REFERENCES

1. Procop GW. Molecular diagnostics for the detection and characterization of microbial pathogens. Clin Infect Dis 2007;45:S99-111.

2. Nikkari S, Lopez FA, Lepp PW, et al. Broad-range bacterial detection and the analysis of unexplained death and critical illness. Emerg Infect Dis 2002;8:188-94.

3. Clarridge JE III. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 2004;17:840-62.

4. Cummings LA, Kurosawa K, Hoogestraat DR, et al. Clinical next generation sequencing outperforms standard microbiological culture for characterizing polymicrobial samples. Clin Chem 2016;62:1465-73.

5. Ranjan R, Rani A, Metwally A, McGee HS, Perkins DL. Analysis of the microbiome: advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun 2016;469:967-77.

6. Wensel CR, Pluznick JL, Salzberg SL, Sears CL. Next-generation sequencing: insights to advance clinical investigations of the microbiome. J Clin Invest 2022;132:e154944.

7. Feigelman R, Kahlert CR, Baty F, et al. Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. Microbiome 2017;5:20.

8. Marotz CA, Sanders JG, Zuniga C, Zaramela LS, Knight R, Zengler K. Improving saliva shotgun metagenomics by chemical host DNA depletion. Microbiome 2018;6:42.

9. Horz HP, Scheer S, Vianna ME, Conrads G. New methods for selective isolation of bacterial DNA from human clinical specimens. Anaerobe 2010;16:47-53.

10. Ahannach S, Delanghe L, Spacova I, et al. Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples. iScience 2021;24:103306.

11. Bruggeling CE, Garza DR, Achouiti S, Mes W, Dutilh BE, Boleij A. Optimized bacterial DNA isolation method for microbiome analysis of human tissues. Microbiologyopen 2021;10:e1191.

12. Goltsman DSA, Sun CL, Proctor DM, et al. Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. Genome Res 2018;28:1467-80.

13. Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nat Rev Microbiol 2018;16:143-55.

14. Malone M, Johani K, Jensen SO, et al. Next generation DNA sequencing of tissues from infected diabetic foot ulcers. EBioMedicine 2017;21:142-9.

15. Thoendel M, Jeraldo PR, Greenwood-Quaintance KE, et al. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing. J Microbiol Methods 2016;127:141-5.

16. Hasan MR, Rawat A, Tang P, et al. Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing. J Clin Microbiol 2016;54:919-27.

17. Castelino M, Eyre S, Moat J, et al. Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform. BMC Microbiol 2017;17:23.

18. Heravi FS, Zakrzewski M, Vickery K, Hu H. Host DNA depletion efficiency of microbiome DNA enrichment methods in infected tissue samples. J Microbiol Methods 2020;170:105856.

19. Amar Y, Lagkouvardos I, Silva RL, et al. Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA. Microbiome 2021;9:123.

20. Charalampous T, Kay GL, Richardson H, et al. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol 2019;37:783-92.

21. Masud T, Kemp E. Corticosteroids in treatment of disseminated tuberculosis in patient with HIV infection. Br Med J 1988;296:464-5.

22. He Y, Fang K, Shi X, et al. Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia. J Transl Med 2022;20:195.

23. Khan MI, Ahhmed A, Shin JH, Baek JS, Kim MY, Kim JD. Green tea seed isolated saponins exerts antibacterial effects against various strains of gram positive and gram negative bacteria, a comprehensive study in vitro and in vivo. Evid Based Complement Alternat Med 2018;2018:3486106.

24. Milani C, Hevia A, Foroni E, et al. Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PLoS One 2013;8:e68739.

25. Handschur M, Karlic H, Hertel C, Pfeilstöcker M, Haslberger AG. Preanalytic removal of human DNA eliminates false signals in general 16S rDNA PCR monitoring of bacterial pathogens in blood. Comp Immunol Microbiol Infect Dis 2009;32:207-19.

26. Milani C, Lugli GA, Duranti S, et al. Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Sci Rep 2015;5:15782.

27. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-60.

28. Milani C, Casey E, Lugli GA, et al. Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX. Microbiome 2018;6:145.

29. Milani C, Lugli GA, Fontana F, et al. METAnnotatorX2: a comprehensive tool for deep and shallow metagenomic data set analyses. mSystems 2021;6:e0058321.

30. Hillmann B, Al-Ghalith GA, Shields-Cutler RR, et al. Evaluating the information content of shallow shotgun metagenomics. mSystems 2018;3:e00069-18.

31. Lupetti A, Barnini S, Morici P, Ghelardi E, Nibbering PH, Campa M. Saponin promotes rapid identification and antimicrobial susceptibility profiling of Gram-positive and Gram-negative bacteria in blood cultures with the Vitek 2 system. Eur J Clin Microbiol Infect Dis 2013;32:493-502.

32. Lee JE, Jo SJ, Park KG, et al. Evaluation of modified saponin preparation method for the direct identification and antimicrobial susceptibility testing from positive blood culture. J Microbiol Methods 2018;154:118-23.

33. Mai-Prochnow A, Clauson M, Hong J, Murphy AB. Gram positive and Gram negative bacteria differ in their sensitivity to cold plasma. Sci Rep 2016;6:38610.

34. Tagousop CN, Tamokou JD, Kengne IC, Ngnokam D, Voutquenne-Nazabadioko L. Antimicrobial activities of saponins from Melanthera elliptica and their synergistic effects with antibiotics against pathogenic phenotypes. Chem Cent J 2018;12:97.

35. Patra AK, Saxena J. The effect and mode of action of saponins on the microbial populations and fermentation in the rumen and ruminant production. Nutr Res Rev 2009;22:204-19.

36. Marquet M, Zöllkau J, Pastuschek J, et al. Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore’s adaptive sequencing. Sci Rep 2022;12:4000.

37. Ganda E, Beck KL, Haiminen N, et al. DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid. mSystems 2021;6:e0061921.

Microbiome Research Reports
ISSN 2771-5965 (Online)

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/