Open Access
Volume 28, 2021
Article Number 1
Number of page(s) 10
Published online 08 January 2021
  1. Adebayo A, Suryavanshi M, Bhute S, Agunloye A, Isokpehi R, Anumudu C, Shouche Y. 2017. The microbiome in urogenital schistosomiasis and induced bladder pathologies. PLoS Neglected Tropical Diseases, 11(8), e0005826. [CrossRef] [PubMed] [Google Scholar]
  2. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M’rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. 2011. Enterotypes of the human gut microbiome. Nature, 473(7346), 174–180. [CrossRef] [PubMed] [Google Scholar]
  3. Ashton JJ, Colquhoun CM, Cleary DW, Coelho T, Haggarty R, Mulder I, Batra A, Afzal NA, Beattie RM, Scott KP, Ennis S. 2017. 16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease. Medicine (Baltimore), 96(26), e7347. [CrossRef] [PubMed] [Google Scholar]
  4. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon J. 2005. Host-bacterial mutualism in the human intestine. Science, 307(5717), 1915–1920. [Google Scholar]
  5. Blais Lecours P, Marsolais D, Cormier Y, Berberi M, Haché C, Bourdages R, Duchaine C. 2014. Increased prevalence of Methanosphaera stadtmanae in inflammatory bowel diseases. PloS One, 9(2), e87734. [Google Scholar]
  6. Bloom SM, Bijanki VN, Nava GM, Sun L, Malvin NP, Donermeyer DL, Dunne WM, Allen PM, Stappenbeck TS. 2011. Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease. Cell Host & Microbe, 9(5), 390–403. [CrossRef] [PubMed] [Google Scholar]
  7. Bor B, Bedree JK, Shi W, McLean JS, He X. 2019. Saccharibacteria (TM7) in the human oral microbiome. Journal of Dental Research, 98(5), 500–509. [CrossRef] [PubMed] [Google Scholar]
  8. Chow J, Lee SM, Shen Y, Khosravi A, Mazmanian S. 2010. Host-bacterial symbiosis in health and disease. Advances in Immunology, 107, 243–274. [CrossRef] [PubMed] [Google Scholar]
  9. Cole J, Chai B, Farris R, Wang Q, Kulam-Syed-Mohideen A, McGarrell D, Bandela A, Cardenas E, Garrity G, Tiedje J. 2007. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Research, 35, D169–D172. [CrossRef] [PubMed] [Google Scholar]
  10. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. 2014. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Research, 42(Database issue), D633–D642. [CrossRef] [PubMed] [Google Scholar]
  11. Collins AJ, Murugkar PP, Dewhirst FE. 2019. Complete genome sequence of strain AC001, a novel cultured member of the human oral microbiome from the candidate Phylum Saccharibacteria (TM7). Microbiology Resource Announcements, 8(42), e01158-19. [CrossRef] [PubMed] [Google Scholar]
  12. Consortium H M P. 2012. Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–214. [CrossRef] [PubMed] [Google Scholar]
  13. Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O’Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P. 2018. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology, 3(1), 8–16. [CrossRef] [PubMed] [Google Scholar]
  14. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, Lakshmanan A, Wade WG. 2010. The human oral microbiome. Journal of Bacteriology, 192(19), 16. [Google Scholar]
  15. Dias LM, Folador ARC, Oliveira AM, Ramos RTJ, Silva A, Baraúna R. 2018. Genomic architecture of the two cold-adapted genera Exiguobacterium and Psychrobacter: evidence of functional reduction in the Exiguobacterium antarcticum B7 Genome. Genome Biology and Evolution, 10(3), 731–741. [CrossRef] [PubMed] [Google Scholar]
  16. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16), 2194–2200. [CrossRef] [PubMed] [Google Scholar]
  17. Fornbacke M, Clarsund M. 2013. Cold-adapted proteases as an emerging class of therapeutics. Infectious Diseases and Therapy, 2(1), 15–26. [CrossRef] [PubMed] [Google Scholar]
  18. Gaci N, Borrel G, Tottey W, O’Toole PW, Brugère J. 2014. Archaea and the human gut: new beginning of an old story. World Journal of Gastroenterology, 20(43), 16062–16078. [CrossRef] [PubMed] [Google Scholar]
  19. Gogleva AA, Kaparullina EN, Doronina NV, Trotsenko Y. 2010. Methylophilus flavus sp. nov. and Methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants. International Journal of Systematic and Evolutionary Microbiology, 60, 2623–2628. [CrossRef] [PubMed] [Google Scholar]
  20. Gong J, Qiu W, Zeng Q, Liu X, Sun X, Li H, Yang Y, Wu A, Bao J, Wang Y, Shu Y, Hu X, Bellanti JA, Zheng SG, Lu Y, Lu Z. 2018. Lack of short-chain fatty acids and overgrowth of opportunistic pathogens define dysbiosis of neuromyelitis optica spectrum disorders: a Chinese pilot study. Multiple Sclerosis, 25, 1352458518790396. [Google Scholar]
  21. Gorvitovskaia A, Holmes S, Huse S. 2016. Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome, 4, 15. [CrossRef] [PubMed] [Google Scholar]
  22. Gózd-Barszczewska A, Kozioł-Montewka M, Barszczewski P, Młodzińska A, Humińska K. 2017. Gut microbiome as a biomarker of cardiometabolic disorders. Annals of Agricultural and Environmental Medicine, 24(3), 416–422. [CrossRef] [Google Scholar]
  23. Guernier V, Brennan B, Yakob L, Milinovich G, Clements A, Soares MR. 2017. Gut microbiota disturbance during helminth infection: Can it affect cognition and behaviour of children? BMC Infectious Diseases, 17(1), 58. [CrossRef] [PubMed] [Google Scholar]
  24. Gülden E, Chao C, Tai N, Pearson JA, Peng J, Majewska-Szczepanik M, Zhou Z, Wong FS, Wen L. 2018. TRIF deficiency protects non-obese diabetic mice from type 1 diabetes by modulating the gut microbiota and dendritic cells. Journal of Autoimmunity, 93, 57–65. [CrossRef] [PubMed] [Google Scholar]
  25. Hams E, Aviello G, Fallon P. 2013. The schistosoma granuloma: friend or foe? Frontiers in Immunology, 4, 89. [CrossRef] [PubMed] [Google Scholar]
  26. He X, McLean JS, Edlund A, Yooseph S, Hall AP, Liu SY, Dorrestein PC, Esquenazi E, Hunter RC, Cheng G, Nelson KE, Lux R, Shi W. 2015. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proceedings of the National Academy of Sciences of the United States of America, 112(1), 244–249. [CrossRef] [PubMed] [Google Scholar]
  27. Henson MA, Phalak P. 2017. Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis. BMC Systems Biology, 11(1), 145. [CrossRef] [PubMed] [Google Scholar]
  28. Holzscheiter M, Layland LE, Loffredo-Verde E, Mair K, Vogelmann R, Langer R, Wagner H, Prazeres da Costa C. 2014. Lack of host gut microbiota alters immune responses and intestinal granuloma formation during schistosomiasis. Clinical and Experimental Immunology, 175(2), 246–257. [CrossRef] [PubMed] [Google Scholar]
  29. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar RD. 2015. Role of the normal gut microbiota. World Journal of Gastroenterology, 21(29), 8787–8803. [CrossRef] [PubMed] [Google Scholar]
  30. Jenkins TP, Peachey LE, Ajami NJ, MacDonald AS, Hsieh MH, Brindley PJ, Cantacessi C, Rinaldi G. 2018. Schistosoma mansoni infection is associated with quantitative and qualitative modifications of the mammalian intestinal microbiota. Scientific Reports, 8(1), 12072. [CrossRef] [PubMed] [Google Scholar]
  31. Katz N, Chaves A, Pellegrino J. 1972. A simple device for quantitative stool thick-smear technique in Schistosomiasis mansoni. Revista do Instituto de Medicina Tropical de São Paulo, 14(6), 397–400. [Google Scholar]
  32. Kay GL, Millard A, Sergeant MJ, Midzi N, Gwisai R, Mduluza T, Ivens A, Nausch N, Mutapi F, Pallen M. 2015. Differences in the faecal microbiome in Schistosoma haematobium infected children vs. uninfected children. PLoS Neglected Tropical Diseases, 9(6), e0003861. [CrossRef] [PubMed] [Google Scholar]
  33. Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RE. 2013. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Computational Biology, 9(1), e1002863. [CrossRef] [PubMed] [Google Scholar]
  34. Lee SC, Tang MS, Lim YA, Choy SH, Kurtz ZD, Cox LM, Gundra UM, Cho I, Bonneau R, Blaser MJ, Chua KH, Loke P. 2014. Helminth colonization is associated with increased diversity of the gut microbiota. PLoS Neglected Tropical Diseases, 8(5), e2880. [CrossRef] [PubMed] [Google Scholar]
  35. Love M, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. [CrossRef] [PubMed] [Google Scholar]
  36. Magoč T, Salzberg S. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (Oxford, England), 27(21), 2957–2963. [CrossRef] [PubMed] [Google Scholar]
  37. Maharshak N, Ringel Y, Katibian D, Lundqvist A, Sartor RB, Carroll IM, Ringel-Kulka T. 2018. Fecal and mucosa-associated intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Digestive Diseases and Sciences, 63(7), 1890–1899. [CrossRef] [PubMed] [Google Scholar]
  38. Mahmoodpoor F, Rahbar Saadat Y, Barzegari A, Ardalan M, Zununi Vahed S. 2017. The impact of gut microbiota on kidney function and pathogenesis. Biomedicine & Pharmacotherapy, 93, 412–419. [CrossRef] [Google Scholar]
  39. McMurdie PJ, Holmes S. 2014. Waste not, want not: Why rarefying microbiome data is inadmissible. PLoS Computational Biology, 10(4), e1003531. [CrossRef] [PubMed] [Google Scholar]
  40. Mejia R, Damania A, Jeun R, Bryan P, Vargas P, Juarez M, Cajal P, Nasser J, Krolewiecki A, Lefoulon E, Long C, Drake E, Cimino R, Slatko B. 2020. Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study. Parasites & Vectors, 13(1), 200. [CrossRef] [PubMed] [Google Scholar]
  41. Momen-Heravi F, Babic A, Tworoger SS, Zhang L, Wu K, Smith-Warner SA, Ogino S, Chan AT, Meyerhardt J, Giovannucci E, Fuchs C, Cho E, Michaud DS, Stampfer MJ, Yu YH, Kim D, Zhang X. 2017. Periodontal disease, tooth loss and colorectal cancer risk: results from the Nurses’ Health Study. International Journal of Cancer, 140(3), 646–652. [CrossRef] [PubMed] [Google Scholar]
  42. Murugkar PP, Collins AJ, Dewhirst FE. 2019. Complete genome sequence of strain pm004, a novel cultured member of the human oral microbiome from the candidate Phylum Saccharibacteria (TM7). Microbiology Resource Announcements, 8(42), e01159-19. [CrossRef] [PubMed] [Google Scholar]
  43. Rizzatti G, Lopetuso LR, Gibiino G, Binda C, Gasbarrini A. 2017. Proteobacteria: a common factor in human diseases. BioMed Research International, 9351507, 7. [Google Scholar]
  44. Rosa BA, Supali T, Gankpala L, Djuardi Y, Sartono E, Zhou Y, Fischer K, Martin J, Tyagi R, Bolay FK, Fischer PU, Yazdanbakhsh M, Mitreva M. 2018. Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia. Microbiome, 6(1), 33. [CrossRef] [PubMed] [Google Scholar]
  45. Safari Z, Gérard P. 2019. The links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD). Cellular and Molecular Life Sciences, 76(8), 1541–1558. [CrossRef] [PubMed] [Google Scholar]
  46. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75(23), 7537–7541. [CrossRef] [PubMed] [Google Scholar]
  47. Schneeberger PHH, Coulibaly JT, Panic G, Daubenberger C, Gueuning M, Frey JE, Keiser J. 2018. Investigations on the interplays between Schistosoma mansoni, praziquantel and the gut microbiome. Parasites & Vectors, 11(1), 168. [CrossRef] [PubMed] [Google Scholar]
  48. Seerangaiyan K, van Winkelhoff AJ, Harmsen HJM, Rossen JWA, Winkel E. 2017. The tongue microbiome in healthy subjects and patients with intra-oral halitosis. Journal of Breath Research, 11(3), 036010. [CrossRef] [PubMed] [Google Scholar]
  49. Sgambato D, Miranda A, Romano L, Romano M. 2017. Gut microbiota and gastric disease. Minerva Gastroenterologica e Dietologica, 63(4), 345–354. [PubMed] [Google Scholar]
  50. Sun LP, Wang W, Zuo YP, Zhang ZQ, Hong QB, Yang GJ, Zhu HR, Liang YS, Yang HT. 2017. An integrated environmental improvement of marshlands: impact on control and elimination of schistosomiasis in marshland regions along the Yangtze River, China. Infectious Diseases of Poverty, 6(1), 72. [CrossRef] [PubMed] [Google Scholar]
  51. Tan Y, Wang Y, Wang Y, Xu D, Huang Y, Wang D, Wang G, Rensing C, Zheng S. 2018. Novel mechanisms of selenate and selenite reduction in the obligate aerobic bacterium Comamonas testosteroni S44. Journal of Hazardous Materials, 359, 129–138. [CrossRef] [PubMed] [Google Scholar]
  52. Toro-Londono M, Bedoya-Urrego K, Garcia-Montoya G, Galvan-Diaz A, Alzate J. 2019. Intestinal parasitic infection alters bacterial gut microbiota in children. PeerJ, 7, e6200. [Google Scholar]
  53. Wu HJ, Ivanov II, Darce J, Hattori K, Shima T, Umesaki Y, Littman DR, Benoist C, Mathis D. 2010. Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity, 32(6), 815–827. [CrossRef] [PubMed] [Google Scholar]
  54. Yuan Z, Yan W, Wen C, Zheng J, Yang N, Sun C. 2020. Enterotype identification and its influence on regulating the duodenum metabolism in chickens. Poultry Science, 99(3), 1515–1527. [CrossRef] [PubMed] [Google Scholar]
  55. Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van‘t Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ. 2018. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. eLife, 7, e37816. [CrossRef] [PubMed] [Google Scholar]
  56. Zhang Y, Wang Y, Jiang Y, Pan W, Liu H, Yin J, Shen Y, Cao J. 2016. T follicular helper cells in patients with acute schistosomiasis. Parasites & Vectors, 9(1), 321. [CrossRef] [PubMed] [Google Scholar]
  57. Zhao Y, Yang S, Li B, Li W, Wang J, Chen Z, Yang J, Tan H, Li J. 2019. Schistosoma japonicum alterations of the mice gut microbiome via ova-induced granuloma. Frontiers in Microbiology, 10, 352. [CrossRef] [PubMed] [Google Scholar]
  58. Zou L, Ruan S. 2015. Schistosomiasis transmission and control in China. Acta Tropica, 143, 51–57. [CrossRef] [PubMed] [Google Scholar]

Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.

Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.

Initial download of the metrics may take a while.