US immigration westernizes the human gut microbiome
Open accessAbstract
Many US immigrant populations develop metabolic diseases post immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of US immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the United States, including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 US-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the United States is associated with immediate loss of gut microbiome diversity and function in which US-associated strains and functions displace native strains and functions. These effects increase with duration of US residence and are compounded by obesity and across generations.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Westernization of the gut microbiota in U.S. immigrants is accompanied by loss of microbial functions and taxa, deteriorating health markers, increased BMI, and rising inflammatory markers.
“Rapid “westernization” of the microbiota has been observed in U.S. immigrants, with loss of microbial functions and taxa accompanied by deteriorating markers of host health, increased BMI, and rising inflammatory markers typical in industrialized populations (Vangay et al., 2018; Sonnenburg and Sonnenburg, 2019).”
From Gut-microbiota-targeted diets modulate human immune status (2021) · cites this paper as Vangay et al., 2018
The data suggest that carbohydrate degradation by participants' microbiota was insufficient to process the increased fiber consumption, consistent with analyses of industrialized microbiomes.
“These data suggest the carbohydrate degradation by participants’ microbiota was insufficient to process the increased fiber consumption, consistent with analyses of industrialized microbiome (Smits et al., 2017; Vangay et al., 2018).”
From Gut-microbiota-targeted diets modulate human immune status (2021) · cites this paper as Vangay et al., 2018
A 2018 study of US first and second-generation immigrants observed loss of fibre-degrading bacterial enzymes that may have been associated with a reduction in dietary fibre consumption after migration from Southeast Asia.
“A 2018 study of US first and second-generation immigrants were observed to have lost fibre-degrading bacterial enzymes that may have been associated with a reduction in dietary fibre consumption after migration from Southeast Asia [104].”
From Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration (2019) · cites this paper as [104]
Consumption of Western-style diets rich in processed, fried and sugar-rich foods and low in plant foods with their constituent fiber and polyphenols can lead to the loss of microbial diversity and function as well as the extinction of important beneficial microbes and expansion of opportunistic pathogens.
“It is evident that the consumption of Western-style diets rich in processed, fried and sugar-rich foods and low in plant foods with their constituent fiber and polyphenols can lead to the loss of microbial diversity and function as well as the extinction of important beneficial microbes and expansion of opportunistic pathogens (13,14), with far-reaching consequences for human health.”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [14]
Long-term consumption of a Western diet in humans and animals can lead to extinction of beneficial microbes, decrease bacterial diversity, and drive the microbiota to a predominant Bacteroides-driven enterotype.
“Long-term consumption of a Western diet in humans and animals can lead to the extinction of beneficial microbes, decrease bacterial diversity, and drive the microbiota to a predominant Bacteroides-driven enterotype (13,14,116,88).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [14]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Cytoscape: A software Environment for integrated models of biomolecular interaction networks
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works
Self-citationProkka: rapid prokaryotic genome annotation
Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,512 · see citing works
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100 · 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
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works
Self-citationLinking long-term dietary patterns with gut microbial enterotypes
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., Knight, R., et al. (2011) · Science · doi:10.1126/science.1208344 · Cited by 6,513 · see citing works
Self-citationO'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357 · see citing works
The carbohydrate-active enzymes database (CAZy) in 2013
Lombard, V., Ramulu, H. G., Drula, É., Coutinho, P. M., & Henrissat, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1178 · Cited by 6,355 · see citing works
De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1005963107 · Cited by 5,579 · see citing works
Conservation evaluation and phylogenetic diversity
Faith, D. (1992) · Biological Conservation · doi:10.1016/0006-3207(92)91201-3 · Cited by 5,495 · see citing works
The United States Department of Agriculture
True, A. C. (1912) · The Annals of the American Academy of Political and Social Science · doi:10.1177/000271621204000113 · Cited by 5,104 · see citing works
Richness 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
metaSPAdes: a new versatile metagenomic assembler
Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496 · see citing works
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395 · see citing works
The Treatment-Naive Microbiome in New-Onset Crohn’s Disease
Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S. J., Yassour, M., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.02.005 · Cited by 3,220 · see citing works
Self-citationGut metagenome in European women with normal, impaired and diabetic glucose control
Karlsson, F. H., Tremaroli, V., Nookaew, I., Bergström, G., Behre, C. J., Fagerberg, B., Nielsen, J., & Bäckhed, F. (2013) · Nature · doi:10.1038/nature12198 · Cited by 3,115 · see citing works
The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey, F. E., Knight, R., & Gordon, J. I. (2009) · Science Translational Medicine · doi:10.1126/scitranslmed.3000322 · Cited by 3,058 · cited 1× · see citing works
“, 2011) and can also respond quickly to dramatic dietary changes (David et al., 2014; Turnbaugh et al., 2009a).”
BackgroundEnvironment dominates over host genetics in shaping human gut microbiota
Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., et al. (2018) · Nature · doi:10.1038/nature25973 · Cited by 2,859 · see citing works
UniFrac: an effective distance metric for microbial community comparison
Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J., & Knight, R. (2011) · The ISME Journal · doi:10.1038/ismej.2010.133 · Cited by 2,825 · see citing works
Self-citationMicrobial degradation of complex carbohydrates in the gut
Flint, H. J., Scott, K. P., Duncan, S. H., Louis, P., & Forano, E. (2012) · Gut Microbes · doi:10.4161/gmic.19897 · Cited by 2,331 · see citing works
Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
Muegge, B. D., Kuczynski, J., Knights, D., Clemente, J. C., González, A., Fontana, L., Henrissat, B., Knight, R., & Gordon, J. I. (2011) · Science · doi:10.1126/science.1198719 · Cited by 1,988 · see citing works
Self-citationUniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H., & the UniProt Consortium (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu739 · Cited by 1,928 · see citing works
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters
Weber, T., Blin, K., Duddela, S., Krug, D., Kim, H. U., Bruccoleri, R. E., Lee, S. Y., Fischbach, M. A., Müller, R., Wohlleben, W., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv437 · Cited by 1,866 · see citing works
dbCAN: a web resource for automated carbohydrate-active enzyme annotation
Yin, Y., Mao, X., Yang, J., Chen, X., Mao, F., & Xu, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks479 · Cited by 1,800 · see citing works
Diet-induced extinctions in the gut microbiota compound over generations
Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016) · Nature · doi:10.1038/nature16504 · Cited by 1,730 · see citing works
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota
Kaoutari, A. E., Armougom, F., Gordon, J. I., Raoult, D., & Henrissat, B. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro3050 · Cited by 1,683 · see citing works
High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity
Hildebrandt, M. A., Hoffmann, C., Sherrill–Mix, S. A., Keilbaugh, S. A., Hamady, M., Chen, Y., Knight, R., Ahima, R. S., Bushman, F., & Wu, G. D. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.08.042 · Cited by 1,576 · cited 1× · see citing works
“The gut microbiome plays a critical role in host metabolism and is heavily influenced by an individual’s long-term diet (Hildebrandt et al., 2009; Wu et al., 2011) and can also respond quickly to dramatic dietary changes (David et al.”
BackgroundAntibiotics, birth mode, and diet shape microbiome maturation during early life
Bokulich, N. A., Chung, J., Battaglia, T., Henderson, N., Jay, M., Li, H., D. Lieber, A., Wu, F., Perez-Perez, G. I., Chen, Y., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad7121 · Cited by 1,469 · see citing works
Gut microbiome of the Hadza hunter-gatherers
Schnorr, S. L., Candela, M., Rampelli, S., Centanni, M., Consolandi, C., Basaglia, G., Turroni, S., Biagi, E., Peano, C., Severgnini, M., et al. (2014) · Nature Communications · doi:10.1038/ncomms4654 · Cited by 1,317 · see citing works
antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
Blin, K., Wolf, T., Chevrette, M. G., Lu, X., Schwalen, C. J., Kautsar, S. A., Duran, H. G. S., Santos, E. L. C. D. L., Kim, H. U., Nave, M., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx319 · Cited by 1,159 · 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
Chang, J. Y., Antonopoulos, D. A., Kalra, A., Tonelli, A., Khalife, W. T., Schmidt, T. M., & Young, V. B. (2008) · The Journal of Infectious Diseases · doi:10.1086/525047 · Cited by 1,010 · see citing works
The core gut microbiome, energy balance and obesity
Turnbaugh, P. J., & Gordon, J. I. (2009) · The Journal of Physiology · doi:10.1113/jphysiol.2009.174136 · Cited by 993 · see citing works
Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania
Smits, S. A., Leach, J., Sonnenburg, E. D., Gonzalez, C. G., Lichtman, J. S., Reid, G., Knight, R., Manjurano, A., Changalucha, J., Elias, J. E., et al. (2017) · Science · doi:10.1126/science.aan4834 · Cited by 886 · see citing works
What are the consequences of the disappearing human microbiota?
Blaser, M. J., & Falkow, S. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2245 · Cited by 859 · see citing works
The microbiome of uncontacted Amerindians
Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., Magris, M., Hidalgo, G., Contreras, M., Noya-Alarcón, Ó., et al. (2015) · Science Advances · doi:10.1126/sciadv.1500183 · Cited by 851 · see citing works
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
Gohl, D. M., Vangay, P., Garbe, J., Maclean, A., Hauge, A., Becker, A., Gould, T. J., Clayton, J. B., Johnson, T. J., Hunter, R. C., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3601 · Cited by 807 · see citing works
Self-citationCompact graphical representation of phylogenetic data and metadata with GraPhlAn
Asnicar, F., Weingart, G., Tickle, T. L., Huttenhower, C., & Segata, N. (2015) · PeerJ · doi:10.7717/peerj.1029 · Cited by 806 · see citing works
Obesity among US immigrant subgroups by duration of residence.
Goel, M., McCarthy, E., Phillips, R., & Wee, C. C. (2004) · Journal of the American Medical Association (JAMA) · doi:10.1001/jama.292.23.2860 · Cited by 719 · see citing works
Compositional Data Analysis: Theory and Applications
(2011) · Wiley eBooks · doi:10.1002/9781119976462 · Cited by 704 · cited 1× · see citing works
“Aitchison’s distances were calculated by first imputing zeros from an abundance OTU table, then applying a centered log ratio transform using the robCompositions R package (Pawlowsky-Glahn and Buccianti, 2011).”
MethodLooking for a Signal in the Noise: Revisiting Obesity and the Microbiome
Sze, M. A., & Schloss, P. D. (2016) · mBio · doi:10.1128/mbio.01018-16 · Cited by 600 · see citing works
Subsistence strategies in traditional societies distinguish gut microbiomes
Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P. M., et al. (2015) · Nature Communications · doi:10.1038/ncomms7505 · Cited by 587 · see citing works
Caspi, R. R., Foerster, H., Fulcher, C., Kaipa, P., Krummenacker, M., Latendresse, M., Paley, S., Rhee, S. Y., Shearer, A. G., Tissier, C. P., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm900 · Cited by 581 · see citing works
The Python Language Reference Manual
van Rossum, G., & Drake, F. L. (2003) · Cited by 457 · see citing works
Lauderdale, D. S., & Rathouz, P. (2000) · International Journal of Obesity · doi:10.1038/sj.ijo.0801365 · Cited by 308 · see citing works
Cohort profile: the Healthy Life in an Urban Setting (HELIUS) study in Amsterdam, The Netherlands
Snijder, M. B., Galenkamp, H., Prins, M., Derks, E. M., Peters, R. J. G., Zwinderman, A. H., & Stronks, K. (2017) · BMJ Open · doi:10.1136/bmjopen-2017-017873 · Cited by 274 · see citing works
Gomez, A., Petrzelkova, K. J., Burns, M. B., Yeoman, C. J., Amato, K. R., Vlckova, K., Modry, D., Todd, A., Jost Robinson, C. A., Remis, M. J., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.02.013 · Cited by 248 · see citing works
McEntyre, J. R., & Ostell, J. (2002) · Cited by 210 · see citing works
Tamarind xyloglucan: a polysaccharide with versatile application potential
Mishra, A., & Malhotra, A. V. (2009) · Journal of Materials Chemistry · doi:10.1039/b911150f · Cited by 182 · see citing works
Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection
Montassier, E., Al-Ghalith, G., Ward, T. L., Corvec, S., Gastinne, T., Potel, G., Moreau, P., de la Cochetière, M., Batard, E., & Knights, D. (2016) · Genome Medicine · doi:10.1186/s13073-016-0301-4 · Cited by 176 · see citing works
Self-citationIntergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice
Schulfer, A. F., Battaglia, T., Alvarez, Y., Bijnens, L., Ruiz, V. E., Ho, M. L., Robinson, S. L., Ward, T., Cox, L. M., Rogers, A. B., et al. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0075-5 · Cited by 160 · see citing works
Self-citationAcculturation and environmental change impacts dietary habits among adult Hmong
Franzén, L., & Smith, C. (2008) · Appetite · doi:10.1016/j.appet.2008.09.012 · Cited by 131 · see citing works
Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity
Zhang, X., Li, J., Krautkramer, K. A., Badri, M. H., Battaglia, T., Borbet, T. C., Koh, H., Ng, S., Sibley, R. A., Li, Y., et al. (2018) · eLife · doi:10.7554/elife.37816 · Cited by 108 · see citing works
Self-citationSHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control
Al‐Ghalith, G. A., Hillmann, B., Ang, K., Shields‐Cutler, R. R., & Knights, D. (2018) · mSystems · doi:10.1128/msystems.00202-17 · Cited by 92 · see citing works
Self-citationThe digestion and absorption of sucrose by the intact rat
Dahlqvist, A., & Thomson, D. L. (1963) · The Journal of Physiology · doi:10.1113/jphysiol.1963.sp007141 · Cited by 73 · see citing works
Pangsri, P., Piwpankaew, Y., Ingkakul, A., et al. (2015) · SpringerPlus · doi:10.1186/s40064-015-1565-7 · Cited by 68 · see citing works
Arcan, C., Larson, N., Bauer, K., Berge, J. M., Story, M. T., & Neumark‐Sztainer, D. (2014) · Journal of the Academy of Nutrition and Dietetics · doi:10.1016/j.jand.2013.11.019 · Cited by 58 · see citing works
Characterization of the gut microbiome in epidemiologic studies: the multiethnic cohort experience
Fu, B. C., Randolph, T. W., Lim, U., Monroe, K. R., Cheng, I. C., Wilkens, L. R., Marchand, L. L., Hullar, M. A. J., & Lampe, J. W. (2016) · Annals of Epidemiology · doi:10.1016/j.annepidem.2016.02.009 · Cited by 54 · see citing works
Kooiman, P. (1971) · Carbohydrate Research · doi:10.1016/s0008-6215(00)81387-7 · Cited by 49 · see citing works
Kwok, L., Zhang, J., Guo, Z., Gesudu, Q., Zheng, Y., Qiao, J., Huo, D., & Zhang, H. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093631 · Cited by 41 · see citing works
Food Consumption Surveys in the US Department of Agriculture
Tippett, K. S., Enns, C. W., & Moshfegh, A. J. (1999) · Nutrition Today · doi:10.1097/00017285-199901000-00007 · Cited by 34 · see citing works
Mulasi-Pokhriyal, U., Smith, C., & Franzen-Castle, L. D. (2011) · Public Health Nutrition · doi:10.1017/s1368980011001649 · Cited by 33 · see citing works
Growth Trajectories of Refugee and Nonrefugee Children in the United States
Dawson-Hahn, E., Pak-Gorstein, S., Matheson, J., Zhou, C., Yun, K., Scott, K., Payton, C., Stein, E., Holland, A., Grow, H. M., et al. (2016) · Pediatrics · doi:10.1542/peds.2016-0953 · Cited by 30 · see citing works
Overweight among Refugee Children after Arrival in the United States
Hervey, K., Chanes, D. V., Klesges, L. M., Fischer, P. R., Trippel, S. J., & Juhn, Y. J. (2009) · Journal of Health Care for the Poor and Underserved · doi:10.1353/hpu.0.0118 · Cited by 25 · see citing works
The carbohydrates of tender kernel of palmyra palm (Borassus flabellifer, L.)
Subrahmanyan, V., Bains, G. S., Natarajan, C. P., et al. (1956) · Archives of Biochemistry and Biophysics · doi:10.1016/0003-9861(56)90392-7 · Cited by 18 · see citing works
The Effect of Living in the United States on Body Mass Index in Refugee Patients
Careyva, B. A., LaNoue, M. D., Bangura, M., de la Paz, A., Gee, A., Patel, N., & Mills, G. D. (2015) · Journal of Health Care for the Poor and Underserved · doi:10.1353/hpu.2015.0046 · Cited by 18 · see citing works
Rashidi, A., Ebadi, M., Shields‐Cutler, R. R., et al. (2018) · Transplantation and Cellular Therapy · doi:10.1016/j.bbmt.2018.01.025 · Cited by 17 · see citing works
Self-citationHeney, J. H., Dimock, C. C., Friedman, J. F., & Lewis, C. (2014) · PubMed · Cited by 16 · see citing works
The guts of obesity: progress and challenges in linking gut microbes to obesity.
Al‐Ghalith, G. A., Vangay, P., & Knights, D. (2015) · PubMed · Cited by 11 · see citing works
Self-citationSuperTracker Incorporates Food Composition Data into Innovative Online Consumer Tool
Britten, P. (2013) · Procedia Food Science · doi:10.1016/j.profoo.2013.04.025 · Cited by 4 · see citing works
Speek, A. J., Speek-Saichua, S., & Schreurs, W. H. P. (1991) · Food Chemistry · doi:10.1016/0308-8146(91)90110-a · Cited by 4 · see citing works
The Gut Microbiota of Bali among the World Populations: Connecting Diet, Urbanisation, and Obesity.
Febinia, C. A. (2016) · The Sydney eScholarship Repository (The University of Sydney) · Cited by 1 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Gut-microbiota-targeted diets modulate human immune status
Wastyk, H. C., Fragiadakis, G. K., Perelman, D., Dahan, D., Merrill, B. D., Yu, F. B., Topf, M., Gonzalez, C. G., Van Treuren, W., Han, S., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.019 · Cited by 1,385 · see citing works
Diet-microbiota interactions and personalized nutrition
Kolodziejczyk, A. A., Zheng, D., & Elinav, E. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0256-8 · Cited by 879 · see citing works
Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration
Leeming, E. R., Johnson, A. J., Spector, T. D., & Le Roy, C. I. (2019) · Nutrients · doi:10.3390/nu11122862 · Cited by 817 · see citing works
Self-citationDaily sampling reveals personalized diet-microbiome associations in humans
Johnson, A. J., Vangay, P., Al-Ghalith, G. A., Hillmann, B. M., Ward, T. L., Shields-Cutler, R. R., Kim, A. D., Shmagel, A. K., Syed, A. N., Walter, J., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.05.005 · Cited by 742 · see citing works
Self-citationPrevotella Diversity, Niches and Interactions with the Human Host
Tett, A., Pasolli, E., Masetti, G., Ercolini, D., & Segata, N. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00559-y · Cited by 748 · see citing works
Carbohydrate-active enzymes (CAZymes) in the gut microbiome
Wardman, J. F., Bains, R. K., Rahfeld, P., & Withers, S. G. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00712-1 · Cited by 597 · see citing works
Sex differences in gut microbiota
Kim, Y. S., Unno, T., Kim, B.-Y., & Park, M.-S. (2020) · The World Journal of Men s Health · doi:10.5534/wjmh.190009 · Cited by 610 · see citing works
Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476 · see citing works
The ancestral and industrialized gut microbiota and implications for human health
Sonnenburg, E. D., & Sonnenburg, J. L. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0191-8 · Cited by 489 · see citing works
The person-to-person transmission landscape of the gut and oral microbiomes
Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05620-1 · Cited by 449 · see citing works
Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health
Berding, K., Vlckova, K., Marx, W., Schellekens, H., Stanton, C., Clarke, G., Jacka, F., Dinan, T. G., & Cryan, J. F. (2021) · Advances in Nutrition · doi:10.1093/advances/nmaa181 · Cited by 451 · see citing works
Wang, D. D., Nguyen, L. H., Li, Y., Yan, Y., Ma, W., Rinott, E., Ivey, K. L., Shai, I., Willett, W. C., Hu, F. B., et al. (2021) · Nature Medicine · doi:10.1038/s41591-020-01223-3 · Cited by 386 · see citing works
Precision medicine in the era of artificial intelligence: implications in chronic disease management
Subramanian, M., Wojtusciszyn, A., Favre, L., Boughorbel, S., Shan, J., Letaief, K. B., Pitteloud, N., & Chouchane, L. (2020) · Journal of Translational Medicine · doi:10.1186/s12967-020-02658-5 · Cited by 362 · see citing works
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303 · see citing works
Gut microbiota diversity across ethnicities in the United States
Brooks, A. W., Priya, S., Blekhman, R., & Bordenstein, S. R. (2018) · PLOS Biology · doi:10.1371/journal.pbio.2006842 · Cited by 304 · see citing works
Human gut microbiome aging clock based on taxonomic profiling and deep learning
Galkin, F., Mamoshina, P., Aliper, A., Lane, E., Moskalev, V., Gladyshev, V. N., & Zhavoronkov, A. (2020) · iScience · doi:10.1016/j.isci.2020.101199 · Cited by 292 · see citing works
Microbiota succession throughout life from the cradle to the grave
Martino, C., Dilmore, A. H., Burcham, Z. M., Metcalf, J. L., Jeste, D., & Knight, R. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00768-z · Cited by 275 · see citing works
Adjusting for age improves identification of gut microbiome alterations in multiple diseases
Ghosh, T. S., Das, M., Jeffery, I. B., & O'Toole, P. W. (2020) · eLife · doi:10.7554/elife.50240 · Cited by 233 · see citing works
“A recent study of the gut microbiome of Thai individuals migrating to the US observed the loss of metabolic functions linked to degradation of dietary fibers like xylan, arabinoxylan, cellobiose, pullulan, glucomannan and resistant starch, with increasing duration of stay leading to a broader loss of microbiome functi…”
BackgroundLeveraging diet to engineer the gut microbiome
Wolter, M., Grant, E. T., Boudaud, M., Steimle, A., Pereira, G. V., Martens, E. C., & Desai, M. S. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-021-00512-7 · Cited by 211 · see citing works
Self-citationPublic human microbiome data are dominated by highly developed countries
Abdill, R. J., Adamowicz, E. M., & Blekhman, R. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001536 · Cited by 221 · see citing works
You’ve got male: Sex and the microbiota-gut-brain axis across the lifespan
Jaggar, M., Rea, K., Spichak, S., Dinan, T. G., & Cryan, J. F. (2020) · Frontiers in Neuroendocrinology · doi:10.1016/j.yfrne.2019.100815 · Cited by 200 · see citing works
Christensen, L., Vuholm, S., Roager, H. M., Nielsen, D. S., Krych, L., Kristensen, M., Astrup, A., & Hjorth, M. F. (2019) · The Journal of Nutrition · doi:10.1093/jn/nxz198 · Cited by 162 · see citing works
Peters, B. A., Lin, J., Qi, Q., Usyk, M., Isasi, C. R., Mossavar-Rahmani, Y., Derby, C. A., Santoro, N., Perreira, K. M., Daviglus, M. L., et al. (2022) · mSystems · doi:10.1128/msystems.00273-22 · Cited by 130 · see citing works
Sims, T. T., Colbert, L. E., Zheng, J., Delgado Medrano, A. Y., Hoffman, K. L., Ramondetta, L., Jazaeri, A., Jhingran, A., Schmeler, K. M., Daniel, C. R., et al. (2019) · Gynecologic Oncology · doi:10.1016/j.ygyno.2019.09.002 · Cited by 100 · see citing works
Tamburini, F. B., Maghini, D., Oduaran, O. H., Brewster, R., Hulley, M. R., Sahibdeen, V., Norris, S. A., Tollman, S., Kahn, K., Wagner, R. G., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27917-x · Cited by 88 · see citing works
The hunt for a healthy microbiome
Eisenstein, M. (2020) · Nature · doi:10.1038/d41586-020-00193-3 · Cited by 84 · see citing works
Geographic Differences in Gut Microbiota Composition Impact Susceptibility to Enteric Infection
Porras, A. M., Shi, Q., Zhou, H., Callahan, R., Montenegro-Bethancourt, G., Solomons, N., & Brito, I. L. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109457 · Cited by 74 · see citing works
From taxonomy to metabolic output: what factors define gut microbiome health?
Wilmanski, T., Rappaport, N., Diener, C., Gibbons, S. M., & Price, N. D. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1907270 · Cited by 73 · see citing works
The human microbiome in clinical translation: from bench to bedside
Bautista, J., Echeverría, C. E., Maldonado-Noboa, I., Ojeda-Mosquera, S., Hidalgo-Tinoco, C., & López-Cortés, A. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1632435 · Cited by 55 · see citing works
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 · see citing works
Deemer, D. G., Voreades, N., Bron, P. A., & Lindemann, S. R. (2025) · Journal of Food Bioactives · doi:10.26599/jfb.2025.95030415 · Cited by 3 · see citing works
Cohort Profile: the SMRU Refugee and Migrant Pregnancy Study in Western Thailand and Eastern Myanmar
McGready, R., J White, N., Nosten, F. H., & Collaborators, S. R. A. M. P. S. (2026) · Wellcome Open Research · doi:10.12688/wellcomeopenres.25582.2 · Cited by 2 · see citing works
Self-citation
- Authors
- Vangay, P., Johnson, A. J., Ward, T. L., Al-Ghalith, G. A., Shields-Cutler, R. R., Hillmann, B. M., Lucas, S. K., Beura, L. K., Thompson, E. A., Till, L. M., Batres, R., Paw, B., Pergament, S. L., Saenyakul, P., Xiong, M., Kim, A. D., Kim, G., Masopust, D., Martens, E. C., Angkurawaranon, C., McGready, R., Kashyap, P. C., Culhane-Pera, K. A., & Knights, D.
- Affiliations
- University of Minnesota (US)
- Mayo Clinic (US)
- Macalester College (US)
- University of Michigan (US)
- Chiang Mai University (TH)
- Mahidol University (TH)
- Corresponding author
- Knights, Dan
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-11
- Volume
- 175
- Issue
- 4
- Pages
- 962-972.e10
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6498444
- OpenAlex
- W2899495835
- Cited by
- 794
- References
- 73
- Citations by year
- 2026: 74 · 2025: 97 · 2024: 108 · 2023: 100 · 2022: 111 · 2021: 113 · 2020: 112 · 2019: 69 · 2018: 9
- FWCI
- 27.56
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 365 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- University of Minnesota Clinical and Translational Science Institute
- University of Minnesota Healthy Foods, Healthy Lives Institute
- Office of Diversity
- Graduate School at the University of Minnesota
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Health Sciences › Medicine › Epidemiology › Adipokines, Inflammation, and Metabolic Diseases
- Keywords
- gut microbiota, immigration, Westernization, metabolic disorders, Hmong people, Karen, microbiome diversity, obesity, intergenerational transmission, host-microbe interactions
- MeSH terms
- Gastrointestinal Microbiome, Adult, Bacteroides, Dietary Fiber, Emigration and Immigration, Humans, Obesity, United States, Prevotella, Asian People, Emigrants and Immigrants, Metagenome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
