Moving pictures of the human microbiome

Search and clustering orders of magnitude faster than BLAST

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A human gut microbial gene catalogue established by metagenomic sequencing

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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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Diversity of the Human Intestinal Microbial Flora

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A core gut microbiome in obese and lean twins

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Vaginal microbiome of reproductive-age women

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Bacterial Community Variation in Human Body Habitats Across Space and Time

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The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

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Development of the Human Infant Intestinal Microbiota

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Moving microbes: the dynamics of transient microbial residence on human skinPreprint

Vandegrift, R., Fahimipour, A. K., Muscarella, M. E., Bateman, A. C., Wymelenberg, K. G. V. D., & Bohannan, B. J. M. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/586008 · Cited by 22

The regulation of fecal microbiota for transplantation: An international perspective for policy and public health

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Proceedings of the 2014 A.S.P.E.N. Research Workshop

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SitePainter: a tool for exploring biogeographical patterns

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Host genetics is associated with the gut microbial community membership rather than the structure

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Re-examining chemically defined liquid diets through the lens of the microbiome

Toni, T., Alverdy, J. C., & Gershuni, V. M. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-021-00519-0 · Cited by 21

Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka

Lai, K. P., Zhu, P., Boncan, D. A. T., Yang, L., Leung, C. C. T., Ho, J. C. H., Lin, X., Chan, T., Kong, R. Y. C., & Tse, W. K. F. (2022) · mSystems · doi:10.1128/msystems.00047-22 · Cited by 20

A tiny fraction of all species forms most of nature: Rarity as a sticky state

van Nes, E. H., Pujoni, D. G. F., Shetty, S. A., Straatsma, G., de Vos, W. M., & Scheffer, M. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2221791120 · Cited by 20

Immunostimulation in the treatment for chronic fatigue syndrome/myalgic encephalomyelitis

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Temporal variation of the microbiome is dependent on body region in a wild mammal (Tamiasciurus hudsonicus)

Bobbie, C. B., Mykytczuk, N., & Schulte‐Hostedde, A. I. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix081 · Cited by 20

Reproducibility of assessing fecal microbiota in chronic constipation

Parthasarathy, G., Chen, J., Chia, N., O’Connor, H. M., Gaskins, H. R., & Bharucha, A. E. (2017) · Neurogastroenterology & Motility · doi:10.1111/nmo.13172 · Cited by 20

MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes

Ma, W., Huang, C., Zhou, Y., Li, J., & Cui, Q. (2017) · Scientific Reports · doi:10.1038/srep40200 · Cited by 20

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification

Sayyari, E., Kawas, B., & Mirarab, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz394 · Cited by 20

Microbial community succession of submerged bones in an aquatic habitat

Kaszubinski, S. F., Receveur, J. P., Nestle, E. D., Pechal, J. L., & Benbow, M. E. (2022) · Journal of Forensic Sciences · doi:10.1111/1556-4029.15036 · Cited by 19

The gut microbiome and obstructive sleep apnea syndrome in children

Liu, W., Du, Q., Zhang, H., & Han, D. (2022) · Sleep Medicine · doi:10.1016/j.sleep.2022.09.022 · Cited by 21

The role of the oral microbiota in the causal effect of adjunctive antibiotics on clinical outcomes in stage III–IV periodontitis patients

Bardenhorst, S. K., Hagenfeld, D., Matern, J., Prior, K., Harks, I., Eickholz, P., Lorenz, K., Kim, T., Kocher, T., Meyle, J., et al. (2024) · Microbiome · doi:10.1186/s40168-024-01945-3 · Cited by 19

Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil

Xie, K., Deng, Y., Zhang, X., Wang, X., Kang, G., Bai, L., & Huang, H. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01796 · Cited by 21

Temporal instability of the post-surgical maxillary sinus microbiota

Koutsourelakis, I., Halderman, A. A., Khalil, S. M., Hittle, L. E., Mongodin, E. F., & Lane, A. P. (2018) · BMC Infectious Diseases · doi:10.1186/s12879-018-3272-9 · Cited by 20

Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology

Qian, G., & Ho, J. W. K. (2020) · Biophysical Reviews · doi:10.1007/s12551-020-00724-2 · Cited by 20

The infant gut microbiota at 12 months of age is associated with human milk exposure but not with maternal pre-pregnancy body mass index or infant BMI-for-age z-scores

Haddad, E. N., Sugino, K. Y., Kerver, J. M., Paneth, N., & Comstock, S. S. (2021) · Current Research in Physiology · doi:10.1016/j.crphys.2021.03.004 · Cited by 22

Host Microbiome Richness Predicts Resistance to Disturbance by Pathogenic Infection in a Vertebrate HostPreprint

Harrison, X. A., Price, S. J., Hopkins, K., Leung, W. T. M., Sergeant, C., & Garner, T. W. J. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/158428 · Cited by 19

A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease

Luna, P. N., Mansbach, J. M., & Shaw, C. A. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008473 · Cited by 17

A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity

Jing, G., Zhang, Y., Liu, L., Wang, Z., Sun, Z., Knight, R. D., Su, X., & Xu, J. (2021) · mSystems · doi:10.1128/msystems.00394-21 · Cited by 18

The Salivary Microbiome and Predicted Metabolite Production Are Associated with Barrett's Esophagus and High-Grade Dysplasia or Adenocarcinoma

Solfisburg, Q. S., Baldini, F., Baldwin-Hunter, B. L., Austin, G. I., Lee, H. H., Park, H., Freedberg, D. E., Lightdale, C. J., Korem, T., & Abrams, J. A. (2023) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-23-0652 · Cited by 19

Association of Host and Microbial Species Diversity across Spatial Scales in Desert Rodent Communities

Gavish, Y., Kedem, H., Messika, I., Cohen, C., Toh, E. C., Munro, D. B., Dong, Q., Fuqua, C., Clay, K., & Hawlena, H. (2014) · PLoS ONE · doi:10.1371/journal.pone.0109677 · Cited by 19

Rules of the game for microbiota

Faust, K., & Raes, J. (2016) · Nature · doi:10.1038/534182a · Cited by 18

Resources and tools for the high-throughput, multi-omic study of intestinal microbiota

Blanco‐Míguez, A., Fdez‐Riverola, F., Sánchez, B., & Lourenço, A. M. G. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx156 · Cited by 16

Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest

Wang, X., Lin, P., & Ho, J. W. K. (2018) · BMC Genomics · doi:10.1186/s12864-017-4340-z · Cited by 18

Approaches to Modulate Biofilm Ecology

Nascimento, M. M. (2019) · Dental Clinics of North America · doi:10.1016/j.cden.2019.07.002 · Cited by 18

The role of the gut microbiome in graft fibrosis after pediatric liver transplantation

Qin, T., Fu, J., & Verkade, H. J. (2020) · Human Genetics · doi:10.1007/s00439-020-02221-8 · Cited by 18

Investigating colonization patterns of the infant gut microbiome during the introduction of solid food and weaning from breastmilk: A cohort study protocol

Dizzell, S. E., Stearns, J. C., Li, J., van Best, N., Bervoets, L., Mommers, M., Penders, J., Morrison, K. M., & Hutton, E. K. (2021) · PLoS ONE · doi:10.1371/journal.pone.0248924 · Cited by 18

Proof-of-principle demonstration of endogenous circadian system and circadian misalignment effects on human oral microbiota

Chellappa, S. L., Engen, P. A., Naqib, A. D., Qian, J., Vujović, N., Rahman, N., Green, S. J., Garaulet, M., Keshavarzian, A., & Scheer, F. A. J. L. (2022) · Kölner Universitäts PublikationsServer (Universität zu Köln) · Cited by 18

Disentangling microbial associations from hidden environmental and technical factors via latent graphical modelsPreprint

Kurtz, Z. D., Bonneau, R., & Müller, C. L. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2019.12.21.885889 · Cited by 19

Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis *,†,‡

Kaszubinski, S. F., Pechal, J. L., Schmidt, C. J., Jordan, H. R., Benbow, M. E., & Meek, M. H. (2019) · Journal of Forensic Sciences · doi:10.1111/1556-4029.14213 · Cited by 18

EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies

Shahin, M., Ji, B. W., & Dixit, P. D. (2023) · npj Systems Biology and Applications · doi:10.1038/s41540-023-00285-6 · Cited by 16

Identification of microbiota dynamics using robust parameter estimation methods

Chung, M., Krueger, J., & Pop, M. (2017) · Mathematical Biosciences · doi:10.1016/j.mbs.2017.09.009 · Cited by 15

Robust and automatic definition of microbiome states

García-Jiménez, B., & Wilkinson, M. D. (2019) · PeerJ · doi:10.7717/peerj.6657 · Cited by 19

Cold Case Experiment Demonstrates the Potential Utility of Aquatic Microbial Community Assembly in Estimating a Postmortem Submersion Interval

Kaszubinski, S. F., Receveur, J. P., Wydra, B., Smiles, K., Wallace, J. R., Babcock, N. J., Weatherbee, C. R., & Benbow, M. E. (2020) · Journal of Forensic Sciences · doi:10.1111/1556-4029.14303 · Cited by 17

Microbial community shift under exposure of dredged sediments from a eutrophic bay

Nascimento, J. R., Easson, C., Jurelevicius, D. D. A., Lopez, J. V., Bidone, E. D., & Sabadini-Santos, E. (2020) · Environmental Monitoring and Assessment · doi:10.1007/s10661-020-08507-8 · Cited by 17

Microbial diversity through an oceanographic lens: refining the concept of ocean provinces through trophic‐level analysis and productivity‐specific length scales

Hörstmann, C., Buttigieg, P. L., John, U., Raes, E. J., Wolf-Gladrow, D. A., Bracher, A. U., & Waite, A. M. (2021) · Environmental Microbiology · doi:10.1111/1462-2920.15832 · Cited by 18

Advances in Machine Learning for Processing and Comparison of Metagenomic Data

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Bacterial community structure and function distinguish gut sites in captive red‐shanked doucs (Pygathrix nemaeus)

Clayton, J. B., Shields‐Cutler, R. R., Hoops, S., Al‐Ghalith, G. A., Sha, J. C. M., Johnson, T. J., & Knights, D. (2019) · American Journal of Primatology · doi:10.1002/ajp.22977 · Cited by 16

Clustering microbiome data using mixtures of logistic normal multinomial models

Fang, Y., & Subedi, S. D. (2023) · Scientific Reports · doi:10.1038/s41598-023-41318-8 · Cited by 17

Factors Influencing Microbiota in Modulating Vaccine Immune Response: A Long Way to Go

Ponziani, F. R., Coppola, G., Rio, P., Caldarelli, M., Borriello, R., Gambassi, G., Gasbarrini, A., & Cianci, R. (2023) · Vaccines · doi:10.3390/vaccines11101609 · Cited by 17

Oral microbiota as a biomarker for predicting the risk of malignancy in indeterminate pulmonary nodules: a prospective multicenter study

Ma, Q., Huang, C., He, J., Zeng, X. F., Qu, Y.-L., Xiang, H., Yang, Z., Mao, L., Zheng, R., Xiao, J., et al. (2024) · International Journal of Surgery · doi:10.1097/js9.0000000000002152 · Cited by 18

Maintenance of Distal Intestinal Structure in the Face of Prolonged Fasting: A Comparative Examination of Species From Five Vertebrate Classes

McCue, M. D., Passement, C. A., & Meyerholz, D. K. (2017) · The Anatomical Record · doi:10.1002/ar.23691 · Cited by 16

BioSankey : Visualization of Microbial Communities Over Time

Platzer, A., Polzin, J., Rembart, K., Han, P., Rauer, D., & Nußbaumer, T. (2018) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2017-0063 · Cited by 16

The Human Microbiome: Getting Personal Eachofusharborsauniquemicrobiome,anditscharacteristicsplayanimportant roleindifferentiatingusfromoneanother

Califf, K. J., González, A., Knight, R. D., & Caporaso, J. G. (2014) · doi:10.1128/microbe.9.410.1 · Cited by 16

Comparison of Meconium Microbiome in Dizygotic and Monozygotic Twins Born by Caesarean Section (CS)

Yang, J., Yao, S., Cheng, K., Xu, L., Hou, L., Wei, Y., Feng, H., Yu, X., Zhang, X., Tong, X.-M., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01139 · Cited by 16

Human Respiratory and Gut Microbiomes—Do They Really Contribute to Respiratory Health?

Durack, J., & Christophersen, C. T. (2020) · Frontiers in Pediatrics · doi:10.3389/fped.2020.00528 · Cited by 18

Having an Anthropocene Body

Mackenzie, A. (2013) · Body & Society · doi:10.1177/1357034x13506470 · Cited by 16

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiomePreprint

Shaiber, A., Willis, A. D., Delmont, T. O., Roux, S., Chen, L.-X., Schmid, A. C., Yousef, M., Watson, A. R., Lolans, K., Esen, Ö. C., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.29.069278 · Cited by 18

A seasonal study of a passive abandoned coalmine drainage remediation system reveals three distinct zones of contaminant levels and microbial communities

Valkanas, M. M., & Trun, N. J. (2018) · MicrobiologyOpen · doi:10.1002/mbo3.585 · Cited by 15

Technical versus biological variability in a synthetic human gut community

van de Velde, C., Joseph, C., Simoens, K., Raes, J., Bernaerts, K., & Faust, K. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2155019 · Cited by 14

Origins of scaling laws in microbial dynamics

Wang, X., & Liu, Y. (2023) · Physical Review Research · doi:10.1103/physrevresearch.5.013004 · Cited by 15

Matrix-entrapped fibers create ecological niches for gut bacterial growth

Bulut, N., Cantu-Jungles, T. M., Zhang, X., Mutlu, Z., Çakmak, M., & Hamaker, B. R. (2023) · Scientific Reports · doi:10.1038/s41598-023-27907-7 · Cited by 15

Effects of altitude on the gut microbiome and metabolomics of Sanhe heifers

Zhang, X., Wang, W., Cao, Z., Yang, H., Wang, Y., & Li, S. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1076011 · Cited by 15

Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem

Galla, G., Praeg, N., Colla, F., Rzehak, T., Illmer, P., Seeber, J., & Hauffe, H. C. (2023) · Scientific Reports · doi:10.1038/s41598-023-30916-1 · Cited by 16

Effect of ginger supplementation on the fecal microbiome in subjects with prior colorectal adenoma

Prakash, A., Rubin, N., Staley, C. M., Onyeaghala, G. C., Wen, Y., Shaukat, A., Milne, G. L., Straka, R. J., Church, T. R., & Prizment, A. E. (2024) · Scientific Reports · doi:10.1038/s41598-024-52658-4 · Cited by 15

Characterization of communal sink drain communities of a university campus

Withey, Z., Goodall, T., MacIntyre, S., & Gweon, H. S. (2021) · Environmental DNA · doi:10.1002/edn3.196 · Cited by 14

Heavy-tailed abundance distributions from stochastic Lotka-Volterra models

Descheemaeker, L., Grilli, J., & de Buyl, S. (2021) · Physical review. E · doi:10.1103/physreve.104.034404 · Cited by 15

IBDs and the pediatric age: Their peculiarities and the involvement of the microbiota

Cococcioni, L., Panelli, S., Varotto-Boccazzi, I., Carlo, D. D., Pistone, D., Leccese, G., Zuccotti, G., & Comandatore, F. (2020) · Digestive and Liver Disease · doi:10.1016/j.dld.2020.10.033 · Cited by 15

The long and the short of it: Nanopore based eDNA metabarcoding of marine vertebrates works; sensitivity and specificity depend on amplicon lengthsPreprint

Doorenspleet, K., Janse, M., Oosterbroek, S., Kamermans, P., Bos, O. G., Wurz, E., Murk, A. J., & Nijland, R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.26.470087 · Cited by 15

Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta‐Omics Data in Personalized and Precision Medicine

Oh, S., & Li, R. W. (2024) · Advanced Science · doi:10.1002/advs.202400458 · Cited by 15

Crystal ball – 2013

Curtis, T., Daran, J.-M. G., Pronk, J. T., Frey, J., Jansson, J. K., Robbins‐Pianka, A., Knight, R. D., Schnürer, A., Smets, B. F., Smid, E. J., et al. (2012) · Microbial Biotechnology · doi:10.1111/1751-7915.12014 · Cited by 15

Temporary establishment of bacteria from indoor plant leaves and soil on human skin

Mhuireach, G. Á., Fahimipour, A. K., Vandegrift, R., Muscarella, M. E., Hickey, R. J., Bateman, A. C., Wymelenberg, K. G. V. D., & Bohannan, B. J. M. (2022) · Environmental Microbiome · doi:10.1186/s40793-022-00457-7 · Cited by 16

Regional biogeography versus intra-annual dynamics of the root and soil microbiome

Bell-Dereske, L. P., Benucci, G. M. N., da Costa, P. B., Bonito, G., Friesen, M. L., Tiemann, L. K., & Evans, S. E. (2023) · Environmental Microbiome · doi:10.1186/s40793-023-00504-x · Cited by 14

Endomicrobiome of in vitro and natural plants deciphering the endophytes-associated secondary metabolite biosynthesis in Picrorhiza kurrooa , a Himalayan medicinal herb

Tamang, A., Swarnkar, M. K., Kumar, P., Kumar, D., Pandey, S. S., & Hallan, V. K. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.02279-23 · Cited by 14

A Catastrophic Biodiversity Loss in the Environment Is Being Replicated on the Skin Microbiome: Is This a Major Contributor to the Chronic Disease Epidemic?

Wallen-Russell, C., Pearlman, N., Wallen-Russell, S., Cretoiu, D., Thompson, D. C., & Voinea, S. C. (2023) · Microorganisms · doi:10.3390/microorganisms11112784 · Cited by 14

Effects of black soldier fly meal feeding on rainbow trout gut microbiota, immune-related gene expression, and Lactococcus petauri resistance

Sayramoğlu, H., Öztürk, R. Ç., Ustaoğlu, D., Terzi̇, Y., Yandı, İ., Kayis, S., Çapkın, E., & Altınok, İ. (2023) · Journal of Insects as Food and Feed · doi:10.1163/23524588-20230057 · Cited by 14

In vitro models of the human microbiota and microbiome

McDonald, J. A. K. (2017) · Emerging Topics in Life Sciences · doi:10.1042/etls20170045 · Cited by 17

Bio‐therapeutics from human milk: prospects and perspectives

Singh, K. S., Singh, B. P., Rokana, N., Singh, N., Kaur, J., Singh, A., & Panwar, H. (2021) · Journal of Applied Microbiology · doi:10.1111/jam.15078 · Cited by 16

Effect of xylanase and β-glucanase on growth performance, activity of digestive enzymes, digestibility, and microbiome diversity of juvenile Nile tilapia fed soybean meal and/or sorghum distillers dried grains with solubles-based diets

de Macêdo, É. S., Urbich, A. V., Nakamura, J. S. T., da Cruz, T. P., Panaczevicz, P. A. P., Wernick, B., Furuya, V. R. B., Pezzato, L. E., Gatlin, D. M., & Furuya, W. M. (2022) · Aquaculture · doi:10.1016/j.aquaculture.2022.739134 · Cited by 14

Human Gut Microbiota in Heart Failure: Trying to Unmask an Emerging Organ

PARASKEVAIDIS, I. A., Xanthopoulos, A. V., Tsougos, E., & Triposkiadis, F. K. (2023) · Biomedicines · doi:10.3390/biomedicines11092574 · Cited by 13

HuMiChip2 for strain level identification and functional profiling of human microbiomes

Tu, Q., Li, J., Shi, Z. J., Chen, Y., Lin, L., Li, J., Wang, H., Yan, J., Zhou, Q., Li, X., et al. (2016) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-016-7910-0 · Cited by 14

The Human Microbiome in Health and Disease

Arnold, W., Hill, E. S., Fei, N., Yee, A. L., Garcia, M. S., Cralle, L. E., & Gilbert, J. A. (2018) · Springer eBooks · doi:10.1007/978-3-319-96830-8_39 · Cited by 14

The power and pitfalls of Dirichlet-multinomial mixture models for ecological count dataPreprint

O’Brien, J. D., Record, N. R., & Countway, P. D. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/045468 · Cited by 13

Gut microbiome and diet contribute to ecological niche differentiation between argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) on the Qinghai-Tibet Plateau

Zhang, M., Liang, C., Li, B., Jiang, F., Song, P., Gu, H., Gao, H., Cai, Z., & Zhang, T. (2025) · Communications Biology · doi:10.1038/s42003-025-08185-7 · Cited by 13

Variable habitat conditions drive species covariation in the human microbiota

Fisher, C. K., Mora, T., & Walczak, A. M. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005435 · Cited by 14

MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis

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Evolutionary dynamics in a varying environment: Continuous versus discrete noise

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