Bacterial Community Variation in Human Body Habitats Across Space and Time
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Growing on You: The human gut and skin harbor diverse microbial communities that are known to vary strikingly among individuals. Here, Costello et al. (p. 1694 , published online 5 November) analyzed microbial diversity among several distinct body habitats (including the gut, mouth, inside the ears and nose, and skin) of the same person at different times. They found that body habitat had more influence on microbial community composition than temporal differences and variation among people. Some skin locations, such as the index finger, back of the knee, and sole of the foot, on occasion harbored higher microbial diversity than the gut or oral cavity.
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The fine structure of the healthy microbiota seems to be unique to individuals; intra-individual differences across time are typically much smaller than differences between individuals.
“the fine structure of the healthy microbiota seems to be unique to individuals; intra-individual differences across time are typically much smaller than differences between individuals (Caporaso et al., 2011;Costello et al., 2009).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Costello et al., 2009
Small day-to-day variations in microbiota composition are generally observed within individuals.
“Within individuals, small day-to-day variations in microbiota composition are generally observed (Costello et al., 2009), but these fluctuations become most obvious when we take a wider view across the lifespan (see Fig. 3).”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Costello et al., 2009
No differences were found in beta diversity; longitudinal fecal samples were more similar within patients than between patients, despite some drift over time in the Chaput study.
“Overall, no differences were identified in beta diversity since, as expected (19), longitudinal fecal samples were more similar within patients as compared to between patients, despite some drift with time in the Chaput study (Fig. S5A and S5C).”
From A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors (2021) · cites this paper as [19]
Short-term longitudinal samplings from half the donors found that individuals are more similar to themselves over time compared with others.
“Study of short-term longitudinal samplings from half the donors found that individuals are more similar to themselves over time compared with others (Costello et al., 2009; Flores et al., 2014; Mehta et al., 2018).”
From Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers (2021) · cites this paper as Costello et al., 2009
Sebaceous environments possess specifically adapted, perhaps lipophilic bacteria.
“Previous studies of skin environments have suggested that sebaceous environments possess specifically adapted, perhaps lipophilic bacteria (Costello et al., 2009; Grice et al., 2009).”
From Nasal Microenvironments and Interspecific Interactions Influence Nasal Microbiota Complexity and S. aureus Carriage (2013) · cites this paper as Costello et al., 2009
A common feature of microbial ecological studies of the anterior naris is dominance of Corynebacterium, Staphylococcus, and Propionibacterium species.
“A common feature of microbial ecological studies of the anterior naris has been the dominance of Corynebacterium, Staphylococcus, and Propionibacterium species (Costello et al., 2009; Frank et al., 2010; Grice et al., 2009; TheHumanMicrobiomeProjectConsortium, 2012; Zhou et al., 2013).”
From Nasal Microenvironments and Interspecific Interactions Influence Nasal Microbiota Complexity and S. aureus Carriage (2013) · cites this paper as Costello et al., 2009
Eruption of primary deciduous dentition introduces new substrata for microbial colonization, thus introducing ecological shifts within the oral microbiome.
“Eruption of primary deciduous dentition introduces new substrata for microbial colonization, thus introducing ecological shifts within the oral microbiome.130, 131”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [130]
Compared with other colonized body sites, the oral microbiome has the largest core set of microbes that are shared among unrelated individuals.
“The NIH Human Microbiome Project assessed the microbial compositions, encompassing both relative abundance and representative microbes, in 9 intraoral sites from 200 participants and found that, compared with other colonized body sites (such as the gut and the skin), the oral microbiome has the largest core set of microbes that are shared among unrelated individuals.130, 159”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [130]
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Cites
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227 · see citing works
Self-citationDiversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · see citing works
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823 · see citing works
Self-citationTurnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091 · see citing works
Self-citationDefining the normal bacterial flora of the oral cavity
Aas, J. A., Paster, B. J., Stokes, L. N., Olsen, I., & Dewhirst, F. E. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.11.5721-5732.2005 · Cited by 3,092 · see citing works
Microbial biogeography: putting microorganisms on the map
Martiny, J. B. H., Bohannan, B. J. M., Brown, J. H., Colwell, R. K., Fuhrman, J. A., Green, J. L., Horner‐Devine, M. C., Kane, M. D., Krumins, J. A., Kuske, C. R., et al. (2006) · Nature Reviews Microbiology · doi:10.1038/nrmicro1341 · Cited by 2,995 · see citing works
Topographical and Temporal Diversity of the Human Skin Microbiome
Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., Program, N. C. S., Bouffard, G. G., Blakesley, R. W., Murray, P. R., et al. (2009) · Science · doi:10.1126/science.1171700 · Cited by 2,953 · see citing works
Lozupone, C., Hamady, M., Kelley, S. T., & Knight, R. D. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01996-06 · Cited by 2,717 · see citing works
Self-citationMICROBIAL ECOLOGY OF THE GASTROINTESTINAL TRACT
Savage, D. C. (1977) · Annual Review of Microbiology · doi:10.1146/annurev.mi.31.100177.000543 · Cited by 2,436 · see citing works
An ecological and evolutionary perspective on human–microbe mutualism and disease
Dethlefsen, L., McFall-Ngai, M., & Relman, D. A. (2007) · Nature · doi:10.1038/nature06245 · Cited by 1,660 · see citing works
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
Hamady, M., Walker, J. J., Harris, J. K., Gold, N. J., & Knight, R. (2008) · Nature Methods · doi:10.1038/nmeth.1184 · Cited by 1,310 · see citing works
Self-citationThe influence of sex, handedness, and washing on the diversity of hand surface bacteria
Fierer, N., Hamady, M., Lauber, C. L., & Knight, R. D. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807920105 · Cited by 1,100 · see citing works
Self-citationRawls, J. F., Mahowald, M. A., Ley, R. E., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.08.043 · Cited by 962 · see citing works
Self-citationMolecular analysis of human forearm superficial skin bacterial biota
Gao, Z., Tseng, C., Pei, Z., & Blaser, M. J. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607077104 · Cited by 660 · see citing works
Lederberg, J. (2000) · Science · doi:10.1126/science.288.5464.287 · Cited by 523 · see citing works
Global diversity in the human salivary microbiomePreprint
Nasidze, I., Li, J., Quinque, D., Tang, K., & Stoneking, M. (2009) · Genome Research · doi:10.1101/gr.084616.108 · Cited by 464 · see citing works
Bacteriology of humans: an ecological perspective
(2008) · Choice Reviews Online · doi:10.5860/choice.46-2078 · Cited by 123 · see citing works
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Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · see citing works
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 · see citing works
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
Self-citationGlobal patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,633 · see citing works
Self-citationPredictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116 · see citing works
Self-citationUltra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839 · see citing works
Self-citationEnterotypes of the human gut microbiome
MetaHIT Consortium (additional members), Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., et al. (2011) · Nature · doi:10.1038/nature09944 · Cited by 7,548 · see citing works
Diversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533 · see citing works
Self-citationRole of the microbiota in immunity and inflammation.
Belkaid, Y., & Hand, T. W. (2014) · Cell · doi:10.1016/j.cell.2014.03.011 · Cited by 5,385 · see citing works
Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286 · see citing works
Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774 · see citing works
Self-citationRichness of human gut microbiome correlates with metabolic markers
Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature · doi:10.1038/nature12506 · Cited by 4,662 · see citing works
Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis
Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., Britt, E. B., Fu, X., Wu, Y., Li, L., et al. (2013) · Nature Medicine · doi:10.1038/nm.3145 · Cited by 4,386 · see citing works
Vaginal microbiome of reproductive-age women
Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S. S. K., McCulle, S. L., Karlebach, S., Gorle, R., Russell, J., Tacket, C. O., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002611107 · Cited by 4,254 · see citing works
Microbial interactions: from networks to models
Faust, K., & Raes, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2832 · Cited by 4,138 · see citing works
Proteobacteria: Microbial signature of dysbiosis in gut microbiota
Shin, N.-R., Whon, T. W., & Bae, J.-W. (2015) · Trends in Biotechnology · doi:10.1016/j.tibtech.2015.06.011 · Cited by 3,954 · see citing works
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788 · see citing works
Self-citationThe impact of the gut microbiota on human health: an integrative view
Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012) · Cell · doi:10.1016/j.cell.2012.01.035 · Cited by 3,710 · see citing works
Self-citationIntroduction to the human gut microbiota
Thursby, E., & Juge, N. (2017) · Biochemical Journal · doi:10.1042/bcj20160510 · Cited by 3,600 · see citing works
The human microbiome: at the interface of health and disease
Cho, I., & Blaser, M. J. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3182 · Cited by 3,449 · see citing works
Grice, E. A., & Segre, J. A. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2537 · Cited by 3,143 · see citing works
Using network analysis to explore co-occurrence patterns in soil microbial communities
Barberán, A., Bates, S. T., Casamayor, E. O., & Fierer, N. (2012) · The ISME Journal · doi:10.1038/ismej.2011.119 · Cited by 3,044 · see citing works
Self-citationByrd, A. L., Belkaid, Y., & Segre, J. A. (2018) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.157 · Cited by 2,806 · see citing works
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
Morgan, X. C., Tickle, T. L., Sokol, H., Gevers, D., Devaney, K. L., Ward, D. V., Reyes, J. A., Shah, S. A., LeLeiko, N., Snapper, S. B., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-9-r79 · Cited by 2,713 · see citing works
Succession of microbial consortia in the developing infant gut microbiome
Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000081107 · Cited by 2,540 · see citing works
Self-citationGut–brain axis: How the microbiome influences anxiety and depression
Foster, J. A., & McVey Neufeld, K.-A. (2013) · Trends in Neurosciences · doi:10.1016/j.tins.2013.01.005 · Cited by 2,460 · see citing works
Taxonomy, Physiology, and Natural Products of Actinobacteria
Barka, E. A., Vatsa, P., Sanchez, L., Vaillant‐Gaveau, N., Jacquard, C., Klenk, H., Clément, C., Ouhdouch, Y., & van Wezel, G. P. (2016) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00019-15 · Cited by 2,244 · see citing works
Baumgart, D. C., & Sandborn, W. J. (2012) · The Lancet · doi:10.1016/s0140-6736(12)60026-9 · Cited by 2,205 · see citing works
The role of the gut microbiota in nutrition and health
Flint, H. J., Scott, K. P., Louis, P., & Duncan, S. H. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.156 · Cited by 2,203 · see citing works
The NIH Human Microbiome ProjectPreprint
The NIH HMP Working Group, Peterson, J. L., Garges, S., Giovanni, M. Y., McInnes, P., Wang, L., Schloss, J. A., Bonazzi, V. R., McEwen, J. E., Wetterstrand, K. A., et al. (2009) · Genome Research · doi:10.1101/gr.096651.109 · Cited by 2,092 · see citing works
Normalization and microbial differential abundance strategies depend upon data characteristics
Weiss, S. J., Xu, Z. Z., Peddada, S. D., Amir, A., Bittinger, K. L., González, A., Lozupone, C., Zaneveld, J., Vázquez‐Baeza, Y., Birmingham, A., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0237-y · Cited by 2,121 · see citing works
Self-citationThe Long-Term Stability of the Human Gut Microbiota
Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058 · see citing works
Self-citationBest practices for analysing microbiomes
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030 · see citing works
Self-citationBayesian community-wide culture-independent microbial source tracking
Knights, D., Kuczynski, J., Charlson, E. S., Zaneveld, J., Mozer, M. C., Collman, R. G., Bushman, F. D., Knight, R. D., & Kelley, S. T. (2011) · Nature Methods · doi:10.1038/nmeth.1650 · Cited by 1,839 · see citing works
Self-citationKong, H. H., Oh, J., Deming, C., Conlan, S., Grice, E. A., Beatson, M. A., Nomicos, E., Polley, E. C., Komarow, H. D., Program, N. C. S., et al. (2012) · Genome Research · doi:10.1101/gr.131029.111 · Cited by 1,808 · see citing works
You are what you eat: Diet, health and the gut microbiota
Zmora, N., Suez, J., & Elinav, E. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0061-2 · Cited by 1,792 · see citing works
Schwabe, R. F., & Jobin, C. (2013) · Nature Reviews Cancer · doi:10.1038/nrc3610 · Cited by 1,689 · see citing works
Coagulase-Negative Staphylococci
Becker, K., Heilmann, C., & Peters, G. (2014) · Clinical Microbiology Reviews · doi:10.1128/cmr.00109-13 · Cited by 1,677 · see citing works
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., Bergerat, A., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2010.118 · Cited by 1,632 · see citing works
The interplay between the intestinal microbiota and the brain
Collins, S. M., Surette, M., & Bercik, P. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2876 · Cited by 1,611 · see citing works
Unravelling the effects of the environment and host genotype on the gut microbiome
Spor, A., Koren, O., & Ley, R. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2540 · Cited by 1,509 · see citing works
Exposure to Environmental Microorganisms and Childhood Asthma
Ege, M. J., Mayer, M., Normand, A.-C., Genuneit, J., Cookson, W. O. C. M., Braun-Fahrländer, C., Heederik, D., Piarroux, R., & von Mutius, E. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1007302 · Cited by 1,529 · see citing works
Microbial co-occurrence relationships in the human microbiome
Faust, K., Sathirapongsasuti, J. F., Izard, J., Segata, N., Gevers, D., Raes, J., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002606 · Cited by 1,527 · see citing works
Gut/brain axis and the microbiota
Mayer, E. A., Tillisch, K., & Gupta, A. (2015) · Journal of Clinical Investigation · doi:10.1172/jci76304 · Cited by 1,503 · see citing works
How glycan metabolism shapes the human gut microbiota
Koropatkin, N. M., Cameron, E. A., & Martens, E. C. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2746 · Cited by 1,419 · see citing works
The Integrative Human Microbiome Project
The Integrative HMP (iHMP) Research Network Consortium, Proctor, L. M., Creasy, H. H., Fettweis, J. M., Lloyd-Price, J., Mahurkar, A., Zhou, W., Buck, G. A., Snyder, M. P., Strauss, J. F., et al. (2019) · Nature · doi:10.1038/s41586-019-1238-8 · Cited by 1,381 · see citing works
The composition of the gut microbiota throughout life, with an emphasis on early life
Rodríguez, J. M., Murphy, K., Stanton, C., Ross, R. P., Kober, O. I., Juge, N., Avershina, E., Rudi, K., Narbad, A., Jenmalm, M. C., et al. (2015) · Microbial Ecology in Health and Disease · doi:10.3402/mehd.v26.26050 · Cited by 1,320 · see citing works
EMPeror: a tool for visualizing high-throughput microbial community data
Vázquez‐Baeza, Y., Pirrung, M., Gonzalez, A., & Knight, R. D. (2013) · GigaScience · doi:10.1186/2047-217x-2-16 · Cited by 1,272 · see citing works
Self-citationJumpertz, R., Le, D. S., Turnbaugh, P. J., Trinidad, C., Bogardus, C., Gordon, J. I., & Krakoff, J. (2011) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.110.010132 · Cited by 1,232 · see citing works
Self-citationThe oral microbiome – an update for oral healthcare professionals
Kilian, M., Chapple, I. L. C., Hannig, M., Marsh, P. D., Meuric, V., Pedersen, A. M. L., Tonetti, M. S., Wade, W. G., & Zaura, E. (2016) · British Dental Journal · doi:10.1038/sj.bdj.2016.865 · Cited by 1,269 · see citing works
Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012) · Nutrition Reviews · doi:10.1111/j.1753-4887.2012.00493.x · Cited by 1,255 · see citing works
Self-citationPaneth cells, antimicrobial peptides and maintenance of intestinal homeostasis
Bevins, C. L., & Salzman, N. H. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2546 · Cited by 1,238 · see citing works
Dynamics of the human gut microbiome in inflammatory bowel disease
Halfvarson, J., Brislawn, C. J., Lamendella, R., Vázquez-Baeza, Y., Walters, W. A., Bramer, L. M., D'Amato, M., Bonfiglio, F., McDonald, D., Gonzalez, A., et al. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.4 · Cited by 1,204 · see citing works
Self-citationHuman oral, gut, and plaque microbiota in patients with atherosclerosis
Koren, O., Spor, A., Felin, J., Fåk, F., Stombaugh, J., Tremaroli, V., Behre, C. J., Knight, R., Fagerberg, B., Ley, R. E., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011383107 · Cited by 1,196 · see citing works
Self-citationJakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009836 · Cited by 1,160 · see citing works
Topographic diversity of fungal and bacterial communities in human skin
NIH Intramural Sequencing Center Comparative Sequencing Program, Findley, K., Oh, J., Yang, J., Conlan, S., Deming, C., Meyer, J. A., Schoenfeld, D., Nomicos, E., Park, M., et al. (2013) · Nature · doi:10.1038/nature12171 · Cited by 1,206 · see citing works
Manichanh, C., Borruel, N., Casellas, F., & Guarner, F. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.152 · Cited by 1,160 · see citing works
Clokie, M. R. J., Millard, A. D., Letarov, A. V., & Heaphy, S. (2011) · Bacteriophage · doi:10.4161/bact.1.1.14942 · Cited by 1,154 · see citing works
Biogeography and individuality shape function in the human skin metagenome
Program, N. C. S., Oh, J., Byrd, A. L., Deming, C., Conlan, S., Kong, H. H., & Segre, J. A. (2014) · Nature · doi:10.1038/nature13786 · Cited by 1,148 · see citing works
Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract
Charlson, E. S., Bittinger, K., Haas, A. R., Fitzgerald, A. S., Frank, I., Yadav, A., Bushman, F. D., & Collman, R. G. (2011) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201104-0655oc · Cited by 1,144 · see citing works
Moving pictures of the human microbiome
Caporaso, J. G., Lauber, C. L., Costello, E. K., Berg-Lyons, D., Gonzalez, A., Stombaugh, J., Knights, D., Gajer, P., Ravel, J., Fierer, N., et al. (2011) · Genome Biology · doi:10.1186/gb-2011-12-5-r50 · Cited by 1,138 · see citing works
Self-citationProbiotics, gut microbiota, and their influence on host health and disease
Sánchez, B., Delgado, S., Blanco‐Míguez, A., Lourenço, A., Gueimonde, M., & Margolles, A. (2017) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201600240 · Cited by 1,104 · see citing works
Compartmentalized Control of Skin Immunity by Resident Commensals
Naik, S., Bouladoux, N., Wilhelm, C., Molloy, M. J., Salcedo, R., Kastenmuller, W., Deming, C., Quinones, M., Koo, L., Conlan, S., et al. (2012) · Science · doi:10.1126/science.1225152 · Cited by 1,092 · see citing works
Cohabiting family members share microbiota with one another and with their dogs
Song, S. J., Lauber, C. L., Costello, E. K., Lozupone, C., Humphrey, G., Berg-Lyons, D., Caporaso, J. G., Knights, D., Clemente, J. C., Nakielny, S., et al. (2013) · eLife · doi:10.7554/elife.00458 · Cited by 1,075 · see citing works
Self-citationSegata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., Huttenhower, C., & Izard, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-6-r42 · Cited by 1,076 · see citing works
Chu, D. M., Ma, J., Prince, A. L., Antony, K. M., Seferovic, M. D., & Aagaard, K. M. (2017) · Nature Medicine · doi:10.1038/nm.4272 · Cited by 1,063 · see citing works
Environmental biodiversity, human microbiota, and allergy are interrelated
Hanski, I., von Hertzen, L., Fyhrquist, N., Koskinen, K., Torppa, K., Laatikainen, T., Karisola, P., Auvinen, P., Paulin, L., Mäkelä, M. J., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205624109 · Cited by 1,063 · see citing works
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Abubucker, S., Segata, N., Goll, J. B., Schubert, A. M., Izard, J., Cantarel, B. L., Rodriguez-Mueller, B., Zucker, J., Thiagarajan, M., Henrissat, B., et al. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002358 · Cited by 1,050 · see citing works
The resilience of the intestinal microbiota influences health and disease
Sommer, F., Anderson, J. M., Bharti, R., Raes, J., & Rosenstiel, P. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.58 · Cited by 1,058 · see citing works
Defining seasonal marine microbial community dynamics
Gilbert, J. A., Steele, J. A., Caporaso, J. G., Steinbrück, L., Reeder, J., Temperton, B., Huse, S. M., McHardy, A. C., Knight, R. D., Joint, I. R., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2011.107 · Cited by 1,044 · see citing works
Self-citationHuman Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer
Chen, W., Liu, F., Ling, Z., Tong, X., & Xiang, C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0039743 · Cited by 1,029 · see citing works
Temporal Stability of the Human Skin Microbiome
Oh, J., Byrd, A. L., Park, M., Kong, H. H., & Segre, J. A. (2016) · Cell · doi:10.1016/j.cell.2016.04.008 · Cited by 1,036 · see citing works
Willing, B. P., Dicksved, J., Halfvarson, J., Andersson, A. F., Lucio, M., Zheng, Z., Järnerot, G., Tysk, C., Jansson, J. K., & Engstrand, L. (2010) · Gastroenterology · doi:10.1053/j.gastro.2010.08.049 · Cited by 1,032 · see citing works
Microbes, Metabolites, and the Gut-Lung Axis
Dang, A. T., & Marsland, B. J. (2019) · Mucosal Immunology · doi:10.1038/s41385-019-0160-6 · Cited by 1,028 · see citing works
Vandeputte, D., Falony, G., Vieira-Silva, S., Tito, R. Y., Joossens, M., & Raes, J. (2016) · Gut · doi:10.1136/gutjnl-2015-309618 · Cited by 1,028 · see citing works
The Intestinal Microbiome in Early Life: Health and Disease
Arrieta, M.-C., Stiemsma, L. T., Amenyogbe, N., Brown, E. M., & Finlay, B. (2014) · Frontiers in Immunology · doi:10.3389/fimmu.2014.00427 · Cited by 1,024 · see citing works
Hidden Fungi, Emergent Properties: Endophytes and Microbiomes
Porras‐Alfaro, A., & Bayman, P. (2011) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-080508-081831 · Cited by 975 · see citing works
Epithelial antimicrobial defence of the skin and intestine
Gallo, R. L., & Hooper, L. V. (2012) · Nature reviews. Immunology · doi:10.1038/nri3228 · Cited by 959 · see citing works
Host lifestyle affects human microbiota on daily timescales
David, L. A., Materna, A. C., Friedman, J., Campos-Baptista, M. I., Blackburn, M. C., Perrotta, A., Erdman, S. E., & Alm, E. J. (2014) · Genome biology · doi:10.1186/gb-2014-15-7-r89 · Cited by 950 · see citing works
The gut microbiome: Relationships with disease and opportunities for therapy
Durack, J., & Lynch, S. V. (2018) · The Journal of Experimental Medicine · doi:10.1084/jem.20180448 · Cited by 955 · see citing works
Burns, A. R., Stephens, W. Z., Stagaman, K., Wong, S., Rawls, J. F., Guillemin, K. J., & Bohannan, B. J. M. (2015) · The ISME Journal · doi:10.1038/ismej.2015.142 · Cited by 943 · see citing works
A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects
Tjalsma, H., Boleij, A., Marchesi, J. R., & Dutilh, B. E. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2819 · Cited by 903 · see citing works
Dynamics and associations of microbial community types across the human body
Ding, T., & Schloss, P. D. (2014) · Nature · doi:10.1038/nature13178 · Cited by 885 · see citing works
Microbiota and diabetes: an evolving relationship
Tilg, H., & Moschen, A. R. (2014) · Gut · doi:10.1136/gutjnl-2014-306928 · Cited by 853 · see citing works
Effects of gut microbes on nutrient absorption and energy regulation
Krajmalnik‐Brown, R., Ilhan, Z., Kang, D., & DiBaise, J. K. (2012) · Nutrition in Clinical Practice · doi:10.1177/0884533611436116 · Cited by 852 · see citing works
Guinane, C. M., & Cotter, P. D. (2013) · Therapeutic Advances in Gastroenterology · doi:10.1177/1756283x13482996 · Cited by 846 · see citing works
The human milk microbiota: Origin and potential roles in health and disease
Fernández, L., Langa, S., Martín, V., Maldonado‐Barragán, A., Jiménez, E., Martı́n, R., & Rodríguez, J. M. (2012) · Pharmacological Research · doi:10.1016/j.phrs.2012.09.001 · Cited by 849 · see citing works
The gut microbiota and obesity: from correlation to causality
Zhao, L. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3089 · Cited by 847 · see citing works
Bäckhed, F., Fraser, C. M., Ringel, Y., Sanders, M. E., Sartor, R. B., Sherman, P. M., Versalovic, J., Young, V., & Finlay, B. B. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.10.012 · Cited by 836 · see citing works
Commensal–dendritic-cell interaction specifies a unique protective skin immune signature
Naik, S., Bouladoux, N., Linehan, J. L., Han, S.-J., Harrison, O. J., Wilhelm, C., Conlan, S., Himmelfarb, S., Byrd, A. L., Deming, C., et al. (2015) · Nature · doi:10.1038/nature14052 · Cited by 820 · see citing works
Host genetic variation impacts microbiome composition across human body sites
Blekhman, R., Goodrich, J. K., Huang, K., Sun, Q., Bukowski, R., Bell, J. T., Spector, T. D., Keinan, A., Ley, R. E., Gevers, D., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0759-1 · Cited by 745 · see citing works
Sartor, R. B., & Wu, G. D. (2017) · Gastroenterology · doi:10.1053/j.gastro.2016.10.012 · Cited by 808 · see citing works
Sex differences and hormonal effects on gut microbiota composition in mice
Org, E., Mehrabian, M., Parks, B. W., Shipkova, P., Liu, X., Drake, T. A., & Lusis, A. J. (2016) · Gut Microbes · doi:10.1080/19490976.2016.1203502 · Cited by 796 · see citing works
Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne
Fitz‐Gibbon, S. T., Tomida, S., Chiu, B.-H., Nguyen, L., Du, C., Liu, M., Elashoff, D. A., Erfe, M. C. B., Loncaric, A., Kim, J., et al. (2013) · Journal of Investigative Dermatology · doi:10.1038/jid.2013.21 · Cited by 777 · see citing works
Characterization of the Diversity and Temporal Stability of Bacterial Communities in Human Milk
Hunt, K. M., Foster, J. A., Forney, L. J., Schütte, U. M. E., Beck, D. L., Abdo, Z., Fox, L. K., Williams, J. E., McGuire, M. K., & McGuire, M. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021313 · Cited by 765 · see citing works
Oral microbiomes: more and more importance in oral cavity and whole body
Gao, L., Xu, T., Huang, G., Jiang, S., Gu, Y., & Chen, F. (2018) · Protein & Cell · doi:10.1007/s13238-018-0548-1 · Cited by 770 · see citing works
The human microbiome: Our second genome
Grice, E. A., & Segre, J. A. (2012) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090711-163814 · Cited by 759 · see citing works
The oral microbiome: Role of key organisms and complex networks in oral health and disease
Sedghi, L., DiMassa, V., Harrington, A., Lynch, S. V., & Kapila, Y. L. (2021) · Periodontology 2000 · doi:10.1111/prd.12393 · Cited by 755 · see citing works
How bacterial pathogens colonize their hosts and invade deeper tissues
Ribet, D., & Cossart, P. (2015) · Microbes and Infection · doi:10.1016/j.micinf.2015.01.004 · Cited by 747 · see citing works
Llewellyn, M. S., Boutin, S., Hoseinifar, S. H., & Derôme, N. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00207 · Cited by 742 · see citing works
- Authors
- Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R.
- Affiliations
- University of Colorado Boulder (US)
- Cooperative Institute for Research in Environmental Sciences (US)
- Washington University in St. Louis (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Knight, Rob
- Venue
- Science
- Published
- 2009-12-18
- Volume
- 326
- Issue
- 5960
- Pages
- 1694-1697
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3602444
- OpenAlex
- W1989889539
- Cited by
- 3,231
- References
- 17
- Citations by year
- 2026: 83 · 2025: 145 · 2024: 160 · 2023: 166 · 2022: 197 · 2021: 230 · 2020: 234 · 2019: 217 · 2018: 233 · 2017: 267 · 2016: 210 · 2015: 217 · 2014: 197 · 2013: 237 · 2012: 192
- FWCI
- 58.17
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- Crohn's and Colitis Foundation
- National Institute of General Medical Sciences (T32GM065103)
- National Institute of Diabetes and Digestive and Kidney Diseases (P50DK064540, P01DK078669, DK78669, DK64540)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Health Sciences › Medicine › Dermatology › Dermatology and Skin Diseases
- Keywords
- human microbiome, bacterial community composition, biogeography, skin microbiome, gut microbiota, oral microbiota, temporal stability, interpersonal variability, community assembly, healthy adults
- MeSH terms
- Adult, Bacteria, DNA, Bacterial, DNA, Ribosomal, Ear Canal, Feces, Female, Hair, Humans, Male, Middle Aged, Mouth, Nose, Phylogeny, RNA, Ribosomal, 16S, Skin, Time Factors, Cluster Analysis, Genes, rRNA, Principal Component Analysis, Biodiversity, Metagenome
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