The microbiome of uncontacted Amerindians

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400

MUSCLE: multiple sequence alignment with high accuracy and high throughput

Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr121 · Cited by 40,166

vegan: Community Ecology Package

Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Sólymos, P., Stevens, M. H. H., Szöcs, E., et al. (2001) · doi:10.32614/cran.package.vegan · Cited by 27,099

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376

Metagenomic biomarker discovery and explanation

Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192

An obesity-associated gut microbiome with increased capacity for energy harvest

Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624

Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts

Manghi, P., Bhosle, A., Wang, K., Marconi, R., Selma‐Royo, M., Ricci, L., Asnicar, F., Golzato, D., Ma, W., Hang, D., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01858-9 · Cited by 84

Impacts of the Human Gut Microbiome on Therapeutics

Vázquez‐Baeza, Y., Callewaert, C., Debelius, J. W., Hyde, E. R., Marotz, C. A., Morton, J. T., Swafford, A. D.-E., Vrbanac, A. F., Dorrestein, P. C., & Knight, R. D. (2017) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-042017-031849 · Cited by 87

Infant gut microbiome is enriched with Bifidobacterium longum ssp. infantis in Old Order Mennonites with traditional farming lifestyle

Seppo, A., Bu, K., Jumabaeva, M., Thakar, J., Choudhury, R. A., Yonemitsu, C., Bode, L., Martina, C. A., Allen, M., Tamburini, S., et al. (2021) · Allergy · doi:10.1111/all.14877 · Cited by 81

The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept

Sharon, I., Quijada, N. M., Pasolli, E., Fabbrini, M., Vitali, F., Agamennone, V., Dötsch, A., Selberherr, E., Grau, J. H., Meixner, M., et al. (2022) · Nutrients · doi:10.3390/nu14142872 · Cited by 83

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics

Gschwind, R., Perović, S. U., Weiss, M., Petitjean, M., Lao, J., Coelho, L. P., & Ruppé, É. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad384 · Cited by 84

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model

Clayton, J. B., Al‐Ghalith, G. A., Long, H. T., Tuan, B. V., Cabana, F., Huang, H., Vangay, P., Ward, T., Minh, V. V., Tam, N. A., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-29277-x · Cited by 81

Mars: new insights and unresolved questions

Changela, H. G., Chatzitheodoridis, E., Antunes, A., Beaty, D., Bouw, K., Bridges, J. C., Čápová, K. A., Cockell, C. S., Conley, C. A., Dadachova, E., et al. (2021) · International Journal of Astrobiology · doi:10.1017/s1473550421000276 · Cited by 80

The Microbiota of the Human Skin

Egert, M., & Simmering, R. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-31248-4_5 · Cited by 86

High-resolution characterization of the human microbiome

Noecker, C. A., McNally, C. P., Eng, A., & Borenstein, E. (2016) · Translational research · doi:10.1016/j.trsl.2016.07.012 · Cited by 81

Factors shaping the composition of the cutaneous microbiota

Szabó, K., Erdei, L., Bolla, B. S., Tax, G., Bíró, T., & Kemény, L. V. (2016) · British Journal of Dermatology · doi:10.1111/bjd.14967 · Cited by 82

In VivoAnalysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis

Thorell, K., Bengtsson‐Palme, J., Liu, O. H.-F., Gonzáles, R. V. P. P., Nookaew, I., Rabeneck, L., Paszat, L., Graham, D. Y., Nielsen, J., Lundin, S. B., et al. (2017) · Infection and Immunity · doi:10.1128/iai.00031-17 · Cited by 77

The Past and Future Biology of the Human Microbiome in an Age of Extinctions

Blaser, M. J. (2018) · Cell · doi:10.1016/j.cell.2018.02.040 · Cited by 77

Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics

Gillings, M. R., Paulsen, I. T., & Tetu, S. G. (2015) · Genes · doi:10.3390/genes6030841 · Cited by 78

Effects of Food Additives on Immune Cells As Contributors to Body Weight Gain and Immune-Mediated Metabolic Dysregulation

Neto, H. A. P., Ausina, P., Gomez, L. S., Leandro, J. G. B., Zancan, P., & Sola‐Penna, M. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.01478 · Cited by 81

Homeostasis in the Gut Microbiota in Chronic Kidney Disease

Bhargava, S., Merckelbach, E., Noels, H., Vohra, A., & Jankowski, J. (2022) · Toxins · doi:10.3390/toxins14100648 · Cited by 77

Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome

Forsberg, K. J., Bhatt, I. V., Schmidtke, D. T., Javanmardi, K., Dillard, K. E., Stoddard, B. L., Finkelstein, I. J., Kaiser, B. K., & Malik, H. S. (2019) · eLife · doi:10.7554/elife.46540 · Cited by 73

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

Zhang, L., Forst, C. V., Gordon, A. L., Gussin, G., Geber, A. B., Fernandez, P. J., Ding, T., Lashua, L. P., Wang, M., Balmaseda, Á., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00803-2 · Cited by 72

Propionate and Alzheimer’s Disease

Killingsworth, J., Sawmiller, D. R., & Shytle, R. D. (2021) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2020.580001 · Cited by 76

Human Gut Microbiome Across Different Lifestyles: From Hunter-Gatherers to Urban Populations

Rosas-Plaza, S., Hernández‐Terán, A., Navarro-Díaz, M., Escalante, A. E., Morales-Espinosa, R., & Cerritos, R. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.843170 · Cited by 78

Characterization of the public transit air microbiome and resistome reveals geographical specificity

Leung, M. H. Y., Tong, X., Bøifot, K. O., Bezdan, D., Butler, D., Danko, D., Gohli, J., Green, D. C., Hernandez, M., Kelly, F. J., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01044-7 · Cited by 67

Increasing the diversity of dietary fibers in a daily-consumed bread modifies gut microbiota and metabolic profile in subjects at cardiometabolic risk

Ranaivo, H., Thirion, F., Béra‐Maillet, C., Guilly, S., Simon, C., Sothier, M., Berghe, L. V. D., Feugier, N., Lambert-Porcheron, S., Dussous, I., et al. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2044722 · Cited by 69

Wicked: The untold story of ciprofloxacin

Conley, Z. C., Bodine, T. J., Chou, A., & Zechiedrich, L. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1006805 · Cited by 70

Exploring the universal healthy human gut microbiota around the World

Piquer-Esteban, S., Ruiz‐Ruiz, S., Arnau, V., Díaz-Villanueva, W., & Moyá, A. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.12.035 · Cited by 72

Application of Microbiome in Forensics

Zhang, J., Liu, W., Simayijiang, H., Hu, P., & Yan, J. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.07.007 · Cited by 75

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

Gounot, J.-S., Chia, M., Bertrand, D., Saw, W., Ravikrishnan, A., Low, A., Ding, Y., Ng, A. H. Q., Tan, L. W. L., Teo, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33782-z · Cited by 66

Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation

Li, F., Armet, A. M., Korpela, K., Liu, J., Quevedo, R. M., Asnicar, F., Seethaler, B., Rusnak, T., Cole, J. L., Zhang, Z., et al. (2025) · Cell · doi:10.1016/j.cell.2024.12.034 · Cited by 77

Insights into human evolution from ancient and contemporary microbiome studies

Schnorr, S. L., Sankaranarayanan, K., Lewis, C. M., & Warinner, C. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.07.003 · Cited by 71

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions

Bundgaard‐Nielsen, C., Hagstrøm, S., & Sørensen, S. (2018) · Scientific Reports · doi:10.1038/s41598-018-35843-0 · Cited by 65

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance

Barelli, C., Albanese, D., Stumpf, R. M., Asangba, A. E., Donati, C., Rovero, F., & Hauffe, H. C. (2020) · mSystems · doi:10.1128/msystems.00061-20 · Cited by 67

The interplay of obesity, gut microbiome and diet in the immune check point inhibitors therapy era

Spyrou, N., Vallianou, N. G., Kadillari, J., & Dalamaga, Μ. (2021) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2021.05.008 · Cited by 66

Neonatal exposure to a wild-derived microbiome protects mice against diet-induced obesity

Hild, B., Dreier, M. S., Oh, J. H., McCulloch, J. A., Badger, J. H., Guo, J., Thefaine, C. E., Umarova, R., Hall, K. D., Gavrilova, O., et al. (2021) · Nature Metabolism · doi:10.1038/s42255-021-00439-y · Cited by 68

Individual signatures and environmental factors shape skin microbiota in healthy dogs

Cuscó, A., Belanger, J. M., Gershony, L. C., Islas‐Trejo, A., Levy, K., Medrano, J. F. F., Sánchez, A., Oberbauer, A. M., & Francino, O. (2017) · Microbiome · doi:10.1186/s40168-017-0355-6 · Cited by 70

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes

Tsukayama, P., Boolchandani, M., Patel, S., Pehrsson, E. C., Gibson, M. K., Chiou, K. L., Jolly, C. J., Rogers, J., Phillips‐Conroy, J. E., & Dantas, G. A. (2018) · mSystems · doi:10.1128/msystems.00016-18 · Cited by 64

Metagenomic Insight into Microbiome and Antibiotic Resistance Genes of High Clinical Concern in Urban and Rural Hospital Wastewater of Northern India Origin: a Major Reservoir of Antimicrobial Resistance

Talat, A., Blake, K. S., Dantas, G. A., & Khan, A. U. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.04102-22 · Cited by 73

Microbial exposure and human health

Sharma, A., & Gilbert, J. A. (2018) · Current Opinion in Microbiology · doi:10.1016/j.mib.2018.08.003 · Cited by 67

Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions

Tomazetto, G., Hahnke, S., Wibberg, D., Pühler, A., Klocke, M., & Schlüter, A. (2018) · Biotechnology Reports · doi:10.1016/j.btre.2018.e00254 · Cited by 64

Individual and household attributes influence the dynamics of the personal skin microbiota and its association network

Leung, M. H. Y., Tong, X., Wilkins, D. E., Cheung, H. H. L., & Lee, P. K. H. (2018) · Microbiome · doi:10.1186/s40168-018-0412-9 · Cited by 66

A systematic review of the impacts of oral tetracycline class antibiotics on antimicrobial resistance in normal human flora

Truong, R., Tang, V., Grennan, T., & Tan, D. H. S. (2022) · JAC-Antimicrobial Resistance · doi:10.1093/jacamr/dlac009 · Cited by 63

Gut Microbiome of the Canadian Arctic Inuit

Girard, C., Tromas, N., Amyot, M., & Shapiro, B. J. (2017) · mSphere · doi:10.1128/msphere.00297-16 · Cited by 65

Think before you prescribe: how dentistry contributes to antibiotic resistance

Sukumar, S., Martin, F. E., Hughes, T., & Adler, C. J. (2019) · Australian Dental Journal · doi:10.1111/adj.12727 · Cited by 65

Genomic and Metagenomic Approaches for Predictive Surveillance of Emerging Pathogens and Antibiotic Resistance

Sukhum, K. V., Diorio‐Toth, L., & Dantas, G. A. (2019) · Clinical Pharmacology & Therapeutics · doi:10.1002/cpt.1535 · Cited by 60

Ultra-Processed Food Is Positively Associated With Depressive Symptoms Among United States Adults

Zheng, L., Sun, J., Yu, X., & Zhang, D. (2020) · Frontiers in Nutrition · doi:10.3389/fnut.2020.600449 · Cited by 65

Virome-associated antibiotic-resistance genes in an experimental aquaculture facility

Colombo, S., Arioli, S., Guglielmetti, S., Lunelli, F., & Mora, D. (2016) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiw003 · Cited by 61

Phytobiome metabolism: beneficial soil microbes steer crop plants' secondary metabolism

Korenblum, E., & Aharoni, A. (2019) · Pest Management Science · doi:10.1002/ps.5440 · Cited by 60

Genomic and metagenomic technologies to explore the antibiotic resistance mobilome

Martínez, J. L., Coque, T. M., Lanza, V. F., de la Cruz, F., & Baquero, F. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13282 · Cited by 61

Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study

Vallès, Y., Inman, C. K., Peters, B. A., Ali, R., Wareth, L. A., Abdulle, A. M., AlSafar, H. S., Anouti, F. A., Dhaheri, A. S. A., Galani, D., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-29730-x · Cited by 60

Gut Microbiota of Wild and Captive Alpine Musk Deer (Moschus chrysogaster)

Sun, Y., Sun, Y., Shi, Z., Liu, Z., Zhao, C. S., Lu, T., Gao, H., Zhu, F., Chen, R., Zhang, J., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.03156 · Cited by 60

New Insights into the Ecology and Physiology of Methanomassiliicoccales from Terrestrial and Aquatic Environments

Cozannet, M., Borrel, G., Roussel, E. G., Moalic, Y., Allioux, M., Amandine, S., Toffin, L. M. A. A., & Alain, K. (2020) · Microorganisms · doi:10.3390/microorganisms9010030 · Cited by 56

Tuning Expectations to Reality: Don’t Expect Increased Gut Microbiota Diversity with Dietary Fiber

Cantu-Jungles, T. M., & Hamaker, B. R. (2023) · Journal of Nutrition · doi:10.1016/j.tjnut.2023.09.001 · Cited by 62

The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults

Barnett, C. R., Nazzal, L., Goldfarb, D. S., & Blaser, M. J. (2015) · The Journal of Urology · doi:10.1016/j.juro.2015.08.070 · Cited by 57

The Role of Every-Day Cosmetics in Altering the Skin Microbiome: A Study Using Biodiversity

Wallen-Russell, C. (2018) · Cosmetics · doi:10.3390/cosmetics6010002 · Cited by 57

The feline cutaneous and oral microbiota are influenced by breed and environment

Older, C. E., Diesel, A. B., Lawhon, S. D., Queiroz, C. R. R., Henker, L. C., & Hoffmann, A. R. (2019) · PLoS ONE · doi:10.1371/journal.pone.0220463 · Cited by 61

Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health

Wasielewski, H., Alcock, J., & Aktipis, A. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13118 · Cited by 58

The Microbiome of the Built Environment and Human Behavior

Stamper, C. E., Hoisington, A. J., Gomez, O. M., Halweg‐Edwards, A. L., Smith, D. G., Bates, K. L., Kinney, K. A., Postolache, T. T., Brenner, L. A., Rook, G. A. W., et al. (2016) · International review of neurobiology · doi:10.1016/bs.irn.2016.07.006 · Cited by 59

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium Difficile in Patients With and Without Inflammatory Bowel Disease

Hirten, R. P., Grinspan, A. M., Fu, S., Luo, Y., Suárez‐Fariñas, M., Rowland, J., Contijoch, E. J., Mogno, I., Yang, N., Luong, T., et al. (2019) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izy398 · Cited by 54

The Cattle Microbiota and the Immune System

Gómez, D. E., Galvão, K. N., Rodriguez-Lecompte, J. C., & Costa, M. (2019) · Veterinary Clinics of North America Food Animal Practice · doi:10.1016/j.cvfa.2019.08.002 · Cited by 55

Development of the oral resistome during the first decade of life

Sukumar, S., Wang, F., Simpson, C. A., Willet, C. E., Chew, T., Hughes, T. E., Bockmann, M. R., Sadsad, R., Martin, F. E., Lydecker, H. W., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36781-w · Cited by 55

Resistance decay in individuals after antibiotic exposure in primary care: a systematic review and meta-analysis

Bakhit, M., Hoffmann, T., Scott, A. M., Beller, E., Rathbone, J., & Mar, C. D. (2018) · BMC Medicine · doi:10.1186/s12916-018-1109-4 · Cited by 58

Stachyose increases intestinal barrier through Akkermansia muciniphila and reduces gut inflammation in germ-free mice after human fecal transplantation

Xi, M., Li, J., Guo, H., An, X., Song, Y., Wei, H., & Ge, W. (2020) · Food Research International · doi:10.1016/j.foodres.2020.109288 · Cited by 55

Response of the human gut and saliva microbiome to urbanization in Cameroon

Lokmer, A., Aflalo, S., Amougou, N., Lafosse, S., Froment, A., Tabe, F. E., Poyet, M., Groussin, M., Said-Mohamed, R., & Ségurel, L. (2020) · Scientific Reports · doi:10.1038/s41598-020-59849-9 · Cited by 46

Antibiotic resistance genes are differentially mobilized according to resistance mechanism

Nielsen, T. K., Browne, P. D., & Hansen, L. H. (2022) · GigaScience · doi:10.1093/gigascience/giac072 · Cited by 53

Beyond the gut: Skin microbiome compositional changes are associated with BMI

Brandwein, M., Katz, I., Katz, A., & Kohen, R. (2019) · Human Microbiome Journal · doi:10.1016/j.humic.2019.100063 · Cited by 58

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers

D’Souza, A. W., Boolchandani, M., Patel, S., Galazzo, G., van Hattem, J. M., Arcilla, M. S., Melles∗, D. C., de Jong, M. D., Schultsz, C., Bootsma, M., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00893-z · Cited by 54

Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections

Sauvaitre, T., Etienne‐Mesmin, L., Sivignon, A., Mosoni, P., Courtin, C. M., de Wiele, T. V., & Blanquet‐Diot, S. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa052 · Cited by 53

Dietary Habits of 2- to 9-Year-Old American Children Are Associated with Gut Microbiome Composition

Herman, D. R., Rhoades, N., Mercado, J., Argueta, P., Lopez, U., & Flores, G. E. (2020) · Journal of the Academy of Nutrition and Dietetics · doi:10.1016/j.jand.2019.07.024 · Cited by 50

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

Monaghan, T. M., Sloan, T. J., Stockdale, S. R., Blanchard, A. M., Emes, R. D., Wilcox, M. H., Biswas, R., Nashine, R. R., Manke, S., Gandhi, J., et al. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1752605 · Cited by 54

Impact of international travel and diarrhea on gut microbiome and resistome dynamics

Boolchandani, M., Blake, K. S., Tilley, D. H., Cabada, M. M., Schwartz, D. J., Patel, S., Morales, M. L., Meza, R. A., Soto, G. M., Isidean, S. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34862-w · Cited by 54

The History of the Intestinal Microbiota and the Gut-Brain Axis

Lewandowska, Z., Figlerowicz, M., & Mazur‐Melewska, K. (2022) · Pathogens · doi:10.3390/pathogens11121540 · Cited by 65

The Microbiome and Mental Health: Looking Back, Moving Forward with Lessons from Allergic Diseases

Logan, A. C., Jacka, F. N., Craig, J. M., & Prescott, S. L. (2016) · Clinical Psychopharmacology and Neuroscience · doi:10.9758/cpn.2016.14.2.131 · Cited by 51

The human gut resistome

Singh, S., Verma, N., & Taneja, N. (2019) · The Indian Journal of Medical Research · doi:10.4103/ijmr.ijmr_1979_17 · Cited by 58

The role of the changing human microbiome in the asthma pandemic

Borbet, T. C., Zhang, X., Mueller, A., & Blaser, M. J. (2019) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2019.10.022 · Cited by 52

The shrinking human gut microbiome

Moeller, A. H. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.04.002 · Cited by 50

Methods in microbiome research: Past, present, and future

Gotschlich, E. C., Colbert, R. A., & Gill, T. (2019) · Best Practice & Research Clinical Rheumatology · doi:10.1016/j.berh.2020.101498 · Cited by 58

Diversity analysis and metagenomic insights into antibiotic and metal resistance among Himalayan hot spring bacteriobiome insinuating inherent environmental baseline levels of antibiotic and metal tolerance

Najar, I. N., Sherpa, M. T., Das, S., Das, S., & Thakur, N. N. (2020) · Journal of Global Antimicrobial Resistance · doi:10.1016/j.jgar.2020.03.026 · Cited by 51

The Conceptual Ecology of the Human Microbiome

Morar, N., & Bohannan, B. J. M. (2019) · The Quarterly Review of Biology · doi:10.1086/703582 · Cited by 51

Diet Quality, Food Groups and Nutrients Associated with the Gut Microbiota in a Nonwestern Population

García-Vega, Á. S., Corrales-Agudelo, V., Reyes, A., & Escobar, J. S. (2020) · Nutrients · doi:10.3390/nu12102938 · Cited by 52

SENSE: Siamese neural network for sequence embedding and alignment-free comparison

Zheng, W., Yang, L., Genco, R. J., Wactawski‐Wende, J., Buck, M. J., & Sun, Y. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty887 · Cited by 51

Derived habitats of indoor microbes are associated with asthma symptoms in Chinese university dormitories

Fu, X., Li, Y., Meng, Y., Yuan, Q., Zhang, Z., Wen, H., Deng, Y., Norbäck, D., Hu, Q., Zhang, X., et al. (2020) · Environmental Research · doi:10.1016/j.envres.2020.110501 · Cited by 57

Microbial transmission from mother to child: improving infant intestinal microbiota development by identifying the obstacles

Daele, E. V., Knol, J., & Belzer, C. (2019) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2019.1680601 · Cited by 49

Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon

Sprockett, D. D., Martin, M. A., Costello, E. K., Burns, A. R., Holmes, S., Gurven, M., & Relman, D. A. (2020) · Nature Communications · doi:10.1038/s41467-020-17541-6 · Cited by 46

The impact of urbanisation on the cardiometabolic health of Indigenous Brazilian peoples: a systematic review and meta-analysis, and data from the Brazilian Health registry

Kramer, C. K., Leitão, C. B., & Viana, L. V. (2022) · The Lancet · doi:10.1016/s0140-6736(22)00625-0 · Cited by 47

Meta Analysis of Skin Microbiome: New Link between Skin Microbiota Diversity and Skin Health with Proposal to Use This as a Future Mechanism to Determine Whether Cosmetic Products Damage the Skin

Wallen-Russell, C., & Wallen-Russell, S. (2017) · Cosmetics · doi:10.3390/cosmetics4020014 · Cited by 46

Holistic View on Health: Two Protective Layers of Biodiversity

Ruokolainen, L., Lehtimäki, J., Karkman, A., Haahtela, T., von Hertzen, L., & Fyhrquist, N. (2017) · Annales Zoologici Fennici · doi:10.5735/086.054.0106 · Cited by 47

Ecosystem Microbiome Science

Zhu, Y., Zhu, D., Rillig, M. C., Yang, Y., Chu, H., Chen, Q., Peñuelas, J., Cui, H., & Gillings, M. R. (2023) · mLife · doi:10.1002/mlf2.12054 · Cited by 48

Skin microbiome and dermatologic disorders

Scharschmidt, T. C., & Segre, J. A. (2025) · Journal of Clinical Investigation · doi:10.1172/jci184315 · Cited by 55

Influence of the microbiota and probiotics in obesity

Fontané, L., Benaiges, D., Goday, A., Llauradó, G., & Pedro‐Botet, J. (2018) · Clínica e Investigación en Arteriosclerosis (English Edition) · doi:10.1016/j.artere.2018.10.002 · Cited by 48

Recipe for a Healthy Gut: Intake of Unpasteurised Milk Is Associated with Increased Lactobacillus Abundance in the Human Gut Microbiome

Butler, M., Bastiaanssen, T. F. S., Long-Smith, C. M., Berding, K., Mörkl, S., Cusack, A.-M., Strain, C., Busca, K., Porteous-Allen, P., Claesson, M. J., et al. (2020) · Nutrients · doi:10.3390/nu12051468 · Cited by 48

Probiotic strains and mechanistic insights for the treatment of type 2 diabetes

Hampe, C. S., & Roth, C. L. (2017) · Endocrine · doi:10.1007/s12020-017-1433-z · Cited by 46

Association of Age With Blood Pressure Across the Lifespan in Isolated Yanomami and Yekwana Villages

Mueller, N. T., Noya-Alarcón, Ó., Contreras, M., Appel, L. J., & Domínguez-Bello, M. G. (2018) · JAMA Cardiology · doi:10.1001/jamacardio.2018.3676 · Cited by 45

The prolonged disruption of a single-course amoxicillin on mice gut microbiota and resistome, and recovery by inulin, Bifidobacterium longum and fecal microbiota transplantation

Lin, H., Wang, Q., Meng, Y., Liu, L., Chen, Z., Zhao, Y., Das, R., Duan, Y., Xu, X., Xue, Y., et al. (2020) · Environmental Pollution · doi:10.1016/j.envpol.2020.114651 · Cited by 46

Nanotechnology as a viable alternative for the removal of antimicrobial resistance determinants from discharged municipal effluents and associated watersheds: A review

Ojemaye, M. O., Adefisoye, M. A., & Okoh, A. I. (2020) · Journal of Environmental Management · doi:10.1016/j.jenvman.2020.111234 · Cited by 45

Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis

Leyva, L. L., Brereton, N. J. B., & Koski, K. G. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.11.057 · Cited by 50

Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care

Guéniche, A., Périn, O., Bouslimani, A., Landemaine, L., Misra, N., Cupferman, S., Aguilar, L., Clavaud, C., Chopra, T., & Khodr, A. (2022) · Pathogens · doi:10.3390/pathogens11020121 · Cited by 47

Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes

Adu‐Oppong, B., Gasparrini, A. J., & Dantas, G. A. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13257 · Cited by 46

Influencia de la microbiota y de los probióticos en la obesidad

Fontané, L., Benaiges, D., Goday, A., Llauradó, G., & Pedro‐Botet, J. (2018) · Clínica e Investigación en Arteriosclerosis · doi:10.1016/j.arteri.2018.03.004 · Cited by 52

Elevated serum ceramides are linked with obesity-associated gut dysbiosis and impaired glucose metabolism

Kayser, B. D., Prifti, E., Lhomme, M., Belda, E., Dao, M. C., Aron‐Wisnewsky, J., Cotillard, A., Kennedy, S., Pons, N., Chatelier, E. L., et al. (2019) · Metabolomics · doi:10.1007/s11306-019-1596-0 · Cited by 47

Station and train surface microbiomes of Mexico City’s metro (subway/underground)

Hernández, A. M., Vargas-Robles, D., Alcaraz, L. D., & Peimbert, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-65643-4 · Cited by 44

Changes in the vaginal microbiota across a gradient of urbanization

Vargas-Robles, D., Morales, N. S., Rodríguez, I., Nieves, T., Godoy‐Vitorino, F., Alcaraz, L. D., Pérez, M.-E., Ravel, J., Forney, L. J., & Domínguez-Bello, M. G. (2020) · Scientific Reports · doi:10.1038/s41598-020-69111-x · Cited by 41

Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes

Sánchez-Quinto, A., Cerqueda‐García, D., Falcón, L. I., Gaona, O., Martínez-Correa, S., Nieto, J., & González‐Santoyo, I. (2020) · Microorganisms · doi:10.3390/microorganisms8101592 · Cited by 45

Microbiota-accessible carbohydrates (MACs) as novel gut microbiome modulators in noncommunicable diseases

Ayakdaş, G., & Ağagündüz, D. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e19888 · Cited by 47

Microbiome of uncontacted Amerindians

Yèagle, P. L. (2015) · Science · doi:10.1126/science.348.6232.298-a · Cited by 43

Antibiotic resistance in remote tribespeople

(2015) · Journal of Paediatrics and Child Health · doi:10.1111/jpc.12992

Preliminary profile of the gut microbiota from amerindians in the Brazilian amazon experiencing a process of transition to urbanization

Alencar, R. M., Martínez, J. G., Machado., V. N., Álzate, J. F., Ojeda, C. P. O., Matias, R. R., Benzaquem, D. C., Santos, M. C. F., de Assunção, E. N., Lira, E. C., et al. (2024) · Brazilian Journal of Microbiology · doi:10.1007/s42770-024-01413-y · Cited by 10

Caracterização taxonômica do microbioma bacteriano intestinal de comunidades ameríndias na Amazônia brasileira

Alencar, R. M. (2017) · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas)

The Uncolonized within the Uncolonized: Scientific Desire and a Speculative Reading of the Indigenous Biome

Geroux, R. (2020) · Theory & Event · doi:10.1353/tae.2020.0062