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

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Metagenomic biomarker discovery and explanation

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

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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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From soil to health: advancing regenerative agriculture for improved food quality and nutrition security

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Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences

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Interactions between the intestinal microbiota and drug metabolism – Clinical implications and future opportunities

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Lethality of First Contact Dysentery Epidemics on Pacific Islands

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Feeding Our Microbiota: Stimulation of the Immune/Semiochemical System and the Potential Amelioration of Non-Communicable Diseases

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Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile

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Savanna Monkeys

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Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History

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The Gut Microbiome of an Indigenous Agropastoralist Population in a Remote Area of Colombia with High Rates of Gastrointestinal Infections and Dysbiosis

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Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes

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Missing microbiomes: global underrepresentation restricts who research will benefit

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Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized

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Comparative study of the gut microbiomes between Western and Indigenous cultures – Implications for health and disease

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Compositional transformations can reasonably introduce phenotype-associated values into sparse features

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Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin

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Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico

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Moving beyond descriptions of diversity: clinical and research implications of bacterial imbalance in chronic rhinosinusitis

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2017 NIH-wide workshop report on “The Human Microbiome: Emerging Themes at the Horizon of the 21st Century”

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Food Additives and Contaminants: Effects on Human Gut Microbiota—A ReviewPreprint

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Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries

Santiago-Rodriguez, T. M., Fornaciari, A., Fornaciari, G., Luciani, S., Marota, I., Vercellotti, G., Toranzos, G. A., Giuffra, V., & Cano, R. J. (2019) · Genes · doi:10.3390/genes10040299 · Cited by 10

Uncovering the gut microbiome and antibiotic resistome of mammals on the Tibetan Plateau

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Study design and rationale for the PAASIM project: a matched cohort study on urban water supply improvements and infant enteric pathogen infection, gut microbiome development and health in Mozambique

Lévy, K., Garn, J. V., Adriano, Z., Muneme, B., Fagnant-Sperati, C. S., Hubbard, S., Júnior, A., Manuel, J. L., Mangamela, M., McGunegill, S., et al. (2023) · BMJ Open · doi:10.1136/bmjopen-2022-067341 · Cited by 12

Identification of body fluid sources based on microbiome antibiotic resistance genes using high-throughput qPCR

Yu, D., Wang, T., Zhang, L., Gao, N., Huang, Y., Zhang, J., & Yan, J. (2025) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2025.103241 · Cited by 10

The Invisible Extinction

Blaser, M. J., & Domínguez-Bello, M. G. (2025) · Annual Review of Microbiology · doi:10.1146/annurev-micro-051024-092416 · Cited by 11

A Latin American perspective on microbiome research

Reyes, A., Durán, C., Rodríguez-Otálora, S., Pugley, D. D., Iraola, G., Domínguez-Bello, M. G., Lawley, T. D., & Tsukayama, P. (2025) · Nature Communications · doi:10.1038/s41467-025-66756-y · Cited by 9

What Can the Gut Microbiota of Animals Teach Us about the Relationship between Nutrition and Burden of Lifestyle Diseases?

Mafra, D., Borges, N. A., Baptista, B. G., Martins, L. F., Borland, G., Shiels, P. G., & Stenvinkel, P. (2024) · Nutrients · doi:10.3390/nu16111789 · Cited by 11

Evolution of the Oral Microbiome and Dental Caries

Adler, C. J., Browne, G. V., Sukumar, S., & Hughes, T. E. (2017) · Current Oral Health Reports · doi:10.1007/s40496-017-0151-1 · Cited by 10

Seasonal change in the gut

Peddada, S. D. (2017) · Science · doi:10.1126/science.aao2997 · Cited by 10

Topical Probiotics Do Not Satisfy New Criteria for Effective Use Due to Insufficient Skin Microbiome Knowledge

Wallen-Russell, C., & Wallen-Russell, S. (2021) · Cosmetics · doi:10.3390/cosmetics8030090 · Cited by 10

A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits

Conteville, L. C., & Vicente, A. C. P. (2022) · Scientific Reports · doi:10.1038/s41598-022-16392-z · Cited by 11

Review on nanotechnology “Impact on the food services industry”

Saini, P., Kamalesu, Lalita, & Manikanika (2023) · Materials Today Proceedings · doi:10.1016/j.matpr.2023.04.377 · Cited by 10

Fecal Microbiome and Resistome Profiling of Healthy and Diseased Pakistani Individuals Using Next-Generation Sequencing

Afridi, O. K., Ali, J., & Chang, J. H. (2021) · Microorganisms · doi:10.3390/microorganisms9030616 · Cited by 10

Peripheral tolerance to insulin is encoded by mimicry in the microbiomePreprint

García, A. R., Paterou, A., Lee, M., Slawinski, H., Wicker, L. S., Todd, J. A., & Pękalski, M. Ł. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2019.12.18.881433 · Cited by 11

Derived ecological niches of indoor microbes are crucial for asthma symptoms in university dormitoriesPreprint

Fu, X., Li, Y., Meng, Y., Yuan, Q., Zhang, Z., Norbäck, D., Deng, Y., Zhang, X., & Sun, Y. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.05.893529 · Cited by 10

Alignment-free comparison of metagenomics sequences via approximate string matching

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Exploring the influences of geographical variation on sequence signatures in the human gut microbiome

Kumar, G., & Bhadury, P. (2023) · Journal of Genetics · doi:10.1007/s12041-023-01448-4 · Cited by 9

Industrialization drives the gut microbiome and resistome of the Chinese populations

Chen, T., Zhang, T., Zhuang, D., Luo, Y., Li, T., Zhao, F., Sang, J., Tang, Z., Jiang, P., Zhang, T., et al. (2025) · mSystems · doi:10.1128/msystems.01372-24 · Cited by 9

Species level and SNP profiling of skin microbiome improve the specificity in identifying forensic fluid and individual

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Diet’s impact on gut microbial assemblage in health and disease

Koletic, C. F., Mrad, A., Martin, A., & Devkota, S. (2025) · Journal of Clinical Investigation · doi:10.1172/jci184319 · Cited by 9

Fiber Sets up the Battleground for Intestinal Prevotella

Wu, M., & Kasper, D. L. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.11.010 · Cited by 9

Interpreting tree ensemble machine learning models with endoR

Ruaud, A., Pfister, N., Ley, R. E., & Youngblut, N. D. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010714 · Cited by 9

Microbiota and probiotics: chances and challenges – a symposium report

Ruxton, C. H. S., Kajita, C., Rocca, P., & Pot, B. (2023) · Gut Microbiome · doi:10.1017/gmb.2023.4 · Cited by 10

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

Advancing microbiome research in Māori populations: insights from recent literature exploring the gut microbiomes of underrepresented and Indigenous peoples

Silk, E. T., Bayer, S. B., Foster, M., Roy, N. C., Taylor, M. W., Vatanen, T., & Gearry, R. B. (2024) · mSystems · doi:10.1128/msystems.00909-24 · Cited by 11

Gut Feelings

Fasano, A., & Flaherty, S. (2021) · The MIT Press eBooks · doi:10.7551/mitpress/11291.001.0001 · Cited by 14

Where the social meets the biological: new ontologies of biosocial race

Chellappoo, A., & Baedke, J. (2023) · Synthese · doi:10.1007/s11229-022-04006-0 · Cited by 12

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: The METS-Microbiome StudyPreprint

Ecklu-Mensah, G., Choo-Kang, C., Maseng, M. G., Donato, S., Bovet, P., Bedu-Addo, K., Plange‐Rhule, J., Forrester, T., Lambert, E. V., Rae, D. E., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.21.533195 · Cited by 10

Exploring the Interplay: Oral–Gut Microbiome Connection and the Impact of Diet and Nutrition

Parveen, S., Alqahtani, A. S., Aljabri, M. Y., Dawood, T., Khan, S. S., Gupta, B., Vempalli, S., Hassan, A. A.-H. A.-A., & Elamin, N. M. H. (2024) · European Journal of General Dentistry · doi:10.1055/s-0044-1786154 · Cited by 11

Skin microbiota diversity among genetically unrelated individuals of Indian origin

Potbhare, R., RaviKumar, A., Munukka, E., Lahti, L., & Ashma, R. (2022) · PeerJ · doi:10.7717/peerj.13075 · Cited by 9

Impaired central tolerance induces changes in the gut microbiota that exacerbate autoimmune hepatitis

Centa, M., Weinstein, E. G., Clemente, J. C., Faith, J. J., Fiel, M. I., Lyallpuri, R., Herbin, O., & Alexandropoulos, K. (2022) · Journal of Autoimmunity · doi:10.1016/j.jaut.2022.102808 · Cited by 8

Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data

Reynoso-García, J., Santiago-Rodríguez, T. M., Narganes-Storde, Y. M., Cano, R. J., & Toranzos, G. A. (2023) · PLoS ONE · doi:10.1371/journal.pone.0292077 · Cited by 8

Race and indigeneity in human microbiome science: microbiomisation and the historiality of otherness

Casal, A. N. (2024) · History & Philosophy of the Life Sciences · doi:10.1007/s40656-024-00614-w · Cited by 9

Savanna Monkeys: The Genus Chlorocebus

Turner, T. R., Schmitt, C. A., & Cramer, J. D. (2019) · Cited by 8

Secondary Metabolite Differences between Naturally Grown and Conventional Coarse Green Tea

Ohta, K., Kawaoka, T., & Funabashi, M. (2020) · Agriculture · doi:10.3390/agriculture10120632 · Cited by 8

Biological Anthropology in 2015: Open Access, Biocultural Interactions, and Social Change

Willermet, C. M. (2016) · American Anthropologist · doi:10.1111/aman.12529 · Cited by 10

Vegetarian Diets and the Microbiome

Orlich, M. J., Segovia‐Siapco, G., & Jung, S. M. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-803968-7.00024-1 · Cited by 8

Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC): Supporting the transition from strategy to action

Fukuda, K., Limmathurotsakul, D., Okeke, I. N., Shetty, N., van Doorn, H. R., Feasey, N., Chiara, F., Zoubiane, G., Jinks, T., Parkhill, J., et al. (2018) · Wellcome Open Research · doi:10.12688/wellcomeopenres.14586.2 · Cited by 8

The Diversity of Pseudomonas species from the Accumulation Zone of Kanchengayao Glacier, North Sikkim, India

Sherpa, M. T., Najar, I. N., Das, S., & Thakur, N. N. (2019) · Journal of Pure and Applied Microbiology · doi:10.22207/jpam.13.1.37 · Cited by 8

Resistome and microbial profiling of pediatric patient’s gut infected with multidrug-resistant diarrhoeagenic Enterobacteriaceae using next-generation sequencing; the first study from Pakistan

Afridi, O. K., Ali, J., & Chang, J. H. (2021) · Libyan Journal of Medicine · doi:10.1080/19932820.2021.1915615 · Cited by 8

Supplementation With Human Foods Affects the Gut Microbiota of Wild Howler Monkeys

Amato, K. R., Back, J. P., Sardaro, M. L. S., & Bicca‐Marques, J. C. (2025) · American Journal of Primatology · doi:10.1002/ajp.70029 · Cited by 7

Fecal microbiota transplantation in pigs: current status and future perspective

Rahman, R., Marcolla, C. S., & Willing, B. P. (2025) · Animal Microbiome · doi:10.1186/s42523-025-00440-w · Cited by 10

From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity

Rivera-Pérez, J. I., González, A. A., & Toranzos, G. A. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.emf-0009-2016 · Cited by 7

Meanings, measurements, and musings on the significance of patterns in human microbiome variation

Schnorr, S. L. (2018) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2018.06.014 · Cited by 8

Ecological Processes and Human Behavior Provide a Framework for Studying the Skin Microbial Metacommunity

Manus, M. B. (2021) · Microbial Ecology · doi:10.1007/s00248-021-01884-8 · Cited by 7

Potential long consequences from internal and external ecology: loss of gut microbiota antifragility in children from an industrialized population compared with an indigenous rural lifestyle

González‐Santoyo, I., Ramírez-Carrillo, E., Sanchez, J. D., & López-Corona, O. (2023) · Journal of Developmental Origins of Health and Disease · doi:10.1017/s2040174423000144 · Cited by 6

Archaebiotics: Archaea as Pharmabiotics for Treating Chronic Disease in Humans?

Hania, W. B., Ballet, N., Vandekerckove, P., Ollivier, B., O’Toole, P. W., & Brugère, J. (2017) · InTech eBooks · doi:10.5772/intechopen.69945 · Cited by 7

Inulin, the gut microbiome and the deeper breath of asthma patients – Novel pathways in asthma treatment

Brehm, C. U., & Pfefferle, P. I. (2019) · EBioMedicine · doi:10.1016/j.ebiom.2019.07.052 · Cited by 7

Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention

Orchanian, S. B., Gauglitz, J. M., Wandro, S., Weldon, K. C., Doty, M. M., Stillwell, K., Hansen, S., Jiang, L., Vargas, F., Rhee, K. E., et al. (2022) · Advanced Biology · doi:10.1002/adbi.202101313 · Cited by 7

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

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. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/177295 · Cited by 7

Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation

Sargsian, S., Mondragón-Palomino, O., Lejeune, A., Ercelen, D., Jin, W., Varghese, A., Lim, Y. A. L., Guo, C., Loke, P., & Cadwell, K. (2024) · Microbiome · doi:10.1186/s40168-024-01793-1 · Cited by 7

Comparative Analysis of the Gut Microbiota of Mongolian Gazelle (Procapra gutturosa) Under Fragmented Habitats

Shi, L., Yang, X., Dou, H., Lyu, T., Wang, L., Zhou, S., Shang, Y., Dong, Y., & Zhang, H. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.830321 · Cited by 6

Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review

Wiscovitch-Russo, R. A., Santiago-Rodríguez, T. M., & Toranzos, G. A. (2023) · Genes · doi:10.3390/genes14020303 · Cited by 6

Exploring the Potential Influence of the Human Gut Microbiota on the Gut Resistome: A Systematic Review

Fri, J., Raphalalani, M., Mavhandu-Ramarumo, L. G., & Bessong, P. O. (2024) · Microbiology Research · doi:10.3390/microbiolres15030107 · Cited by 9

Wild-Mouse-Derived Gut Microbiome Transplantation in Laboratory Mice Partly Alleviates House-Dust-Mite-Induced Allergic Airway Inflammation

Islam, M. Z., Jozipović, D., Atienza, P., Krych, Ł., Correia, B. S. B., Bertram, H. C., Hansen, A. K., & Hansen, C. H. F. (2024) · Microorganisms · doi:10.3390/microorganisms12122499 · Cited by 6

Microbial Cycling of Methane

Kalyuzhnaya, M., Collins, D., & Chistoserdova, L. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.90670-8 · Cited by 6

First insight into oral microbiome diversity in Papua New Guineans reveals a specific regional signature

Pedro, N., Brucato, N., Cavadas, B., Lisant, V., Camacho, R. C., Kinipi, C., Leavesley, M., Pereira, L., & Ricaut, F. (2022) · Molecular Ecology · doi:10.1111/mec.16702 · Cited by 7

Factors Affecting the Composition of the Human Microbiome

Imchen, M., Salim, S. A., Kumavath, R., & Busi, S. (2023) · Springer eBooks · doi:10.1007/978-981-99-1463-0_3 · Cited by 6

Gut microbiome dysbiosis is associated with host genetics in the Norwegian Lundehund

Melis, C., Billing, A. M., Wold, P.-A., & Ludington, W. B. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1209158 · Cited by 6

Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits

Yersin, S., Garneau, J. R., Schneeberger, P. H. H., Osman, K. A., Cercamondi, C. I., Muhummed, A. M., Tschopp, R., Zinsstag, J., & Vonaesch, P. (2023) · Scientific Reports · doi:10.1038/s41598-023-47748-8 · Cited by 6

Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region

Balcha, E. S., Gómez, F., Gemeda, M. T., Belayneh, F., Abera, S., Cavalazzi, B., & Woldesemayat, A. A. (2023) · Antibiotics · doi:10.3390/antibiotics12121697 · Cited by 6

From wolves to humans: oral microbiome resistance to transfer across mammalian hosts

Podar, N. A., Carrell, A. A., Cassidy, K. A., Klingeman, D. M., Yang, Z. K., Stahler, E. E., Smith, D. W., Stahler, D. R., & Podar, M. (2024) · mBio · doi:10.1128/mbio.03342-23 · Cited by 8

Impact of Early-Life Antibiotic Use on Gut Microbiota of Infants

Wang Xiu, Y., Wang Guo, Z., Wen, Y., Su, T., & Yuan, Y. (2017) · Journal of Microbial & Biochemical Technology · doi:10.4172/1948-5948.1000369 · Cited by 7

Re-purposing is needed for beneficial bugs, not for the drugs

Ram, H. H., & Dastager, S. G. (2018) · International Microbiology · doi:10.1007/s10123-018-00049-x · Cited by 7

A New Benchmark to Determine What Healthy Western Skin Looks Like in Terms of Biodiversity Using Standardised Methodology

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Different Types and Functional Effects of Probiotics on Human Health through Regulating Glucose Homeostasis

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