Microbiome diversity is a modifiable virulence factor for cryptosporidiosis

References

• Chalmers RM, Davies AP, Tyler K. Cryptosporidium. Microbiology (Reading). 2019;165(5):500–14. doi: 10.1099/mic.0.000764
   PubMed Web of Science ®Google Scholar
• Carey MA, Medlock GL, Alam M, et al. Megasphaera in the stool microbiota is negatively associated with diarrheal cryptosporidiosis. Clin Infect Dis. 2021;73(6):e1242–e51. doi: 10.1093/cid/ciab207
   PubMed Web of Science ®Google Scholar
• Nader JL, Mathers TC, Ward BJ, et al. Evolutionary genomics of anthroponosis in Cryptosporidium. Nat Microbiol. 2019;4(5):826–836. doi: 10.1038/s41564-019-0377-x
   PubMed Web of Science ®Google Scholar
• Girma M, Teshome W, Petros B, et al. Cryptosporidiosis and isosporiasis among HIV-positive individuals in south Ethiopia: a cross sectional study. BMC Infect Dis. 2014;14(1):100. doi: 10.1186/1471-2334-14-100
   PubMedGoogle Scholar
• Kotloff KL, Nataro JP, Blackwelder WC, et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the global enteric multicenter study, GEMS): a prospective, case-control study. Lancet. 2013;382(9888):209–222. doi: 10.1016/S0140-6736(13)60844-2
   PubMed Web of Science ®Google Scholar
• Bouzid M, Hunter PR, Chalmers RM, et al. Cryptosporidium pathogenicity and virulence. Clin Microbiol Rev. 2013;26(1):115–134. doi: 10.1128/CMR.00076-12
   PubMed Web of Science ®Google Scholar
• Caradonna T, Marangi M, Del Chierico F, et al. Detection and prevalence of protozoan parasites in ready-to-eat packaged salads on sale in Italy. Food Microbiol. 2017;67:67–75. doi: 10.1016/j.fm.2017.06.006
   PubMed Web of Science ®Google Scholar
• Current WL, Garcia LS. Cryptosporidiosis. Clin Microbiol Rev. 1991;4(3):325–358. doi: 10.1128/CMR.4.3.325
   PubMed Web of Science ®Google Scholar
• English ED, Guérin A, Tandel J, et al. Live imaging of the Cryptosporidium parvum life cycle reveals direct development of male and female gametes from type I meronts. PLoS Biol. 2022;20(4):e3001604. doi: 10.1371/journal.pbio.3001604
   PubMed Web of Science ®Google Scholar
• Guérin A, Striepen B. The biology of the intestinal intracellular parasite Cryptosporidium. Cell Host Microbe. 2020;28(4):509–515. doi: 10.1016/j.chom.2020.09.007
   PubMed Web of Science ®Google Scholar
• Chey WD, Kurlander J, Eswaran S. Irritable bowel syndrome: a clinical review. JAMA. 2015;313(9):949–958. doi: 10.1001/jama.2015.0954
   PubMed Web of Science ®Google Scholar
• Winter G, Hart RA, Charlesworth RPG, et al. Gut microbiome and depression: what we know and what we need to know. Rev Neurosci. 2018;29(6):629–643. doi: 10.1515/revneuro-2017-0072
   PubMed Web of Science ®Google Scholar
• Cresci GA, Bawden E. Gut microbiome: what we do and Don’t know. Nutr Clin Pract. 2015;30(6):734–746. doi: 10.1177/0884533615609899
   PubMed Web of Science ®Google Scholar
• Belizário JE, Faintuch J, Garay-Malpartida M. Gut microbiome dysbiosis and immunometabolism: new frontiers for treatment of metabolic diseases. Mediators Inflamm. 2018;2018:2037838. doi: 10.1155/2018/2037838
   PubMed Web of Science ®Google Scholar
• Grigor’eva IN. Gallstone disease, obesity and the Firmicutes/Bacteroidetes ratio as a possible biomarker of gut dysbiosis. J Pers Med. 2020;11(1):13. doi: 10.3390/jpm11010013
   PubMed Web of Science ®Google Scholar
• Wieërs G, Verbelen V, Van Den Driessche M, et al. Do probiotics during in-hospital antibiotic treatment prevent colonization of gut microbiota with multi-drug-resistant bacteria? A randomized placebo-controlled trial comparing saccharomyces to a mixture of Lactobacillus, Bifidobacterium, and saccharomyces. Front Public Health. 2021;8: doi: 10.3389/fpubh.2020.578089
   PubMed Web of Science ®Google Scholar
• Laurent F, Lacroix-Lamandé S. Innate immune responses play a key role in controlling infection of the intestinal epithelium by Cryptosporidium. Int J Parasitol. 2017;47(12):711–721. doi: 10.1016/j.ijpara.2017.08.001
   PubMed Web of Science ®Google Scholar
• Thaiss CA, Zmora N, Levy M, et al. The microbiome and innate immunity. Nature. 2016;535(7610):65–74. doi: 10.1038/nature18847
   PubMed Web of Science ®Google Scholar
• Kamada N, Seo SU, Chen GY, et al. Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol. 2013;13(5):321–335. doi: 10.1038/nri3430
   PubMed Web of Science ®Google Scholar
• Sherwin WB, Chao A, Jost L, et al. Information Theory Broadens the Spectrum of Molecular Ecology and evolution. Trends Ecol Evol. 2017;32(12):948–963. doi: 10.1016/j.tree.2017.09.012
   PubMed Web of Science ®Google Scholar
• Kim BR, Shin J, Guevarra R, et al. Deciphering diversity indices for a better understanding of microbial communities. J Microbiol Biotechnol. 2017;27(12):2089–2093. doi: 10.4014/jmb.1709.09027
   PubMed Web of Science ®Google Scholar
• Lemos LN, Fulthorpe RR, Triplett EW, et al. Rethinking microbial diversity analysis in the high throughput sequencing era. J Microbiol Methods. 2011;86(1):42–51. doi: 10.1016/j.mimet.2011.03.014
   PubMed Web of Science ®Google Scholar
• Simpson EH. Measurement of diversity. Nature. 1949;163(4148):688–. doi: 10.1038/163688a0
   Web of Science ®Google Scholar
• Rarefaction WA. Alpha diversity, and statistics. Front Microbiol. 2019;10:2407. doi: 10.3389/fmicb.2019.02407
   PubMed Web of Science ®Google Scholar
• Walters KE, Martiny JBH, Nabout JC. Alpha-, beta-, and gamma-diversity of bacteria varies across habitats. PLoS One. 2020;15(9):e0233872. doi: 10.1371/journal.pone.0233872
   PubMed Web of Science ®Google Scholar
• Sepkoski JJ Jr. Alpha, beta, or gamma: where does all the diversity go? Paleobiology. 1988;14(3):221–234. doi: 10.1017/S0094837300011969
   Web of Science ®Google Scholar
• Kers JG, Saccenti E. The power of microbiome studies: some considerations on which alpha and beta metrics to use and how to report results. Front Microbiol. 2021;12:796025. doi: 10.3389/fmicb.2021.796025
   PubMed Web of Science ®Google Scholar
• Munn Z, Stern C, Aromataris E, et al. What kind of systematic review should I conduct? A proposed typology and guidance for systematic reviewers in the medical and health sciences. BMC Med Res Methodol. 2018;18(1):5. doi: 10.1186/s12874-017-0468-4
   PubMed Web of Science ®Google Scholar
• Page MJ, McKenzie JE, Bossuyt PM, et al. The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. PLOS Med. 2021;18(3):e1003583. doi: 10.1371/journal.pmed.1003583
   PubMed Web of Science ®Google Scholar
• Ras R, Huynh K, Desoky E, et al. Perturbation of the intestinal microbiota of mice infected with Cryptosporidium parvum. Int J Parasitol. 2015;45(8):567–573. doi: 10.1016/j.ijpara.2015.03.005
   PubMed Web of Science ®Google Scholar
• Mammeri M, Chevillot A, Thomas M, et al. Cryptosporidium parvum-infected neonatal mice show gut microbiota remodelling using high-throughput sequencing analysis: preliminary results. Acta Parasitol. 2019;64(2):268–275. doi: 10.2478/s11686-019-00044-w
   PubMed Web of Science ®Google Scholar
• Mammeri M, Obregón DA, Chevillot A, et al. Cryptosporidium parvum infection depletes butyrate Producer bacteria in goat kid microbiome. Front Microbiol. 2020;11:548737. doi: 10.3389/fmicb.2020.548737
   PubMed Web of Science ®Google Scholar
• McKenney EA, Greene LK, Drea CM, et al. Down for the count: cryptosporidium infection depletes the gut microbiome in Coquerel’s sifakas. Microb Ecol Health Dis. 2017;28(1):1335165. doi: 10.1080/16512235.2017.1335165
   PubMedGoogle Scholar
• Charania R, Wade BE, McNair NN, et al. Changes in the microbiome of Cryptosporidium-infected mice correlate to differences in susceptibility and infection levels. Microorganisms. 2020;8(6):879. doi: 10.3390/microorganisms8060879
   PubMed Web of Science ®Google Scholar
• Alak JI, Wolf BW, Mdurvwa EG, et al. Effect of Lactobacillus reuteri on intestinal resistance to Cryptosporidium parvum infection in a murine model of acquired immunodeficiency syndrome. J Infect Dis. 1997;175(1):218–221. doi: 10.1093/infdis/175.1.218
   PubMed Web of Science ®Google Scholar
• Pickerd N, Tuthill D. Resolution of cryptosporidiosis with probiotic treatment. Postgrad Med J. 2004;80(940):112–113. doi: 10.1136/pmj.2003.014175
   PubMed Web of Science ®Google Scholar
• Oliveira BCM, Widmer G, Schaffner DW. Probiotic product enhances susceptibility of mice to cryptosporidiosis. Appl Environ Microbiol. 2018;84(21). doi: 10.1128/AEM.01408-18
   PubMed Web of Science ®Google Scholar
• Ichikawa-Seki M, Motooka D, Kinami A, et al. Specific increase of Fusobacterium in the faecal microbiota of neonatal calves infected with Cryptosporidium parvum. Sci Rep. 2019;9(1):12517. doi: 10.1038/s41598-019-48969-6
   PubMedGoogle Scholar
• Oliveira BCM, Bresciani KDS, Widmer G, et al. Deprivation of dietary fiber enhances susceptibility of mice to cryptosporidiosis. PLoS Negl Trop Dis. 2019;13(9):e0007411. doi: 10.1371/journal.pntd.0007411
   PubMed Web of Science ®Google Scholar
• VanDussen KL, Funkhouser-Jones LJ, Akey ME, et al. Neonatal mouse gut metabolites influence Cryptosporidium parvum infection in intestinal epithelial cells. MBio. 2020;11(6). doi: 10.1128/mBio.02582-20
   PubMed Web of Science ®Google Scholar
• Karpe AV, Hutton ML, Mileto SJ, et al. Cryptosporidiosis modulates the gut microbiome and metabolism in a murine infection model. Metabolites. 2021;11(6):380. doi: 10.3390/metabo11060380
   PubMed Web of Science ®Google Scholar
• Shannon CE. The mathematical theory of communication. 1963. MD Comput. 1997;14(4):306–317.
   PubMedGoogle Scholar
• Bourriaud C, Akoka S, Goupry S, et al. Butyrate production from lactate by human colonic microflora. Reprod Nutr Dev. 2002;42(1):S55–S.
   PubMedGoogle Scholar
• Stoeva MK, Garcia-So J, Justice N, et al. Butyrate-producing human gut symbiont, Clostridium butyricum, and its role in health and disease. Gut Microbes. 2021;13(1):1–28. doi: 10.1080/19490976.2021.1907272
   PubMed Web of Science ®Google Scholar
• Kim ET, Lee SJ, Kim TY, et al. Dynamic changes in fecal microbial communities of neonatal dairy calves by aging and Diarrhea. Animals (Basel). 2021;11(4):1113. doi: 10.3390/ani11041113
   PubMedGoogle Scholar
• Jandhyala SM, Talukdar R, Subramanyam C, et al. Role of the normal gut microbiota. World J Gastroenterol. 2015;21(29):8787–8803. doi: 10.3748/wjg.v21.i29.8787
   PubMed Web of Science ®Google Scholar
• Magne F, Gotteland M, Gauthier L, et al. The Firmicutes/Bacteroidetes ratio: a relevant marker of gut dysbiosis in obese patients? Nutrients. 2020;12(5):1474. doi: 10.3390/nu12051474
   PubMed Web of Science ®Google Scholar
• Stojanov S, Berlec A, Štrukelj B. The influence of probiotics on the Firmicutes/Bacteroidetes ratio in the treatment of obesity and inflammatory bowel disease. Microorganisms. 2020;8(11):1715. doi: 10.3390/microorganisms8111715
   PubMed Web of Science ®Google Scholar
• Chappell CL, Darkoh C, Shimmin L, et al. Fecal indole as a biomarker of susceptibility to Cryptosporidium infection. Infect Immun. 2016;84(8):2299–2306. doi: 10.1128/IAI.00336-16
   PubMed Web of Science ®Google Scholar
• Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015;33(9):496–503. doi: 10.1016/j.tibtech.2015.06.011
   PubMed Web of Science ®Google Scholar
• Gilbert JA, Quinn RA, Debelius J, et al. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 2016;535(7610):94–103. doi: 10.1038/nature18850
   PubMed Web of Science ®Google Scholar
• Markowiak P, Śliżewska K. Effects of probiotics, prebiotics, and Synbiotics on human health. Nutrients. 2017;9(9):1021. doi: 10.3390/nu9091021
   PubMed Web of Science ®Google Scholar
• Kelly SM, Munoz-Munoz J, van Sinderen D. Plant glycan metabolism by bifidobacteria. Front Microbiol. 2021;12:609418. doi: 10.3389/fmicb.2021.609418
   PubMed Web of Science ®Google Scholar
• Simpson HL, Campbell BJ. Review article: dietary fibre-microbiota interactions. Aliment Pharmacol Ther. 2015;42(2):158–179. doi: 10.1111/apt.13248
   PubMed Web of Science ®Google Scholar
• Hills RD Jr., Pontefract BA, Mishcon HR, et al. Gut microbiome: profound implications for diet and disease. Nutrients. 2019;11(7):1613. doi: 10.3390/nu11071613
   PubMed Web of Science ®Google Scholar