Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem?
Open accessAbstract
Most of the Human diseases affecting westernized countries are associated with dysbiosis and loss of microbial diversity in the gut microbiota. The Western way of life, with a wide use of antibiotics and other environmental triggers, may reduce the number of bacterial predators leading to a decrease in microbial diversity of the Human gut. We argue that this phenomenon is similar to the process of ecosystem impoverishment in macro ecology where human activity decreases ecological niches, the size of predator populations, and finally the biodiversity. Such pauperization is fundamental since it reverses the evolution processes, drives life backward into diminished complexity, stability, and adaptability. A simple therapeutic approach could thus be to reintroduce bacterial predators and restore a bacterial diversity of the host microbiota.
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?
While the inherited genome is essentially stable for the lifetime of the host, the microbiome is immensely diverse, dynamic, and responsive to external input, enhancing its potential as a target for therapeutic intervention.
“While our inherited genome is essentially stable for the lifetime of the host, the microbiome is immensely diverse (Mosca et al., 2016;Pasolli et al., 2019), dynamic (Lloyd-Price et al., 2017), and responsive to external input, enhancing its potential as a target for therapeutic intervention”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Mosca et al., 2016
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
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
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
Food Web Complexity and Species Diversity
Paine, R. T. (1966) · The American Naturalist · doi:10.1086/282400 · Cited by 5,361 · cited 1× · see citing works
“In 1966, Paine was the first to observe a decrease of mussel species in a marine ecosystem when removing the starfishes (Paine, 1966).”
BackgroundInduction of Colonic Regulatory T Cells by Indigenous <i>Clostridium</i> Species
Atarashi, K., Tanoue, T., Shima, T., Imaoka, A., Kuwahara, T., Momose, Y., Cheng, G., Yamasaki, S., Saito, T., Ohba, Y., et al. (2011) · Science · doi:10.1126/science.1198469 · Cited by 3,752 · see citing works
Status and Ecological Effects of the World’s Largest Carnivores
Ripple, W. J., Estes, J. A., Beschta, R. L., Wilmers, C. C., Ritchie, E. G., Hebblewhite, M., Berger, J., Elmhagen, B., Letnic, M., Nelson, M. P., et al. (2014) · Science · doi:10.1126/science.1241484 · Cited by 3,667 · see citing works
Vrieze, A., Van Nood, E., Holleman, F., Salojärvi, J., Kootte, R. S., Bartelsman, J. F. W. M., Dallinga–Thie, G. M., Ackermans, M. T., Serlie, M. J., Oozeer, R., et al. (2012) · Gastroenterology · doi:10.1053/j.gastro.2012.06.031 · Cited by 2,913 · see citing works
Global Prevalence of and Risk Factors for Irritable Bowel Syndrome: A Meta-analysis
Lovell, R. M., & Ford, A. C. (2012) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2012.02.029 · Cited by 2,155 · see citing works
Eder, W., Ege, M. J., & von Mutius, E. (2006) · New England Journal of Medicine · doi:10.1056/nejmra054308 · Cited by 1,621 · 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
Jakobsson, H. E., Abrahamsson, T. R., Jenmalm, M. C., Harris, K., Quince, C., Jernberg, C., Björkstén, B., Engstrand, L., & Andersson, A. F. (2014) · Gut · doi:10.1136/gutjnl-2012-303249 · Cited by 1,011 · 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
Low gut microbiota diversity in early infancy precedes asthma at school age
Abrahamsson, T. R., Jakobsson, H. E., Andersson, A. F., Björkstén, B., Engstrand, L., & Jenmalm, M. C. (2014) · Clinical & Experimental Allergy · doi:10.1111/cea.12253 · Cited by 750 · see citing works
Explaining Microbial Population Genomics through Phage Predation
Rodriguez-Valera, F., Martin-Cuadrado, A.-B., Rodriguez-Brito, B., Pašić, L., Thingstad, T. F., Rohwer, F., & Mira, A. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2235 · Cited by 663 · see citing works
Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation
Jenq, R. R., Ubeda, C., Taur, Y., Menezes, C. C., Khanin, R., Dudakov, J. A., Liu, C., West, M. L., Singer, N. V., Equinda, M. J., et al. (2012) · Journal of Experimental Medicine · doi:10.1084/jem.20112408 · Cited by 626 · see citing works
Buffie, C. G., Jarchum, I., Equinda, M., Lipuma, L., Gobourne, A., Viale, A., Ubeda, C., Xavier, J., & Pamer, E. G. (2012) · Infection and Immunity · doi:10.1128/iai.05496-11 · Cited by 596 · cited 1× · see citing works
“ATB profoundly alter the structure of the intestinal microbiota (Buffie et al., 2012) and reduce the bacterial diversity (Dethlefsen et al., 2008; Pérez-Cobas et al., 2013; Zhao et al., 2014).”
BackgroundSchaubeck, M., Clavel, T., Calasan, J., Lagkouvardos, I., Haange, S. B., Jehmlich, N., Basic, M., Dupont, A., Hornef, M., Bergen, M. V., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-309333 · Cited by 447 · see citing works
Carroll, I. M., Ringel‐Kulka, T., Siddle, J. P., & Ringel, Y. (2012) · Neurogastroenterology & Motility · doi:10.1111/j.1365-2982.2012.01891.x · Cited by 425 · see citing works
Jalanka-Tuovinen, J., Salonen, A., Nikkilä, J., Immonen, O., Kekkonen, R., Lahti, L., Palva, A., & de Vos, W. M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023035 · Cited by 340 · see citing works
Prebiotics and probiotics; modifying and mining the microbiota
Quigley, E. M. M. (2010) · Pharmacological Research · doi:10.1016/j.phrs.2010.01.004 · Cited by 238 · see citing works
The role of gut microbiota in human obesity: Recent findings and future perspectives
Tagliabue, A., & Elli, M. (2013) · Nutrition, Metabolism and Cardiovascular Diseases · doi:10.1016/j.numecd.2012.09.002 · Cited by 118 · see citing works
Dotterud, C. K., Avershina, E., Sekelja, M., Simpson, M. R., Rudi, K., Storrø, O., Johnsen, R., & Øien, T. (2015) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0000000000000781 · Cited by 112 · see citing works
Flagged first, then by citations
Research works printed but not linked: 110
- Ahn J. Sinha R. Pei Z. Dominianni C. Wu J. Shi J.. (2013). Human gut microbiome and risk for colorectal cancer. J. Natl. Cancer Inst. 105, 1907– 1911. 10.1093/jnci/djt300 24316595 PMC3866154 · DOI · Paper page
- Allison S. D. Martiny J. B. H. (2008). Resistance, resilience, and redundancy in microbial communities. Proc. Natl. Acad. Sci. U.S.A. 105, 11512– 11519. 10.1073/pnas.0801925105 18695234 PMC2556421 · DOI
- Amre D. K. Lambrette P. Law L. Krupoves A. Chotard V. Costea F.. (2006). Investigating the hygiene hypothesis as a risk factor in pediatric onset crohn's disease: a case-control study. Am. J. Gastroenterol. 101, 1005– 1011. 10.1111/j.1572-0241.2006.00526.x 16573775 · DOI
- Andersson T. Ahlbom A. Magnusson C. Carlsson S. (2014). Prevalence and incidence of diabetes in stockholm county 1990-2010. PLoS ONE 9: e104033. 10.1371/journal.pone.0104033 25121976 PMC4133405 · DOI
- Atladottir H. O. Gyllenberg D. Langridge A. Sandin S. Hansen S. N. Leonard H.. (2015). The increasing prevalence of reported diagnoses of childhood psychiatric disorders: a descriptive multinational comparison. Eur. Child Adolesc. Psychiatry 24, 173– 183. 10.1007/s00787-014-0553-8 24796725 · DOI
- Atterbury R. J. Hobley L. Till R. Lambert C. Capeness M. J. Lerner T. R.. (2011). Effects of orally administered Bdellovibrio bacteriovorus on the well-being and salmonella colonization of young chicks. Appl. Environ. Microbiol. 77, 5794– 5803. 10.1128/AEM.00426-11 21705523 PMC3165243 · DOI
- Betrán A. P. Merialdi M. Lauer J. A. Bing-Shun W. Thomas J. Van Look P.. (2007). Rates of caesarean section: analysis of global, regional and national estimates. Paediatr. Perinat. Epidemiol. 21, 98– 113. 10.1111/j.1365-3016.2007.00786.x 17302638 · DOI
- Bhargava P. Mowry E. M. (2014). Gut microbiome and multiple sclerosis. Curr. Neurol. Neurosci. Rep. 14: 492. 10.1007/s11910-014-0492-2 25204849 · DOI · Paper page
- Bodansky H. J. Staines A. Stephenson C. Haigh D. Cartwright R. (1992). Evidence for an environmental effect in the aetiology of insulin dependent diabetes in a transmigratory population. BMJ 304, 1020– 1022. 10.1136/bmj.304.6833.1020 1586783 PMC1881717 · DOI
- Butchart S. H. M. Walpole M. Collen B. van Strien A. Scharlemann J. P. W. Almond R. E. A.. (2010). Global biodiversity: indicators of recent declines. Science 328, 1164– 1168. 10.1126/science.1187512 20430971 · DOI · Paper page
- Cahenzli J. Köller Y. Wyss M. Geuking M. B. McCoy K. D. (2013). Intestinal microbial diversity during early-life colonization shapes long-term IgE levels. Cell Host Microbe 14, 559– 570. 10.1016/j.chom.2013.10.004 24237701 PMC4049278 · DOI · Paper page
- Carrière J. (2014). Infectious etiopathogenesis of Crohn's disease. World J. Gastroenterol. 20: 12102. 10.3748/wjg.v20.i34.12102 25232246 PMC4161797 · DOI
- Cosson P. Soldati T. (2008). Eat, kill or die: when amoeba meets bacteria. Curr. Opin. Microbiol. 11, 271– 276. 10.1016/j.mib.2008.05.005 18550419 · DOI
- Costello E. K. Stagaman K. Dethlefsen L. Bohannan B. J. M. Relman D. A. (2012). The application of ecological theory toward an understanding of the human microbiome. Science 336, 1255– 1262. 10.1126/science.1224203 22674335 PMC4208626 · DOI · Paper page
- Cotillard A. Kennedy S. P. Kong L. C. Prifti E. Pons N. Le Chatelier E.. (2013). Dietary intervention impact on gut microbial gene richness. Nature 500, 585– 588. 10.1038/nature12480 23985875 · DOI · Paper page
- Creatore M. I. Moineddin R. Booth G. Manuel D. H. DesMeules M. McDermott S.. (2010). Age- and sex-related prevalence of diabetes mellitus among immigrants to Ontario, Canada. Can. Med. Assoc. J. 182, 781– 789. 10.1503/cmaj.091551 20403889 PMC2871200 · DOI
- Dashiff A. Junka R. A. Libera M. Kadouri D. E. (2011). Predation of human pathogens by the predatory bacteria Micavibrio aeruginosavorus and Bdellovibrio bacteriovorus: predation by M. aeruginosavorus and B. bacteriovorus. J. Appl. Microbiol. 110, 431– 444. 10.1111/j.1365-2672.2010.04900.x 21114596 · DOI
- Debast S. B. Bauer M. P. Kuijper E. J. on behalf of the Committee (2014). European society of clinical microbiology and infectious diseases: update of the treatment guidance document for Clostridium difficile infection. Clin. Microbiol. Infect. 20, 1– 26. 10.1111/1469-0691.12418 24118601 · DOI
- De Goffau M. C. Luopajarvi K. Knip M. Ilonen J. Ruohtula T. Harkonen T.. (2013). Fecal microbiota composition differs between children with -cell autoimmunity and those without. Diabetes 62, 1238– 1244. 10.2337/db12-0526 23274889 PMC3609581 · DOI
- Dethlefsen L. Huse S. Sogin M. L. Relman D. A. (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6: e280. 10.1371/journal.pbio.0060280 19018661 PMC2586385 · DOI · Paper page
- Dey N. Soergel D. A. Repo S. Brenner S. E. (2013). Association of gut microbiota with post-operative clinical course in Crohn's disease. BMC Gastroenterol. 13: 131. 10.1186/1471-230X-13-131 23964800 PMC3848607 · DOI
- Dolliver H. Gupta S. (2008). Antibiotic losses in leaching and surface runoff from manure-amended agricultural land. J. Environ. Qual. 37, 1227– 1237. 10.2134/jeq2007.0392 18453442 · DOI
- Durbán A. Abellán J. J. Jiménez-Hernández N. Salgado P. Ponce M. Ponce J. (2012). Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome: microbial diversity in irritable bowel syndrome. Environ. Microbiol. Rep. 4, 242– 247. 10.1111/j.1758-2229.2012.00327.x 23757279 · DOI
- Dwidar M. Monnappa A. K. Mitchell R. J. (2012). The dual probiotic and antibiotic nature of Bdellovibrio bacteriovorus. BMB Rep. 45, 71– 78. 10.5483/BMBRep.2012.45.2.71 22360883 · DOI
- Elmqvist T. Folke C. Nyström M. Peterson G. Bengtsson J. Walker B. (2003). Response diversity, ecosystem change, and resilience. Front. Ecol. Environ. 1: 488– 494. 10.1890/1540-9295(2003)001[0488:RDECAR]2.0.CO;2 · DOI · Paper page
- Faust K. Raes J. (2012). Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538– 550. 10.1038/nrmicro2832 22796884 · DOI
- Gallet R. Tully T. Evans M. E. K. (2009). Ecological conditions affect evolutionary trajectory in a predator-prey system. Evolution 63, 641– 651. 10.1111/j.1558-5646.2008.00559.x 19154363 · DOI
- Giongo A. Gano K. A. Crabb D. B. Mukherjee N. Novelo L. L. Casella G.. (2010). Toward defining the autoimmune microbiome for type 1 diabetes. ISME J. 5, 82– 91. 10.1038/ismej.2010.92 20613793 PMC3105672 · DOI · Paper page
- Graf D. Di Cagno R. Fåk F. Flint H. J. Nyman M. Saarela M.. (2015). Contribution of diet to the composition of the human gut microbiota. Microb. Ecol. Health Dis. 26: 26164. 10.3402/mehd.v26.26164 25656825 PMC4318938 · DOI
- Grüber C. Illi S. Plieth A. Sommerfeld C. Wahn U. (2002). Cultural adaptation is associated with atopy and wheezing among children of Turkish origin living in Germany. Clin. Exp. Allergy 32, 526– 531. 10.1046/j.0954-7894.2002.01331.x 11972597 · DOI
- Guarner F. (2014). Decade in review—gut microbiota: the gut microbiota era marches on. Nat. Rev. Gastroenterol. Hepatol. 11, 647– 649. 10.1038/nrgastro.2014.156 25201043 · DOI
- Hammond S. R. English D. R. McLeod J. G. (2000). The age-range of risk of developing multiple sclerosis: evidence from a migrant population in Australia. Brain J. Neurol. 123(Pt. 5), 968– 974. 10.1093/brain/123.5.968 10775541 · DOI
- Harjutsalo V. Sjöberg L. Tuomilehto J. (2008). Time trends in the incidence of type 1 diabetes in Finnish children: a cohort study. Lancet 371, 1777– 1782. 10.1016/S0140-6736(08)60765-5 18502302 · DOI · Paper page
- Holling C. S. (1973). Resilience and Stability of Ecological Systems. Annu. Rev. Ecol. Syst. 4, 1– 23. 10.1146/annurev.es.04.110173.000245 · DOI · Paper page
- Horton D. B. Scott F. I. Haynes K. Putt M. E. Rose C. D. Lewis J. D.. (2015). Antibiotic exposure and juvenile idiopathic arthritis: a case-control study. Pediatrics 136, e333– e343. 10.1542/peds.2015-0036 26195533 PMC4516942 · DOI
- Hughes T. P. (1994). Catastrophes, phase shifts, and large-scale degradation of a Caribbean coral reef. Science 265, 1547– 1551. 10.1126/science.265.5178.1547 17801530 · DOI
- Hunt D. E. Ward C. S. (2015). A network-based approach to disturbance transmission through microbial interactions. Front. Microbiol. 6: 1182. 10.3389/fmicb.2015.01182 26579091 PMC4621455 · DOI
- Huttenhower C. Gevers D. Knight R. Abubucker S. Badger J. H. Chinwalla A. T.. (2012). Structure, function and diversity of the healthy human microbiome. Nature 486, 207– 214. 10.1038/nature11234 22699609 PMC3564958 · DOI · Paper page
- Hviid A. Svanstrom H. Frisch M. (2011). Antibiotic use and inflammatory bowel diseases in childhood. Gut 60, 49– 54. 10.1136/gut.2010.219683 20966024 · DOI
- Iebba V. Santangelo F. Totino V. Nicoletti M. Gagliardi A. De Biase R. V.. (2013). Higher prevalence and abundance of Bdellovibrio bacteriovorus in the human gut of healthy subjects. PLoS ONE 8: e61608. 10.1371/annotation/b08ddcc9-dfdb-4fc1-b2ac-5a4af3051a91 23613881 PMC3628794 · DOI
- Iebba V. Totino V. Santangelo F. Gagliardi A. Ciotoli L. Virga A.. (2014). Bdellovibrio bacteriovorus directly attacks Pseudomonas aeruginosa and Staphylococcus aureus Cystic fibrosis isolates. Front. Microbiol. 5: 280. 10.3389/fmicb.2014.00280 24926292 PMC4046265 · DOI
- Ismail I. H. Oppedisano F. Joseph S. J. Boyle R. J. Licciardi P. V. Robins-Browne R. M.. (2012). Reduced gut microbial diversity in early life is associated with later development of eczema but not atopy in high-risk infants: microbial diversity and infant eczema. Pediatr. Allergy Immunol. 23, 674– 681. 10.1111/j.1399-3038.2012.01328.x 22831283 · DOI
- Kadouri D. E. To K. Shanks R. M. Q. Doi Y. (2013). Predatory bacteria: a potential ally against multidrug-resistant gram-negative pathogens. PLoS ONE 8: e63397. 10.1371/journal.pone.0063397 23650563 PMC3641118 · DOI
- Kang D.-W. Park J. G. Ilhan Z. E. Wallstrom G. LaBaer J. Adams J. B.. (2013). Reduced incidence of prevotella and other fermenters in intestinal microflora of autistic children. PLoS ONE 8: e68322. 10.1371/journal.pone.0068322 23844187 PMC3700858 · DOI · Paper page
- Koenig J. E. Spor A. Scalfone N. Fricker A. D. Stombaugh J. Knight R.. (2011). Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. U.S.A. 108(Suppl. 1), 4578– 4585. 10.1073/pnas.1000081107 20668239 PMC3063592 · DOI · Paper page
- Kostic A. D. Gevers D. Siljander H. Vatanen T. Hyötyläinen T. Hämäläinen A.-M.. (2015). The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe 17, 260– 273. 10.1016/j.chom.2015.01.001 25662751 PMC4689191 · DOI
- Kuehni C. E. Strippoli M.-P. Low N. Silverman M. (2007). Asthma in young south Asian women living in the United Kingdom: the importance of early life. Clin. Exp. Allergy 37, 47– 53. 10.1111/j.1365-2222.2006.02627.x 17210041 · DOI
- Latvala J. von Hertzen L. Lindholm H. Haahtela T. (2005). Trends in prevalence of asthma and allergy in Finnish young men: nationwide study, 1966-2003. BMJ 330, 1186– 1187. 10.1136/bmj.38448.603924.AE 15849204 PMC558015 · DOI · Paper page
- Lehtinen P. Ashorn M. Iltanen S. Jauhola R. Jauhonen P. Kolho K.-L.. (2011). Incidence trends of pediatric inflammatory bowel disease in Finland, 1987-2003, a nationwide study. Inflamm. Bowel Dis. 17, 1778– 1783. 10.1002/ibd.21550 21744433 · DOI
- Lessios H. A. Robertson D. R. Cubit J. D. (1984). Spread of diadema mass mortality through the Caribbean. Science 226, 335– 337. 10.1126/science.226.4672.335 17749884 · DOI
- Letnic M. Ritchie E. G. Dickman C. R. (2012). Top predators as biodiversity regulators: the dingo Canis lupus dingo as a case study. Biol. Rev. 87, 390– 413. 10.1111/j.1469-185X.2011.00203.x 22051057 · DOI · Paper page
- Ley R. E. Lozupone C. A. Hamady M. Knight R. Gordon J. I. (2008). Worlds within worlds: evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 6, 776– 788. 10.1038/nrmicro1978 18794915 PMC2664199 · DOI
- Lin A. Bik E. M. Costello E. K. Dethlefsen L. Haque R. Relman D. A.. (2013). Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS ONE 8: e53838. 10.1371/journal.pone.0053838 23349750 PMC3551965 · DOI · Paper page
- Lohi S. Mustalahti K. Kaukinen K. Laurila K. Collin P. Rissanen H.. (2007). Increasing prevalence of coeliac disease over time: increasing Prevalence Of Coeliac Disease. Aliment. Pharmacol. Ther. 26, 1217– 1225. 10.1111/j.1365-2036.2007.03502.x 17944736 · DOI
- Loozen G. Boon N. Pauwels M. Slomka V. Rodrigues Herrero E. Quirynen M.. (2015). Effect of Bdellovibrio bacteriovorus HD100 on multispecies oral communities. Anaerobe 35, 45– 53. 10.1016/j.anaerobe.2014.09.011 25252124 · DOI
- Lozupone C. A. Stombaugh J. I. Gordon J. I. Jansson J. K. Knight R. (2012). Diversity, stability and resilience of the human gut microbiota. Nature 489, 220– 230. 10.1038/nature11550 22972295 PMC3577372 · DOI · Paper page
- Manichanh C. Rigottier-Gois L. Bonnaud E. Gloux K. Pelletier E. Frangeul L.. (2006). Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55, 205– 211. 10.1136/gut.2005.073817 16188921 PMC1856500 · DOI · Paper page
- Martínez I. Stegen J. C. Maldonado-Gómez M. X. Eren A. M. Siba P. M. Greenhill A. R.. (2015). The gut microbiota of rural papua new guineans: composition, diversity patterns, and ecological processes. Cell Rep. 11, 527– 538. 10.1016/j.celrep.2015.03.049 25892234 · DOI · Paper page
- Martinez J. L. (2009). Environmental pollution by antibiotics and by antibiotic resistance determinants. Environ. Pollut. 157, 2893– 2902. 10.1016/j.envpol.2009.05.051 19560847 · DOI
- Matsuoka K. Kanai T. (2015). The gut microbiota and inflammatory bowel disease. Semin. Immunopathol. 37, 47– 55. 10.1007/s00281-014-0454-4 25420450 PMC4281375 · DOI · Paper page
- Mayr W. T. Pittock S. J. McClelland R. L. Jorgensen N. W. Noseworthy J. H. Rodriguez M. (2003). Incidence and prevalence of multiple sclerosis in Olmsted County, Minnesota, 1985-2000. Neurology 61, 1373– 1377. 10.1212/01.WNL.0000094316.90240.EB 14638958 · DOI
- McFall-Ngai M. (2007). Adaptive immunity: care for the community. Nature 445, 153– 153. 10.1038/445153a 17215830 · DOI
- McFall-Ngai M. Hadfield M. G. Bosch T. C. Carey H. V. Domazet-Lošo T. Douglas A. E.. (2013). Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. U.S.A. 110, 3229– 3236. 10.1073/pnas.1218525110 23391737 PMC3587249 · DOI
- Michail S. Durbin M. Turner D. Griffiths A. M. Mack D. R. Hyams J.. (2012). Alterations in the gut microbiome of children with severe ulcerative colitis. Inflamm. Bowel Dis. 18, 1799– 1808. 10.1002/ibd.22860 22170749 PMC3319508 · DOI
- Mills S. Shanahan F. Stanton C. Hill C. Coffey A. Ross R. P. (2013). Movers and shakers: influence of bacteriophages in shaping the mammalian gut microbiota. Gut Microbes 4, 4– 16. 10.4161/gmic.22371 23022738 PMC3555884 · DOI
- Molodecky N. A. Soon I. S. Rabi D. M. Ghali W. A. Ferris M. Chernoff G.. (2012). Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology 142, 46– 54.e42. 10.1053/j.gastro.2011.10.001 22001864 · DOI · Paper page
- Monnappa A. K. Dwidar M. Seo J. K. Hur J.-H. Mitchell R. J. (2014). Bdellovibrio bacteriovorus inhibits staphylococcus aureus biofilm formation and invasion into human epithelial cells. Sci. Rep. 4: 3811. 10.1038/srep03811 24448451 PMC3898049 · DOI
- Morton E. R. Lynch J. Froment A. Lafosse S. Heyer E. Przeworski M.. (2015). Variation in rural african gut microbiota is strongly correlated with colonization by entamoeba and subsistence. PLoS Genet. 11: e1005658. 10.1371/journal.pgen.1005658 26619199 PMC4664238 · DOI · Paper page
- Ng S. C. Bernstein C. N. Vatn M. H. Lakatos P. L. Loftus E. V. Tysk C.. (2013). Geographical variability and environmental risk factors in inflammatory bowel disease. Gut 62, 630– 649. 10.1136/gutjnl-2012-303661 23335431 · DOI
- Nyström M. Folke C. Moberg F. (2000). Coral reef disturbance and resilience in a human-dominated environment. Trends Ecol. Evol. 15, 413– 417. 10.1016/S0169-5347(00)01948-0 10998519 · DOI
- Ochman H. Worobey M. Kuo C.-H. Ndjango J.-B. N. Peeters M. Hahn B. H.. (2010). Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biol. 8: e1000546. 10.1371/journal.pbio.1000546 21103409 PMC2982803 · DOI
- OECD (2013). Caesarean sections, in Health at a Glance (Organisation for Economic Co-operation and Development), 98– 99. Available online at: http://www.oecd-ilibrary.org/content/chapter/health_glance-2013-39-en (Accessed September 9, 2014).
- Orel R. (2014). Intestinal microbiota, probiotics and prebiotics in inflammatory bowel disease. World J. Gastroenterol. 20: 11505. 10.3748/wjg.v20.i33.11505 25206258 PMC4155344 · DOI
- Pérez-Cobas A. E. Artacho A. Knecht H. Ferrús M. L. Friedrichs A. Ott S. J.. (2013). Differential effects of antibiotic therapy on the structure and function of human gut microbiota. PLoS ONE 8: e80201. 10.1371/journal.pone.0080201 24282523 PMC3839934 · DOI · Paper page
- Petersen C. Round J. L. (2014). Defining dysbiosis and its influence on host immunity and disease: how changes in microbiota structure influence health. Cell. Microbiol. 16, 1024– 1033. 10.1111/cmi.12308 24798552 PMC4143175 · DOI
- Pinheiro P. S. Sherman R. L. Trapido E. J. Fleming L. E. Huang Y. Gomez-Marin O.. (2009). Cancer Incidence in First Generation U.S. Hispanics: Cubans, Mexicans, Puerto Ricans, and New Latinos. Cancer Epidemiol. Biomarkers Prev. 18, 2162– 2169. 10.1158/1055-9965.EPI-09-0329 19661072 · DOI
- Reyes A. Haynes M. Hanson N. Angly F. E. Heath A. C. Rohwer F.. (2010). Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334– 338. 10.1038/nature09199 20631792 PMC2919852 · DOI
- Reyes A. Wu M. McNulty N. P. Rohwer F. L. Gordon J. I. (2013). Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proc. Natl. Acad. Sci.U.S.A. 110, 20236– 20241. 10.1073/pnas.1319470110 24259713 PMC3864308 · DOI · Paper page
- Ronn R. McCaig A. E. Griffiths B. S. Prosser J. I. (2002). Impact of protozoan grazing on bacterial community structure in soil microcosms. Appl. Environ. Microbiol. 68, 6094– 6105. 10.1128/AEM.68.12.6094-6105.2002 12450833 PMC134433 · DOI
- Russell S. L. Gold M. J. Hartmann M. Willing B. P. Thorson L. Wlodarska M.. (2012). Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep. 13, 440– 447. 10.1038/embor.2012.32 22422004 PMC3343350 · DOI · Paper page
- Sarmah A. K. Meyer M. T. Boxall A. B. A. (2006). A global perspective on the use, sales, exposure pathways, occurrence, fate and effects of veterinary antibiotics (VAs) in the environment. Chemosphere 65, 725– 759. 10.1016/j.chemosphere.2006.03.026 16677683 · DOI · Paper page
- Schippa S. Iebba V. Barbato M. Di Nardo G. Totino V. Checchi M. P. (2010). A distinctive “microbial signature” in celiac pediatric patients. BMC Microbiol. 10: 175 10.1186/1471-2180-10-175 20565734 PMC2906462 · DOI
- Schnorr S. L. Candela M. Rampelli S. Centanni M. Consolandi C. Basaglia G.. (2014). Gut microbiome of the Hadza hunter-gatherers. Nat. Commun. 5: 3654. 10.1038/ncomms4654 24736369 PMC3996546 · DOI · Paper page
- Schwartz B. S. Pollak J. Bailey-Davis L. Hirsch A. G. Cosgrove S. E. Nau C.. (2015). Antibiotic use and childhood body mass index trajectory. Int. J. Obes. 10.1038/ijo.2015.218. [Epub ahead of print]. 26486756 PMC4821740 · DOI
- Sha S. Liang J. Chen M. Xu B. Liang C. Wei N.. (2014). Systematic review: faecal microbiota transplantation therapy for digestive and nondigestive disorders in adults and children. Aliment. Pharmacol. Ther. 39, 1003– 1032. 10.1111/apt.12699 24641570 · DOI
- Sha S. Xu B. Wang X. Zhang Y. Wang H. Kong X.. (2013). The biodiversity and composition of the dominant fecal microbiota in patients with inflammatory bowel disease. Diagn. Microbiol. Infect. Dis. 75, 245– 251. 10.1016/j.diagmicrobio.2012.11.022 23276768 · DOI
- Shade A. Peter H. Allison S. D. Baho D. L. Berga M. Bürgmann H.. (2012). Fundamentals of microbial community resistance and resilience. Front. Microbiol. 3: 417. 10.3389/fmicb.2012.00417 23267351 PMC3525951 · DOI
- Shanks R. M. Q. Davra V. R. Romanowski E. G. Brothers K. M. Stella N. A. Godboley D.. (2013). An eye to a kill: using predatory bacteria to control gram-negative pathogens associated with ocular infections. PLoS ONE 8: e66723. 10.1371/journal.pone.0066723 23824756 PMC3688930 · DOI
- Shaw S. Y. Blanchard J. F. Bernstein C. N. (2010). Association between the use of antibiotics in the first year of life and pediatric inflammatory bowel disease. Am. J. Gastroenterol. 105, 2687– 2692. 10.1038/ajg.2010.398 20940708 · DOI
- Simpson H. L. Campbell B. J. (2015). Review article: dietary fibre–microbiota interactions. Aliment. Pharmacol. Ther. 42, 158– 179. 10.1111/apt.13248 26011307 PMC4949558 · DOI · Paper page
- Sockett R. E. Lambert C. (2004). Bdellovibrio as therapeutic agents: a predatory renaissance? Nat. Rev. Microbiol. 2, 669– 675. 10.1038/nrmicro959 15263901 · DOI
- Stein R. R. Bucci V. Toussaint N. C. Buffie C. G. Rätsch G. Pamer E. G.. (2013). Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput. Biol. 9: e1003388. 10.1371/journal.pcbi.1003388 24348232 PMC3861043 · DOI
- Stewart C. J. Marrs E. C. L. Nelson A. Lanyon C. Perry J. D. Embleton N. D.. (2013). Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis. PLoS ONE 8: e73465. 10.1371/journal.pone.0073465 24023682 PMC3758342 · DOI
- Stolp H. Starr M. P. (1963). Bdellovibrio bacteriovorus gen. et sp. n., a predatory, ectoparasitic, and bacteriolytic microorganism. Antonie Van Leeuwenhoek 29, 217– 248. 10.1007/BF02046064 14068454 · DOI
- Strauch E. Schwudke D. Linscheid M. (2007). Predatory mechanisms of Bdellovibrio and like organisms. Future Microbiol. 2, 63– 73. 10.2217/17460913.2.1.63 17661676 · DOI
- Suau A. Bonnet R. Sutren M. Godon J.-J. Gibson G. R. Collins M. D.. (1999). Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65, 4799– 4807. 10543789 PMC91647
- Szpak P. Orchard T. J. Salomon A. K. Gröcke D. R. (2013). Regional ecological variability and impact of the maritime fur trade on nearshore ecosystems in southern Haida Gwaii (British Columbia, Canada): evidence from stable isotope analysis of rockfish (Sebastes spp.) bone collagen. Archaeol. Anthropol. Sci. 5, 159– 182. 10.1007/s12520-013-0122-y · DOI
- Thaiss C. A. Zeevi D. Levy M. Zilberman-Schapira G. Suez J. Tengeler A. C.. (2014). Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell 159, 514– 529. 10.1016/j.cell.2014.09.048 25417104 · DOI · Paper page
- Turnbaugh P. J. Hamady M. Yatsunenko T. Cantarel B. L. Duncan A. Ley R. E.. (2009). A core gut microbiome in obese and lean twins. Nature 457, 480– 484. 10.1038/nature07540 19043404 PMC2677729 · DOI · Paper page
- Ungaro R. Bernstein C. N. Gearry R. Hviid A. Kolho K.-L. Kronman M. P. (2014). Antibiotics associated with increased risk of new-onset crohn's disease but not ulcerative colitis: a meta-analysis. Am. J. Gastroenterol. 109, 1728– 1738. 10.1038/ajg.2014.246 (Accessed November 6, 2014). 25223575 · DOI
- Van Essche M. Quirynen M. Sliepen I. Loozen G. Boon N. Van Eldere J. (2011). Killing of anaerobic pathogens by predatory bacteria: bacterial predation on anaerobic pathogens. Mol. Oral Microbiol. 26, 52– 61. 10.1111/j.2041-1014.2010.00595.x 21214872 · DOI
- Vellend M. (2010). Conceptual synthesis in community ecology. Q. Rev. Biol. 85, 183– 206. 10.1086/652373 20565040 · DOI
- Vrieze A. de Groot P. F. Kootte R. S. Knaapen M. van Nood E. Nieuwdorp M. (2013). Fecal transplant: a safe and sustainable clinical therapy for restoring intestinal microbial balance in human disease? Best Pract. Res. Clin. Gastroenterol. 27, 127– 137. 10.1016/j.bpg.2013.03.003 23768558 · DOI
- Wang M. Karlsson C. Olsson C. Adlerberth I. Wold A. E. Strachan D. P.. (2008). Reduced diversity in the early fecal microbiota of infants with atopic eczema. J. Allergy Clin. Immunol. 121, 129– 134. 10.1016/j.jaci.2007.09.011 18028995 · DOI
- Wier A. M. Nyholm S. V. Mandel M. J. Massengo-Tiassé R. P. Schaefer A. L. Koroleva I.. (2010). Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proc. Natl. Acad. Sci. U.S.A. 107, 2259– 2264. 10.1073/pnas.0909712107 20133870 PMC2836665 · DOI
- Wu G. D. Compher C. Chen E. Z. Smith S. A. Shah R. D. Bittinger K.. (2016). Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut 65, 63– 72. 10.1136/gutjnl-2014-308209 25431456 PMC4583329 · DOI · Paper page
- Yatsunenko T. Rey F. E. Manary M. J. Trehan I. Dominguez-Bello M. G. Contreras M.. (2012). Human gut microbiome viewed across age and geography. Nature 486, 222– 227. 10.1038/nature11053 22699611 PMC3376388 · DOI · Paper page
- Zeissig S. Blumberg R. S. (2014). Life at the beginning: perturbation of the microbiota by antibiotics in early life and its role in health and disease. Nat. Immunol. 15, 307– 310. 10.1038/ni.2847 24646587 · DOI
- Zelezniak A. Andrejev S. Ponomarova O. Mende D. R. Bork P. Patil K. R. (2015). Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc. Natl. Acad. Sci. U.S.A. 112, 6449– 6454. 10.1073/pnas.1421834112 25941371 PMC4443341 · DOI · Paper page
- Zhao J. Murray S. LiPuma J. J. (2014). Modeling the impact of antibiotic exposure on human microbiota. Sci. Rep. 4: 4345. 10.1038/srep04345 24614401 PMC3949250 · DOI
Cited by
Sorted by citations
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
Dysbiosis and the immune system
Levy, M., Kolodziejczyk, A. A., Thaiss, C. A., & Elinav, E. (2017) · Nature Reviews Immunology · doi:10.1038/nri.2017.7 · Cited by 1,769 · see citing works
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
Health Benefits of Heat-Killed (Tyndallized) Probiotics: An Overview
Piqué, N., Berlanga, M., & Miñana-Galbis, D. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20102534 · Cited by 642 · see citing works
The gut microbiome in human neurological disease: A review
Tremlett, H., Bauer, K. C., Appel‐Cresswell, S., Finlay, B. B., & Waubant, E. (2017) · Annals of Neurology · doi:10.1002/ana.24901 · Cited by 535 · see citing works
The Relationship Between the Human Genome and Microbiome Comes into View
Goodrich, J. K., Davenport, E. R., Clark, A. G., & Ley, R. E. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155532 · Cited by 311 · 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
Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications
Le Bastard, Q., Al‐Ghalith, G. A., Grégoire, M., Chapelet, G., Javaudin, F., Dailly, E., Batard, E., Knights, D., & Montassier, E. (2018) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.14451 · Cited by 263 · see citing works
Diet-driven microbiota dysbiosis is associated with vagal remodeling and obesity
Sen, T., Cawthon, C. R., Ihde, B. T., Hajnal, A., DiLorenzo, P. M., de La Serre, C. B., & Czaja, K. (2017) · Physiology & Behavior · doi:10.1016/j.physbeh.2017.02.027 · Cited by 239 · see citing works
Gut inflammation and dysbiosis in human motor neuron disease
Rowin, J., Xia, Y., Jung, B., & Sun, J. (2017) · Physiological Reports · doi:10.14814/phy2.13443 · Cited by 224 · see citing works
“Dysbiosis (e.g., loss of microbial diversity in the gut microbiota) are correlated with intestinal inflammation and change in intestinal integrity (Sun and Chang 2014; Mosca et al. 2016).”
BackgroundChidambaram, S. B., Essa, M. M., Rathipriya, A. G., Bishir, M., Ray, B., Mahalakshmi, A. M., Tousif, A. H., Sakharkar, M. K., Kashyap, R. S., Friedland, R. P., et al. (2022) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2021.107988 · Cited by 204 · see citing works
Klimenko, N. S., Tyakht, A. V., Popenko, A. S., Vasiliev, A. S., Altukhov, I. A., Ischenko, D. S., Shashkova, T. I., Efimova, D. A., Nikogosov, D. A., Osipenko, D. A., et al. (2018) · Nutrients · doi:10.3390/nu10050576 · Cited by 123 · see citing works
Approaches and advances in the genetic causes of autoimmune disease and their implications
Inshaw, J. R. J., Cutler, A. J., Burren, O. S., Stefana, M. I., & Todd, J. A. (2018) · Nature Immunology · doi:10.1038/s41590-018-0129-8 · Cited by 70 · see citing works
Koopen, A. M., Almeida, E. L., Attaye, I., Witjes, J. J., Rampanelli, E., Majait, S., Kemper, M., Levels, J. H. M., Schimmel, A. W. M., Herrema, H., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.662159 · Cited by 64 · see citing works
Stanisavljević, S., Čepić, A., Bojić, S., Veljović, K., Mihajlović, S., Đedović, N., Jevtić, B., Momčilović, M., Lazarević, M., Mostarica Stojković, M., et al. (2019) · Scientific Reports · doi:10.1038/s41598-018-37505-7 · Cited by 43 · see citing works
Moody microbiome: Challenges and chances
Kuo, P.-H., & Chung, Y.-C. E. (2019) · Journal of the Formosan Medical Association · doi:10.1016/j.jfma.2018.09.004 · Cited by 40 · see citing works
Tomofuji, Y., Kishikawa, T., Maeda, Y., Ogawa, K., Otake-Kasamoto, Y., Kawabata, S., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100219 · Cited by 35 · see citing works
The endocannabinoid system: a bridge between alzheimer’s disease and gut microbiota
Bisogno, T., Lauritano, A., & Piscitelli, F. (2021) · Life · doi:10.3390/life11090934 · Cited by 16 · see citing works
Oey, O., Liu, Y.-Y., Sunjaya, A. F., Simadibrata, D. M., Khattak, M. A., & Gray, E. (2022) · World Journal of Clinical Oncology · doi:10.5306/wjco.v13.i11.929 · Cited by 15 · see citing works
- Authors
- Mosca, A., Leclerc, M., & Hugot, J. P.
- Affiliations
- Inserm (FR)
- AgroParisTech (FR)
- Corresponding author
- Mosca, Alexis
- Venue
- Frontiers in Microbiology
- Publisher
- Frontiers Media SA
- Published
- 2016-03-31
- Volume
- 7
- Pages
- 455-455
- ISSN
- 1664-302X (ISSN-L)
- PMC
- PMC4815357
- OpenAlex
- W2324431491
- Cited by
- 612
- References
- 21
- Citations by year
- 2026: 33 · 2025: 42 · 2024: 72 · 2023: 86 · 2022: 120 · 2021: 89 · 2020: 59 · 2019: 53 · 2018: 30 · 2017: 24 · 2016: 3
- FWCI
- 19.06
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Frontiers in Microbiology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Laboratoire d'Excellence Inflamex (ANR-11-IDEX-0005-02)
- Agence Nationale de la Recherche (ANR 11 IDEX 0005-02, IDEX-0005, ANR-11-IDEX, ANR-11-IDEX-0005)
- Institut National de la Santé et de la Recherche Médicale
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Keywords
- gut microbiota diversity, dysbiosis, bacterial predators, microbial diversity loss, antibiotic use, biodiversity loss, ecological niche, human disease, microbiota restoration
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