Characterization of the gut microbial community of obese patients following a weight-loss intervention using whole metagenome shotgun sequencing
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BACKGROUND/OBJECTIVES: Cross-sectional studies suggested that obesity is promoted by the gut microbiota. However, longitudinal data on taxonomic and functional changes in the gut microbiota of obese patients are scarce. The aim of this work is to study microbiota changes in the course of weight loss therapy and the following year in obese individuals with or without co-morbidities, and to asses a possible predictive value of the gut microbiota with regard to weight loss maintenance. SUBJECTS/METHODS: Sixteen adult patients, who followed a 52-week weight-loss program comprising low calorie diet, exercise and behavioral therapy, were selected according to their weight-loss course. Over two years, anthropometric and metabolic parameters were assessed and microbiota from stool samples was functionally and taxonomically analyzed using DNA shotgun sequencing. RESULTS: Overall the microbiota responded to the dietetic and lifestyle intervention but tended to return to the initial situation both at the taxonomical and functional level at the end of the intervention after one year, except for an increase in Akkermansia abundance which remained stable over two years (12.7x103 counts, 95%CI: 322-25100 at month 0; 141x103 counts, 95%CI: 49-233x103 at month 24; p = 0.005). The Firmicutes/Bacteroidetes ratio was higher in obese subjects with metabolic syndrome (0.64, 95%CI: 0.34-0.95) than in the "healthy obese" (0.27, 95%CI: 0.08-0.45, p = 0.04). Participants, who succeeded in losing their weight consistently over the two years, had at baseline a microbiota enriched in Alistipes, Pseudoflavonifractor and enzymes of the oxidative phosphorylation pathway compared to patients who were less successful in weight reduction. CONCLUSIONS: Successful weight reduction in the obese is accompanied with increased Akkermansia numbers in feces. Metabolic co-morbidities are associated with a higher Firmicutes/Bacteroidetes ratio. Most interestingly, microbiota differences might allow discrimination between successful and unsuccessful weight loss prior to intervention.
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Several studies of different diets associated weight loss with enrichment of Akkermansia muciniphila.
“Several studies of different diets associated weight loss with enrichment of A muciniphila.86, 93, 98, 99”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [99]
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Matthews, D. R., Hosker, J. P., Rudenski, A. S., Naylor, B. A., Treacher, D. F., & Turner, R. C. (1985) · Diabetologia · doi:10.1007/bf00280883 · Cited by 31,502 · see citing works
Toprak, Ö., Kurt, H., Sarı, Y., Şarkış, C., Us, H., & Kırık, A. (2017) · Kidney & Blood Pressure Research · doi:10.1159/000468530 · Cited by 29,769 · see citing works
vegan: Community Ecology Package
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Sólymos, P., Stevens, M. H. H., Szöcs, E., et al. (2001) · doi:10.32614/cran.package.vegan · Cited by 27,099 · see citing works
Modern Applied Statistics with S
Venables, W., & Ripley, B. (2010) · Statisctics and computing/Statistics and computing · doi:10.1007/978-0-387-21706-2 · Cited by 16,188 · see citing works
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444 · 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
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785 · see citing works
SPECIES ASSEMBLAGES AND INDICATOR SPECIES:THE NEED FOR A FLEXIBLE ASYMMETRICAL APPROACH
Dufrêne, M., & Legendre, P. (1997) · Ecological Monographs · doi:10.1890/0012-9615(1997)067[0345:saaist]2.0.co;2 · Cited by 8,346 · see citing works
Enterotypes 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
Changes of Intestinal Functions in Liver Cirrhosis
Fukui, H., & Wiest, R. (2016) · Inflammatory Intestinal Diseases · doi:10.1159/000444436 · Cited by 6,820 · see citing works
The gut microbiota as an environmental factor that regulates fat storage
Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245 · see citing works
Obesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176 · see citing works
Quality control and preprocessing of metagenomic datasets
Schmieder, R., & Edwards, R. A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr026 · Cited by 4,989 · see citing works
Everard, A., Belzer, C., Geurts, L., Ouwerkerk, J. P., Druart, C., Bindels, L. B., Guiot, Y., Derrien, M., Muccioli, G. G., Delzenne, N. M., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219451110 · Cited by 4,511 · see citing works
The COG database: a tool for genome-scale analysis of protein functions and evolution
Tatusov, R. L. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.33 · Cited by 4,480 · see citing works
Abdominal obesity and metabolic syndrome
Després, J.-P., & Lemieux, I. (2006) · Nature · doi:10.1038/nature05488 · Cited by 4,354 · see citing works
Species Assemblages and Indicator Species: The Need for a Flexible Asymmetrical Approach
Dufrêne, M., & Legendre, P. (1997) · Ecological Monographs · doi:10.2307/2963459 · Cited by 4,154 · see citing works
Human Genetics Shape the Gut Microbiome
Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.053 · Cited by 3,164 · see citing works
Bedogni, G., Bellentani, S., Miglioli, L., Masutti, F., Passalacqua, M., Castiglione, A., & Tiribelli, C. (2006) · BMC Gastroenterology · doi:10.1186/1471-230x-6-33 · Cited by 3,054 · see citing works
Modern Applied Statistics with S Fourth edition
Venables, W. N., & Ripley, B. D. (2002) · Cited by 2,538 · see citing works
Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5
Vijay-Kumar, M., Aitken, J. D., Carvalho, F. A., Cullender, T. C., Mwangi, S., Srinivasan, S., Sitaraman, S. V., Knight, R., Ley, R. E., & Gewirtz, A. T. (2010) · Science · doi:10.1126/science.1179721 · Cited by 2,068 · see citing works
Human gut microbiota in obesity and after gastric bypass
Zhang, H., DiBaise, J. K., Zuccolo, A., Kudrna, D., Braidotti, M., Yu, Y., Parameswaran, P., Crowell, M. D., Wing, R., Rittmann, B. E., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812600106 · Cited by 1,880 · see citing works
Dietary intervention impact on gut microbial gene richness
Cotillard, A., Kennedy, S. P., Kong, L. C., Prifti, E., Pons, N., Le Chatelier, E., Almeida, M., Quinquis, B., Levenez, F., Galleron, N., et al. (2013) · Nature · doi:10.1038/nature12480 · Cited by 1,832 · see citing works
Regulation of inflammation by short chain fatty acids
Vinolo, M. A. R., Rodrigues, H. G., Nachbar, R. T., & Curi, R. (2011) · Nutrients · doi:10.3390/nu3100858 · Cited by 1,724 · see citing works
OPLS discriminant analysis: combining the strengths of PLS-DA and SIMCA classification
Bylesjö, M., Rantalainen, M., Cloarec, O., Nicholson, J. K., Holmes, E., & Trygg, J. (2006) · Journal of Chemometrics · doi:10.1002/cem.1006 · Cited by 1,475 · see citing works
S<scp>UCCESSFUL</scp> W<scp>EIGHT</scp> L<scp>OSS</scp> M<scp>AINTENANCE</scp>
Wing, R. R., & Hill, J. O. (2001) · Annual Review of Nutrition · doi:10.1146/annurev.nutr.21.1.323 · Cited by 1,382 · see citing works
Jumpertz, 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
Human colonic microbiota associated with diet, obesity and weight loss
Duncan, S. H., Lobley, G. E., Holtrop, G., Ince, J., Johnstone, A. M., Louis, P., & Flint, H. J. (2008) · International Journal of Obesity · doi:10.1038/ijo.2008.155 · Cited by 1,222 · see citing works
Ramirez-Farias, C., Slezak, K., Fuller, Z., Duncan, A., Holtrop, G., & Louis, P. (2008) · British Journal of Nutrition · doi:10.1017/s0007114508019880 · Cited by 822 · see citing works
Microbes inside—from diversity to function: the case of Akkermansia
Belzer, C., & de Vos, W. M. (2012) · The ISME Journal · doi:10.1038/ismej.2012.6 · Cited by 715 · see citing works
Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome
Saulnier, D. M., Riehle, K., Mistretta, T., Diaz, M., Mandal, D., Raza, S., Weidler, E. M., Qin, X., Coarfa, C., Milosavljevic, A., et al. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.06.072 · Cited by 672 · see citing works
Salonen, A., Lahti, L., Salojärvi, J., Holtrop, G., Korpela, K., Duncan, S. H., Date, P., Farquharson, F., Johnstone, A. M., Lobley, G. E., et al. (2014) · The ISME Journal · doi:10.1038/ismej.2014.63 · Cited by 626 · see citing works
Intestinal Dysbiosis Associated with Systemic Lupus Erythematosus
Hevia, A., Milani, C., López, P., Cuervo, A., Arboleya, S., Duranti, S., Turroni, F., González, S., Suárez, A., Gueimonde, M., et al. (2014) · mBio · doi:10.1128/mbio.01548-14 · Cited by 620 · see citing works
Rossi, M., Corradini, C., Amaretti, A., Nicolini, M., Pompei, A., Zanoni, S., & Matteuzzi, D. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.10.6150-6158.2005 · Cited by 546 · see citing works
Intestinal Microbiota, Microbial Translocation, and Systemic Inflammation in Chronic HIV Infection
Dinh, D. M., Volpe, G. E., Duffalo, C., Bhalchandra, S., Tai, A., Kane, A. V., WANKE, C. A., & Ward, H. (2014) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiu409 · Cited by 531 · see citing works
Bajaj, J. S., Hylemon, P. B., Ridlon, J. M., Heuman, D. M., Daita, K., White, M. B., Monteith, P., Noble, N. A., Sikaroodi, M., & Gillevet, P. M. (2012) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00152.2012 · Cited by 525 · see citing works
Contribution of diet to the composition of the human gut microbiota
Gräf, D., Cagno, R. D., Fåk, F., Flint, H. J., NYMAN, M. E., Saarela, M., & Watzl, B. (2015) · Microbial Ecology in Health and Disease · doi:10.3402/mehd.v26.26164 · Cited by 520 · see citing works
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees
Zhang, H., Gao, S., Lercher, M. J., Hu, S., & Chen, W. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks576 · Cited by 501 · see citing works
Dietary effects on human gut microbiome diversity
Xu, Z., & Knight, R. (2015) · British Journal Of Nutrition · doi:10.1017/s0007114514004127 · Cited by 456 · see citing works
Xu, J. Y., Lian, F., Zhao, L., Zhao, Y., Chen, X., Zhang, X., Guo, Y., Zhang, C., Zhou, Q., Xue, Z., et al. (2014) · The ISME Journal · doi:10.1038/ismej.2014.177 · Cited by 423 · see citing works
A review of the potential mechanisms for the lowering of colorectal oncogenesis by butyrate
Fung, K. Y. C., Cosgrove, L. J., Lockett, T. J., Head, R. J., & Topping, D. L. (2012) · British Journal Of Nutrition · doi:10.1017/s0007114512001948 · Cited by 357 · see citing works
McHardy, I. H., Li, X., Tong, M., Ruegger, P., Jacobs, J., Borneman, J., Anton, P., & Braun, J. (2013) · Microbiome · doi:10.1186/2049-2618-1-26 · Cited by 234 · see citing works
Abdominal Ultrasound for Diagnosis of Nonalcoholic Fatty Liver Disease (NAFLD)
Mishra, P., & Younossi, Z. M. (2007) · The American Journal of Gastroenterology · doi:10.1111/j.1572-0241.2007.01520.x · Cited by 211 · see citing works
Bischoff, S. C., Damms-Machado, A., Betz, C., Herpertz, S., Legenbauer, T., Löw, T., Wechsler, J. G., Bischoff, G., Austel, A., & Ellrott, T. (2011) · International Journal of Obesity · doi:10.1038/ijo.2011.107 · Cited by 168 · see citing works
Self-citationRautio, M., Eerola, E., Väisänen, M., Molitoris, D. R., Lawson, P. A., Collins, M. D., & Jousimies-Somer, H. R. (2003) · Systematic and Applied Microbiology · doi:10.1078/072320203322346029 · Cited by 168 · see citing works
Irigaray, P., Ogier, V., Jacquenet, S., Notet, V., Sibille, P., Méjean, L., Bihain, B. E., & Yen, F. T. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2006.05159.x · Cited by 147 · see citing works
Subdoligranulum variabile gen. nov., sp. nov. from human feces
Holmstrøm, K., Collins, M. D., Møller, T., Falsen, E., & Lawson, P. A. (2004) · Anaerobe · doi:10.1016/j.anaerobe.2004.01.004 · Cited by 146 · see citing works
Kim, H., Kam, S., & Lee, D. (2014) · Environmental Research · doi:10.1016/j.envres.2014.08.032 · Cited by 60 · see citing works
Impact of a very low-energy diet on the fecal microbiota of obese individuals
Simões, C. D., Maukonen, J., Scott, K. P., Virtanen, K. A., Pietiläinen, K. H., & Saarela, M. (2014) · European Journal of Nutrition · doi:10.1007/s00394-013-0645-0 · Cited by 39 · see citing works
Leifer, C. A., McConkey, C., Li, S., Chassaing, B., Gewirtz, A. T., & Ley, R. E. (2014) · Immunology Letters · doi:10.1016/j.imlet.2014.07.017 · Cited by 34 · see citing works
Validation and comparison of two computerized methodsof obtaining a diet history
Landig, J., Erhardt, J. G., Bode, J. C., & Bode, C. (1998) · Clinical Nutrition · doi:10.1016/s0261-5614(98)80004-6 · Cited by 32 · see citing works
Flagged first, then by citations
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Global burden of colorectal cancer: emerging trends, risk factors and prevention strategies
Keum, N., & Giovannucci, E. L. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0189-8 · Cited by 2,690 · see citing works
Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer
Song, M., Chan, A. T., & Sun, J. (2020) · Gastroenterology · doi:10.1053/j.gastro.2019.06.048 · Cited by 752 · see citing works
De la Cuesta-Zuluaga, J., Mueller, N., Álvarez-Quintero, R., Velásquez-Mejía, E., Sierra, J., Corrales-Agudelo, V., Carmona, J., Abad, J., & Escobar, J. (2018) · Nutrients · doi:10.3390/nu11010051 · Cited by 533 · 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 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
Zhou, X., Baumann, R., Gao, X., Mendoza, M., Singh, S., Sand, I. K., Xia, Z., Cox, L. M., Chitnis, T., Yoon, H., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.021 · Cited by 319 · see citing works
Action and function of Akkermansia muciniphila in microbiome ecology, health and disease
Ottman, N., Geerlings, S. Y., Aalvink, S., de Vos, W. M., & Belzer, C. (2017) · Best Practice & Research Clinical Gastroenterology · doi:10.1016/j.bpg.2017.10.001 · Cited by 290 · see citing works
The Intestinal Microbiota in Metabolic Disease
Woting, A., & Blaut, M. (2016) · Nutrients · doi:10.3390/nu8040202 · Cited by 284 · see citing works
Hersoug, L., Möller, P., & Loft, S. H. (2018) · Nutrition Research Reviews · doi:10.1017/s0954422417000269 · Cited by 246 · see citing works
Fabbiano, S., Suárez-Zamorano, N., Chevalier, C., Lazarević, V., Kieser, S., Rigo, D., Léo, S., Veyrat‐Durebex, C., Gaïa, N., Maresca, M., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.08.005 · Cited by 227 · see citing works
Seganfredo, F. B., Blume, C. A., Moehlecke, M., Giongo, A., Casagrande, D. S., Spolidoro, J. V. N., Padoin, A. V., Schaan, B. D., & Mottin, C. C. (2017) · Obesity Reviews · doi:10.1111/obr.12541 · Cited by 228 · see citing works
From correlation to causality: the case of Subdoligranulum
Hul, M. V., Roy, T. L., Prifti, E., Dao, M. C., Paquot, A., Zucker, J., Delzenne, N. M., Muccioli, G. G., Clément, K., & Cani, P. D. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1849998 · Cited by 221 · see citing works
Houtman, T. A., Eckermann, H. A., Smidt, H., & de Weerth, C. (2022) · Scientific Reports · doi:10.1038/s41598-022-07176-6 · Cited by 216 · see citing works
Codiversification of gut microbiota with humans
Suzuki, T. A., Fitzstevens, J. L., Schmidt, V. T., Enav, H., Huus, K. E., Mbong Ngwese, M., Grießhammer, A., Pfleiderer, A., Adegbite, B. R., Zinsou, J. F., et al. (2022) · Science · doi:10.1126/science.abm7759 · Cited by 210 · see citing works
Caloric restriction disrupts the microbiota and colonization resistance
von Schwartzenberg, R. J., Bisanz, J. E., Lyalina, S., Spanogiannopoulos, P., Ang, Q. Y., Cai, J., Dickmann, S., Friedrich, M., Liu, S.-Y., Collins, S. L., et al. (2021) · Nature · doi:10.1038/s41586-021-03663-4 · Cited by 211 · see citing works
Modulation of the gut microbiota by metformin improves metabolic profiles in aged obese mice
Lee, H., Lee, Y., Kim, J., An, J., Lee, S., Kong, H., Song, Y., Lee, C.-K., & Kim, K. (2018) · Gut Microbes · doi:10.1080/19490976.2017.1405209 · Cited by 203 · see citing works
Maifeld, A., Bartolomaeus, H., Löber, U., Avery, E. G., Steckhan, N., Markó, L., Wilck, N., Hamad, I., Šušnjar, U., Mähler, A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22097-0 · Cited by 202 · see citing works
Lai, Z.-L., Tseng, C.-H., Ho, H. J., Cheung, C., Lin, J.-Y., Chen, Y., Cheng, F.-C., Hsu, Y., Lin, J., El-Omar, E. M., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-33893-y · Cited by 192 · see citing works
Pan, S., Zhu, C., Zhao, X., & Coelho, L. P. (2022) · Nature Communications · doi:10.1038/s41467-022-29843-y · Cited by 195 · see citing works
Hibberd, A. A., Yde, C. C., Ziegler, M. L., Honoré, A. H., Saarinen, M., Lahtinen, S. J., Stahl, B., Jensen, H. M., & Stenman, L. K. (2018) · Beneficial Microbes · doi:10.3920/bm2018.0028 · Cited by 179 · see citing works
Comparative analysis of gut microbiota associated with body mass index in a large Korean cohort
Yun, Y., Kim, H.-N., Kim, S. E., Heo, S. G., Chang, Y., Ryu, S., Shin, H., & Kim, H. (2017) · BMC Microbiology · doi:10.1186/s12866-017-1052-0 · Cited by 176 · see citing works
The Gut Microbiome in Hypertension
Avery, E. G., Bartolomaeus, H., Maifeld, A., Markó, L., Wiig, H., Wilck, N., Rosshart, S. P., Forslund, S. K., & Müller, D. N. (2021) · Circulation Research · doi:10.1161/circresaha.121.318065 · Cited by 174 · see citing works
Rinott, E., Meir, A. Y., Tsaban, G., Zelicha, H., Kaplan, A., Knights, D., Tuohy, K. M., Scholz, M., Koren, O., Stampfer, M. J., et al. (2022) · Genome Medicine · doi:10.1186/s13073-022-01015-z · Cited by 174 · see citing works
Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island
Nakayama, J., Yamamoto, A., Conde, L. A., Higashi, K., Sonomoto, K., Tan, J. D., & Lee, Y. K. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00197 · Cited by 163 · see citing works
Kim, J., Lee, H., An, J., Song, Y., Lee, C., Kim, K., & Kong, H. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01947 · Cited by 163 · see citing works
Pham, V. T., Fehlbaum, S., Seifert, N., Richard, N., Bruins, M. J., Sybesma, W., Rehman, A., & Steinert, R. E. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1875774 · Cited by 158 · see citing works
Negative binomial mixed models for analyzing microbiome count data
Zhang, X., Mallick, H., Tang, Z., Zhang, L., Cui, X., Benson, A. K., & Yi, N. (2017) · BMC Bioinformatics · doi:10.1186/s12859-016-1441-7 · Cited by 156 · see citing works
A prospective longitudinal study on the microbiota composition in amyotrophic lateral sclerosis
Di Gioia, D., Bozzi Cionci, N., Baffoni, L., Amoruso, A., Pane, M., Mogna, L., Gaggìa, F., Lucenti, M. A., Bersano, E., Cantello, R., et al. (2020) · BMC Medicine · doi:10.1186/s12916-020-01607-9 · Cited by 151 · see citing works
Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation
Korpela, K. (2018) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-030117-012830 · Cited by 153 · see citing works
Lee, C. B., Chae, S. U., Jo, S. J., Jerng, U. M., & Bae, S. K. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22073566 · Cited by 149 · see citing works
Konjaku flour reduces obesity in mice by modulating the composition of the gut microbiota
Kang, Y., Li, Y., Du, Y., Guo, L., Chen, M., Huang, X., Fang, Y., Hong, J., & Kong, X. (2018) · International Journal of Obesity · doi:10.1038/s41366-018-0187-x · Cited by 136 · see citing works
Factors affecting weight loss variability in obesity
Dent, R., McPherson, R., & Harper, M.-E. (2020) · Metabolism · doi:10.1016/j.metabol.2020.154388 · Cited by 131 · see citing works
Gut dysbiosis is associated with primary hypothyroidism with interaction on gut-thyroid axis
Su, X., Zhao, Y., Li, Y., Ma, S., & Wang, Z. (2020) · Clinical Science · doi:10.1042/cs20200475 · Cited by 127 · see citing works
Nishijima, S., Stankevič, E., Aasmets, O., Schmidt, T., Nagata, N., Keller, M. I., Ferretti, P., Juel, H. B., Fullam, A., Robbani, S. M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.10.022 · Cited by 127 · see citing works
Koutoukidis, D. A., Jebb, S. A., Zimmerman, M., Otunla, A. A., Henry, J. A., Ferrey, A. E., Schofield, E., Kinton, J., Aveyard, P. N., & Marchesi, J. R. (2022) · Gut Microbes · doi:10.1080/19490976.2021.2020068 · Cited by 123 · see citing works
Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins
Marques, C., Fernandes, I., Meireles, M., Faria, A., Spencer, J. P. E., Mateus, N. F. D. C. B., & Calhau, C. (2018) · Scientific Reports · doi:10.1038/s41598-018-29744-5 · Cited by 118 · see citing works
Green Tea and Its Relation to Human Gut Microbiome
Pérez-Burillo, S., Navajas-Porras, B., López-Maldonado, A., Hinojosa-Nogueira, D., Pastoriza, S., & Rufián‐Henares, J. Á. (2021) · Molecules · doi:10.3390/molecules26133907 · Cited by 117 · see citing works
The Equine Gastrointestinal Microbiome: Impacts of Age and Obesity
Morrison, P. K., Newbold, C. J., Jones, E., Worgan, H. J., Grove‐White, D., Dugdale, A., Barfoot, C. F., Harris, P. A., & Argo, C. M. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03017 · Cited by 127 · see citing works
The Baseline Gut Microbiota Directs Dieting-Induced Weight Loss Trajectories
Jie, Z., Yu, X., Liu, Y., Sun, L., Chen, P., Ding, Q., Gao, Y., Zhang, X., Yu, M., Liu, Y., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2021.01.029 · Cited by 116 · see citing works
Gut Microbiota and Host Metabolism: From Proof of Concept to Therapeutic Intervention
Cani, P. D., de Hase, E. M., & Hul, M. V. (2021) · Microorganisms · doi:10.3390/microorganisms9061302 · Cited by 111 · see citing works
Gut microbiota as important modulator of metabolism in health and disease
Wang, X., Zhang, A., Miao, J.-H., Sun, H. J., Yan, G., Wu, F., & Wang, X.-J. (2018) · RSC Advances · doi:10.1039/c8ra08094a · Cited by 105 · see citing works
He, C., Peng, C., Wang, H., Ouyang, Y., Zhu, Z., Shu, X., Zhu, Y., & Lü, N. (2019) · Helicobacter · doi:10.1111/hel.12590 · Cited by 104 · see citing works
Morissette, A., Kropp, C., Songpadith, J.-P., Moreira, R. J., Costa, J., Mariné-Casadó, R., Pilon, G., Varin, T. V., Dudonné, S., Boutekrabt, L., et al. (2020) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00560.2019 · Cited by 105 · see citing works
Song, J., Tian, W. J., Kwok, L., Wang, Y. L., Shang, Y. N., Menghe, B., & Wang, J. G. (2017) · British Journal Of Nutrition · doi:10.1017/s0007114517002380 · Cited by 100 · see citing works
Beisner, J., Gonzalez‐Granda, A., Basrai, M., Damms-Machado, A., & Bischoff, S. C. (2020) · Nutrients · doi:10.3390/nu12113444 · Cited by 103 · see citing works
Self-citationHan, G., Lee, J.-Y., Jin, G.-D., Park, J., Choi, Y. H., Chae, B. J., Kim, E. B., & Choi, Y. (2017) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-017-8304-7 · Cited by 99 · see citing works
A review on gut microbiota: a central factor in the pathophysiology of obesity
Cunningham, A., Stephens, J. W., & Harris, D. A. (2021) · Lipids in Health and Disease · doi:10.1186/s12944-021-01491-z · Cited by 101 · see citing works
Dietary Interventions to Modulate the Gut Microbiome—How Far Away Are We From Precision Medicine
Filippis, F. D., Vitaglione, P., Cuomo, R., Canani, R. B., & Ercolini, D. (2018) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izy080 · Cited by 87 · see citing works
Protective effects of Bacillus probiotics against high-fat diet-induced metabolic disorders in mice
Kim, B., Kwon, J., Kim, M., Park, H., Ji, Y., Holzapfel, W. H., & Hyun, C. (2018) · PLoS ONE · doi:10.1371/journal.pone.0210120 · Cited by 88 · see citing works
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study
Jian, C., Silvestre, M. P., Middleton, D., Korpela, K., Jalo, E., Broderick, D. T. J., de Vos, W. M., Fogelholm, M., Taylor, M. W., Raben, A., et al. (2022) · Genome Medicine · doi:10.1186/s13073-022-01053-7 · Cited by 87 · see citing works
Gut Microbiota in Obesity and Metabolic Abnormalities: A Matter of Composition or Functionality?
Morán‐Ramos, S., López-Contreras, B. E., & Canizales‐Quinteros, S. (2017) · Archives of Medical Research · doi:10.1016/j.arcmed.2017.11.003 · Cited by 86 · see citing works
Pei, Y., Otieno, D., Gu, I., Lee, S., Parks, J. S., Schimmel, K. A., & Kang, H. W. (2020) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2020.108532 · Cited by 82 · see citing works
Ecology and molecular targets of hypermutation in the global microbiome
Roux, S., Paul, B. G., Bagby, S. C., Nayfach, S., Allen, M. A., Attwood, G. T., Cavicchioli, R., Chistoserdova, L., Gruninger, R. J., Hallam, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23402-7 · Cited by 81 · see citing works
Microbiota and Obesity: Where Are We Now?
Ballini, A., Scacco, S., Boccellino, M., Santacroce, L., & Arrigoni, R. (2020) · Biology · doi:10.3390/biology9120415 · Cited by 78 · see citing works
Effect of Food Thermal Processing on the Composition of the Gut Microbiota
Pérez-Burillo, S., Pastoriza, S., Jiménez‐Hernández, N., D’Auria, G., Francino, M. P., & Rufián‐Henares, J. Á. (2018) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.8b04077 · Cited by 77 · see citing works
Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria
Shetty, S. A., Kuipers, B., Atashgahi, S., Aalvink, S., Smidt, H., & de Vos, W. M. (2022) · npj Biofilms and Microbiomes · doi:10.1038/s41522-022-00275-2 · Cited by 75 · see citing works
Martemucci, G., Fracchiolla, G., Muraglia, M., Tardugno, R., Dibenedetto, R. S., & D‘Alessandro, A. G. (2023) · Antioxidants · doi:10.3390/antiox12122091 · Cited by 81 · see citing works
Microbiota Transplant in the Treatment of Obesity and Diabetes: Current and Future Perspectives
Napolitano, M., & Covașă, M. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.590370 · Cited by 75 · see citing works
Pérez-Burillo, S., Pastoriza, S., Fernández‐Arteaga, A., Luzón, G., Jiménez‐Hernández, N., D’Auria, G., Francino, M. P., & Rufián‐Henares, J. Á. (2019) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.8b06604 · Cited by 75 · see citing works
Podlesny, D., Arze, C., Dörner, E., Verma, S., Dutta, S., Walter, J., & Fricke, W. F. (2022) · Microbiome · doi:10.1186/s40168-022-01251-w · Cited by 73 · see citing works
Connection between gut microbiome and the development of obesity
Zhi, C., Huang, J., Wang, J., Cao, H., Bai, Y., Guo, J., & Su, Z. (2019) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-019-03623-x · Cited by 69 · see citing works
de la Cuesta‐Zuluaga, J., Corrales-Agudelo, V., Carmona, J. A., Abad, J. M., & Escobar, J. S. (2017) · International Journal of Obesity · doi:10.1038/ijo.2017.281 · Cited by 68 · see citing works
Jian, C., Luukkonen, P. K., Sädevirta, S., Yki‐Järvinen, H., & Salonen, A. (2020) · Clinical Nutrition · doi:10.1016/j.clnu.2020.05.008 · Cited by 67 · see citing works
Pisanu, S., Palmas, V., Madau, V., Casula, E., Deledda, A., Cusano, R., Uva, P., Vascellari, S., Boi, F., Loviselli, A., et al. (2020) · Nutrients · doi:10.3390/nu12092707 · Cited by 66 · see citing works
The equine gastrointestinal microbiome: impacts of weight-loss
Morrison, P. K., Newbold, C. J., Jones, E., Worgan, H. J., Grove‐White, D., Dugdale, A., Barfoot, C. F., Harris, P. A., & Argo, C. M. (2020) · BMC Veterinary Research · doi:10.1186/s12917-020-02295-6 · Cited by 65 · see citing works
Lifestyle modifications result in alterations in the gut microbiota in obese children
Cho, K. Y. (2021) · BMC Microbiology · doi:10.1186/s12866-020-02002-3 · Cited by 65 · see citing works
Effects of three different mannans on obesity and gut microbiota in high-fat diet-fed C57BL/6J mice
Song, Y., Shen, H., Liu, T., Pan, B., Alwis, S. D., Zhang, W., Luo, X., Li, Z., Wang, N., Ma, W., et al. (2021) · Food & Function · doi:10.1039/d0fo03331f · Cited by 65 · see citing works
The evolution and competitive strategies of Akkermansia muciniphila in gut
Kim, J.-S., Kang, S. W., Lee, J. H., Park, S., & Lee, J. (2022) · Gut Microbes · doi:10.1080/19490976.2021.2025017 · Cited by 61 · see citing works
Dietary Influences on Gut Microbiota with a Focus on Metabolic Syndrome
Thomas, M. S., Blesso, C. N., Calle, M. C., Chun, O. K., Puglisi, M. J., & Fernández, M. L. (2022) · Metabolic Syndrome and Related Disorders · doi:10.1089/met.2021.0131 · Cited by 63 · see citing works
Rondanelli, M., Gasparri, C., Peroni, G., Faliva, M. A., Naso, M., Perna, S., Bazire, P., Sajoux, I., Maugeri, R., & Rigon, C. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2021.662591 · Cited by 60 · see citing works
Song, H., Shen, X., Chu, Q., & Zheng, X. (2021) · Journal of the Science of Food and Agriculture · doi:10.1002/jsfa.11535 · Cited by 61 · see citing works
Nondigestible Oligosaccharides with Anti-Obesity Effects
Liu, Y., Chen, J., Tan, Q., Deng, X., Tsai, P.-J., Chen, P.-H., Ye, M., Guo, J., & Su, Z. (2019) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.9b06079 · Cited by 58 · see citing works
Shomorony, I., Cirulli, E. T., Huang, L., Napier, L. A., Heister, R., Hicks, M. A., Cohen, I. V., Yu, H., Swisher, C. L., Schenker-Ahmed, N. M., et al. (2020) · Genome Medicine · doi:10.1186/s13073-019-0705-z · Cited by 58 · see citing works
The Gut Microbiota during a Behavioral Weight Loss Intervention
Stanislawski, M. A., Frank, D. N., Borengasser, S. J., Ostendorf, D. M., Ir, D., Jambal, P., Bing, K., Wayland, L. T., Siebert, J., Bessesen, D. H., et al. (2021) · Nutrients · doi:10.3390/nu13093248 · Cited by 59 · see citing works
Sleep and circadian disruption and the gut microbiome-possible links to dysregulated metabolism
Withrow, D., Bowers, S. J., Depner, C. M., González, A., Reynolds, A. C., & Wright, K. P. (2020) · Current Opinion in Endocrine and Metabolic Research · doi:10.1016/j.coemr.2020.11.009 · Cited by 58 · see citing works
Porcari, S., CICCARESE, C., Heidrich, V., Rondinella, D., Quaranta, G., Severino, A., Arduini, D., Buti, S., Fornarini, G., Primi, F., et al. (2026) · Nature Medicine · doi:10.1038/s41591-025-04189-2 · Cited by 56 · see citing works
Attaye, I., Warmbrunn, M. V., Boot, A. N. A. F., van der Wolk, S. C., Hutten, B. A., Daams, J. G., Herrema, H., & Nieuwdorp, M. (2022) · Gastroenterology · doi:10.1053/j.gastro.2022.02.011 · Cited by 54 · see citing works
Mitrović, M., Stanković-Popović, V., Tolinački, M., Golić, N., Bajić, S. S., Veljović, K., Nastasijević, B. J., Soldatović, I., Svorcan, P., & Dimkovic, N. B. (2022) · Journal of Renal Nutrition · doi:10.1053/j.jrn.2022.07.008 · Cited by 56 · see citing works
Wang, J., Feng, W., Zhang, S., Chen, L., Sheng, Y., Tang, F., He, J., Xu, X., Ao, H., & Peng, C. Y. (2019) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2019.111887 · Cited by 52 · see citing works
Lane, M., Howland, G., West, M., Hockey, M., Marx, W., Loughman, A., O’Hely, M., Jacka, F., & Rocks, T. (2020) · Obesity Research & Clinical Practice · doi:10.1016/j.orcp.2020.04.006 · Cited by 50 · see citing works
Djurić, Z. (2016) · Translational research · doi:10.1016/j.trsl.2016.07.017 · Cited by 49 · see citing works
Pepsin egg white hydrolysate modulates gut microbiota in Zucker obese rats
Requena, T., Miguel, M., Garcés‐Rimón, M., Martínez‐Cuesta, M. C., López‐Fandiño, R., & Peláez, C. (2017) · Food & Function · doi:10.1039/c6fo01571a · Cited by 49 · see citing works
Liu, Z., Liu, M., Meng, J., Wang, L., & Chen, M. (2023) · Journal of Future Foods · doi:10.1016/j.jfutfo.2023.07.004 · Cited by 45 · see citing works
Djurić, Z., Bassis, C. M., Plegue, M. A., Ren, J., Chan, R., Sidahmed, E., Turgeon, D. K., Ruffin, M. T., Kato, I., & Sen, A. (2017) · Journal of the Academy of Nutrition and Dietetics · doi:10.1016/j.jand.2017.09.013 · Cited by 45 · see citing works
The Gut/Lung Microbiome Axis in Obesity, Asthma, and Bariatric Surgery: A Literature Review
Kim, Y. J., Womble, J. T., Gunsch, C. K., & Ingram, J. L. (2021) · Obesity · doi:10.1002/oby.23107 · Cited by 45 · see citing works
Zhao, W., Duan, C.-C., Liu, Y., Lu, G., Lyu, Q., Liu, X., Zheng, J., Zhao, X., Wang, S., & Zhao, H. (2023) · Journal of Zhejiang University SCIENCE B · doi:10.1631/jzus.b2200491 · Cited by 44 · see citing works
Prescott, S. L., Millstein, R. A., Katzman, M. A., & Logan, A. C. (2016) · International Journal of Biodiversity · doi:10.1155/2016/2718275 · Cited by 45 · see citing works
Enteroendocrine cells: the gatekeepers of microbiome-gut-brain communication
Grundeken, E., & Aidy, S. E. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00810-x · Cited by 41 · see citing works
Zhou, L., Xiao, X., Zhang, Q., Zheng, J., Li, M., Wang, X., Deng, M., Zhai, X., & Liu, J. Y. (2019) · Food & Function · doi:10.1039/c9fo01046g · Cited by 41 · see citing works
Modeling gut-brain interactions in zebrafish
de Abreu, M. S., Giacomini, A. C. V. V., Sysoev, M., Demin, K. A., Alekseeva, P. A., Spagnoli, S., & Kalueff, A. V. (2019) · Brain Research Bulletin · doi:10.1016/j.brainresbull.2019.03.003 · Cited by 40 · see citing works
DeBenedictis, J. N., Nymo, S., Ollestad, K. H., Boyesen, G. A., Rehfeld, J. F., Holst, J. J., Truby, H., Kulseng, B. E., & Martins, C. (2020) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/clinem/dgaa202 · Cited by 40 · see citing works
Dong, T. S., Katzka, W. R., Yang, J. C., Chang, C., Arias-Jayo, N., Lagishetty, V., Balioukova, A., Chen, Y., Dutson, E., Li, Z., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2167170 · Cited by 37 · see citing works
Wang, A., Dongcheng, C., Zhang, H., Li, Q., Yan, Z., Qiu, Y., Xu, H., & Keji, C. (2019) · Pharmacological Research · doi:10.1016/j.phrs.2019.02.018 · Cited by 37 · see citing works
Fasting intervention and its clinical effects on the human host and microbiome
Forslund, S. K. (2022) · Journal of Internal Medicine · doi:10.1111/joim.13574 · Cited by 36 · see citing works
Song, H., Shen, X., Deng, R., Chu, Q., & Zheng, X. (2022) · European Journal of Nutrition · doi:10.1007/s00394-021-02771-1 · Cited by 36 · see citing works
Cuevas‐Sierra, A., Milagro, F. I., Guruceaga, E., Cuervo, M., Goñi, L., García‐Granero, M., Martínez, J. A., & Riezu‐Boj, J. I. (2022) · Clinical Nutrition · doi:10.1016/j.clnu.2022.06.008 · Cited by 36 · see citing works
The Microbiome as a Therapy in Pouchitis and Ulcerative Colitis
LeBlanc, J., Segal, J. P., Braz, L. M. D. C., & Hart, A. L. (2021) · Nutrients · doi:10.3390/nu13061780 · Cited by 35 · see citing works
Liu, Q., Zhang, Z., Ji, P., Liu, J., Chen, B., Mingyao, E., Qi, H., Hou, T., Huang, Q., Ding, L., et al. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.131872 · Cited by 34 · see citing works
Song, Z., Du, H., Zhang, M. H., Nie, Y., & Xu, Y. (2019) · Microorganisms · doi:10.3390/microorganisms7120606 · Cited by 34 · see citing works
Dietary restrictions modulate the gut microbiota: Implications for health and disease
Schmidt, N. S., & Lorentz, A. (2021) · Nutrition Research · doi:10.1016/j.nutres.2021.03.001 · Cited by 34 · see citing works
- Authors
- Louis, S., Tappu, R.-M., Damms-Machado, A., Huson, D. H., & Bischoff, S. C.
- Affiliations
- University of Hohenheim (DE)
- University of Tübingen (DE)
- Corresponding author
- Bischoff, Stephan C.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2016-02-26
- Volume
- 11
- Issue
- 2
- Pages
- e0149564
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC4769288
- OpenAlex
- W2281452758
- Cited by
- 269
- References
- 51
- Citations by year
- 2026: 14 · 2025: 21 · 2024: 21 · 2023: 26 · 2022: 41 · 2021: 45 · 2020: 30 · 2019: 23 · 2018: 20 · 2017: 21 · 2016: 7
- FWCI
- 12.23
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- National University of Singapore (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Bundesministerium für Bildung und Forschung (01GI1122H)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Epidemiology › Adipokines, Inflammation, and Metabolic Diseases
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- gut microbiota, obesity, weight loss, Akkermansia, Firmicutes/Bacteroidetes ratio, metabolic syndrome, weight loss maintenance, hypocaloric diet, lifestyle intervention, microbial biomarkers, Alistipes
- MeSH terms
- Bacillota, Gastrointestinal Microbiome, Adult, Female, Humans, Insulin Resistance, Male, Middle Aged, Obesity, Weight Loss, Bacteroidetes, Gastrointestinal Tract, Metagenome
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