O. (2020) · Journal of soil science and plant nutrition · doi:10.1007/s42729-019-00124-w · Cited by 29

CAMISIM: Simulating metagenomes and microbial communitiesPreprint

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Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation

Mubayi, V., Ahern, C. B., Całusińska, M., & O’Malley, M. (2024) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00077 · Cited by 29

Molecular epidemiology in current times

Tümmler, B. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15238 · Cited by 28

Breast milk urea as a nitrogen source for urease positiveBifidobacterium infantis

Schimmel, P., Kleinjans, L., Bongers, R. S., Knol, J., & Belzer, C. (2021) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiab019 · Cited by 28

Revealing the role of Plant Growth Promoting Rhizobacteria in suppressive soils against Fusarium oxysporum f.sp. cubense based on metagenomic analysis

Nisrina, L., Effendi, Y., & Pancoro, A. (2021) · Heliyon · doi:10.1016/j.heliyon.2021.e07636 · Cited by 28

A comprehensive review for gut microbes: technologies, interventions, metabolites and diseases

Qi, C., Wang, P., Fu, T., Lu, M., Cai, Y., Chen, X., & Cheng, L. (2020) · Briefings in Functional Genomics · doi:10.1093/bfgp/elaa029 · Cited by 28

Shotgun metagenomic analysis reveals new insights into bacterial community profiles in tempeh

Yulandi, A., Suwanto, A., Waturangi, D. E., & Wahyudi, A. T. (2020) · BMC Research Notes · doi:10.1186/s13104-020-05406-6 · Cited by 27

Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap

Aitmanaitė, L., Širmonaitis, K., & Russo, G. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241813786 · Cited by 28

Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes

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MAPK Cascades in Plant Microbiota Structure and Functioning

Gerrewey, T. V., & Chung, H. S. (2024) · The Journal of Microbiology · doi:10.1007/s12275-024-00114-3 · Cited by 27

Metagenomics-based evaluation of groundwater microbial profiles in response to treated wastewater discharge

Zaouri, N., Jumat, M. R., Cheema, T., & Hong, P. (2019) · Environmental Research · doi:10.1016/j.envres.2019.108835 · Cited by 27

Topsoil Bacterial Community Changes and Nutrient Dynamics Under Cereal Based Climate-Smart Agri-Food Systems

Choudhary, M., Jat, H. S., Datta, A., Sharma, P. C., Rajashekar, B., & Jat, M. L. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01812 · Cited by 27

Identification of Bacterial and Fungal Communities in the Roots of Orchids and Surrounding Soil in Heavy Metal Contaminated Area of Mining Heaps

Böhmer, M., Ozdín, D., Račko, M., Lichvár, M., Budiš, J., & Szemes, T. (2020) · Applied Sciences · doi:10.3390/app10207367 · Cited by 27

First report of mitochondrial COI in foraminifera and implications for DNA barcoding

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Clostridium butyricum Potentially Improves Immunity and Nutrition through Alteration of the Microbiota and Metabolism of Elderly People with Malnutrition in Long-Term Care

Liu, L., Chen, X., Liu, L., & Qin, H. (2022) · Nutrients · doi:10.3390/nu14173546 · Cited by 27

Bacterial diversity in the aquatic system in India based on metagenome analysis—a critical review

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The hidden diversity of microbes in ballast water and sediments revealed by metagenomic sequencing

Xue, Z., Tian, W. D., Han, Y., Zhen, F., Wang, Y., & Zhang, W. (2023) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2023.163666 · Cited by 28

In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning

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Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats

Becker, C. C., Weber, L., Zgliczynski, B., Sullivan, C., Sandin, S. A., Muller, E. M., Clark, A. S., Soule, M. C. K., Longnecker, K., Kujawinski, E. B., et al. (2023) · PNAS Nexus · doi:10.1093/pnasnexus/pgad287 · Cited by 27

Innovative metagenomic approaches for detection of microbial communities involved in biodeteriorattion of cultural heritage

Perito, B., & Cavalieri, D. (2018) · IOP Conference Series Materials Science and Engineering · doi:10.1088/1757-899x/364/1/012074 · Cited by 27

Experimental manipulation of selfish genetic elements links genes to microbial community function

Quistad, S. D., Doulcier, G., & Rainey, P. B. (2020) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2019.0681 · Cited by 27

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experimentsPreprint

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Bridging the Gap from Enterotypes to Personalized Dietary Recommendations: A Metabolomics Perspective on Microbiome Research

Bartsch, M., Hahn, A., & Berkemeyer, S. (2023) · Metabolites · doi:10.3390/metabo13121182 · Cited by 28

Exploration of genes encoding KEGG pathway enzymes in rhizospheric microbiome of the wild plant Abutilon fruticosum

Abulfaraj, A. A., Shami, A., Alotaibi, N. M., Alomran, M. M., Aloufi, A. S., Al‐Andal, A., AlHamdan, N. R., Alshehrei, F. M., Sefrji, F. O., Alsaadi, K. H., et al. (2024) · AMB Express · doi:10.1186/s13568-024-01678-4 · Cited by 29

Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential

Bulow, C., Langdon, A. E., Hink, T., Wallace, M. A., Reske, K. A., Patel, S., Sun, X., Seiler, S. M., Jones, S., Kwon, J. H., et al. (2018) · mSphere · doi:10.1128/mspheredirect.00588-18 · Cited by 28

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples

Casimiro‐Soriguer, C. S., Loucera, C., Pérez-Florido, J., López-López, D., & Dopazo, J. (2019) · Biology Direct · doi:10.1186/s13062-019-0246-9 · Cited by 27

Recovery of human gut microbiota genomes with third-generation sequencing

Li, Y., Jin, Y., Zhang, J., Pan, H., Wu, L., Liu, D., Liu, J., Hu, J., & Shen, J. (2021) · Cell Death and Disease · doi:10.1038/s41419-021-03829-y · Cited by 26

Targeting current and future threats: recent methodological trends in environmental antimicrobial resistance research and their relationships to risk assessment

Burch, T. R., Newton, R. J., Kimbell, L. K., LaMartina, E. L., O'Malley, K., Thomson, S. M., Marshall, C. W., & McNamara, P. J. (2022) · Environmental Science: Water Research & Technology · doi:10.1039/d2ew00087c · Cited by 26

Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution

Kiefl, E., Esen, O. C., Miller, S. E., Kroll, K. L., Willis, A. D., Rappé, M. S., Pan, T., & Eren, A. M. (2023) · Science Advances · doi:10.1126/sciadv.abq4632 · Cited by 26

Environmental metagenome classification for constructing a microbiome fingerprint

Kawulok, J., Kawulok, M., & Deorowicz, S. (2019) · Biology Direct · doi:10.1186/s13062-019-0251-z · Cited by 25

Comparison of microbiome samples: methods and computational challenges

Comin, M., Camillo, B. D., Pizzi, C., & Vandin, F. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa121 · Cited by 29

Metagenome-Assembled Genome Binning Methods with Short Reads Disproportionately Fail for Plasmids and Genomic IslandsPreprint

Maguire, F., Jia, B., Gray, K. L., Lau, W. Y. V., Beiko, R. G., & Brinkman, F. S. L. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.31.997171 · Cited by 26

nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profilingPreprint

Stamouli, S., Beber, M. E., Normark, T., Christensen, T. A., Li, L., Borry, M., Jamy, M., community, N.-C., & Yates, J. A. F. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.20.563221 · Cited by 30

An integrated neuroimaging-omics approach for the gut-brain communication pathways in Alzheimer’s disease

Sheng, C., Du, W., Liang, Y., Xu, P., Ding, Q., Chen, X., Jia, S., & Wang, X. (2023) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2023.1211979 · Cited by 28

Emerging roles of intratumor microbiota in cancer: tumorigenesis and management strategies

Shi, Z., Li, Z., & Zhang, M. (2024) · Journal of Translational Medicine · doi:10.1186/s12967-024-05640-7 · Cited by 26

Seasonal variations of microbial communities and viral diversity in fishery-enhanced marine ranching sediments: insights into metabolic potentials and ecological interactions

Chen, C.-Z., Li, P., Liu, L., Sun, Y.-J., Ju, W.-M., & Li, Z. (2024) · Microbiome · doi:10.1186/s40168-024-01922-w · Cited by 25

Addressing Learning Needs on the Use of Metagenomics in Antimicrobial Resistance Surveillance

Duarte, A. S. R., Stärk, K. D. C., Munk, P., Leekitcharoenphon, P., Bossers, A., Luiken, R. E. C., Sarrazin, S., Lukjančenko, O., Pamp, S. J., Bortolaia, V., et al. (2020) · Frontiers in Public Health · doi:10.3389/fpubh.2020.00038 · Cited by 25

Optimizing Microbiota Profiles for Athletes

Mancin, L., Rollo, I., Mota, J. F., Piccini, F., Carletti, M., Susto, G. A., Valle, G., & Paoli, A. (2020) · Exercise and Sport Sciences Reviews · doi:10.1249/jes.0000000000000236 · Cited by 26

Microbial Activity in Subterranean Ecosystems: Recent Advances

Martín-Pozas, T., González-Pimentel, J. L., Jurado, V., Cuezva, S., Domínguez-Moñino, I., Fernández‐Cortés, Á., Cañaveras, J. C., Moral, S. S., & Sáiz‐Jiménez, C. (2020) · Applied Sciences · doi:10.3390/app10228130 · Cited by 25

Microbiota as Drivers and as Therapeutic Targets in Ocular and Tissue Specific Autoimmunity

Salvador, R., Zhang, A., Horai, R., & Caspi, R. R. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.606751 · Cited by 25

Next steps after 15 stimulating years of human gut microbiome research

Clavel, T., Horz, H., Segata, N., & Vehreschild, M. J. G. T. (2021) · Microbial Biotechnology · doi:10.1111/1751-7915.13970 · Cited by 26

Development and validation of a high throughput SARS-CoV-2 whole genome sequencing workflow in a clinical laboratory

Rosenthal, S. H., Gerasimova, A., Ruiz-Vega, R., Livingston, K., Kagan, R., Liu, Y., Anderson, B., Owen, R., Bernstein, L., Smolgovsky, A., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-06091-0 · Cited by 20

High-throughput identification and quantification of single bacterial cells in the microbiota

Jin, J., Yamamoto, R., Takeuchi, T., Cui, G., Miyauchi, E., Hojo, N., Ikuta, K., Ohno, H., & Shiroguchi, K. (2022) · Nature Communications · doi:10.1038/s41467-022-28426-1 · Cited by 25

Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis

Wang, H., Yang, G. X., Hu, Y., Lam, P. M. W., Sangha, K. K., Siciliano, D., Swenerton, A., Miller, R. R., Tilley, P. A. G., von Dadelszen, P., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-10869-7 · Cited by 25

FragGeneScanRs: faster gene prediction for short reads

der Jeugt, F. V., Dawyndt, P., & Mesuere, B. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04736-5 · Cited by 25

Contribution of −Omics Technologies in the Study of Porphyromonas gingivalis during Periodontitis Pathogenesis: A Minireview

Nuñez-Belmar, J., Morales-Olavarría, M., Vicencio, E., Vernal, R., Cárdenas, J. P., & Cortéz, C. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms24010620 · Cited by 27

Profiling Microbial Communities in Idiopathic Granulomatous Mastitis

Ong, S. S., Xu, J. Y., Sim, C. K., Khng, A. J., Ho, P. J., Kwan, P. K. W., Ravikrishnan, A., Tan, K.-T. B., Tan, Q. T., Tan, E. Y., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24021042 · Cited by 24

Taxonomy and Species Diversity of Sourdough Lactic Acid Bacteria

Vuyst, L. D., González-Alonso, V., Wardhana, Y. R., & Pradal, I. (2023) · Springer eBooks · doi:10.1007/978-3-031-23084-4_6 · Cited by 25

Metagenomic Sequencing Analysis Identifies Cross-Cohort Gut Microbial Signatures Associated With Age-Related Macular Degeneration

Xue, W., Peng, P., Wen, X., Meng, H., Qin, Y., Deng, T., Guo, S., Chen, T., Li, X., Liang, J., et al. (2023) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.64.5.11 · Cited by 25

The predictive power of phylogeny on growth rates in soil bacterial communities

Walkup, J., Dang, C., Mau, R. L., Hayer, M., Schwartz, E., Stone, B. W., Hofmockel, K., Koch, B. J., Purcell, A. M., Pett‐Ridge, J., et al. (2023) · ISME Communications · doi:10.1038/s43705-023-00281-1 · Cited by 25

The gut microbiota perspective for interventions in MS

Żołędziewska, M. (2019) · Autoimmunity Reviews · doi:10.1016/j.autrev.2019.03.016 · Cited by 25

Cultural isolation of spore-forming bacteria in human feces using bile acids

Tanaka, M., Onizuka, S., Mishima, R., & Nakayama, J. (2020) · Scientific Reports · doi:10.1038/s41598-020-71883-1 · Cited by 25

Advances in molecular diagnostic testing for central nervous system infections

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The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives

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