Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Keisam, Santosh ^a,b   Romi, Wahengbam ^a,b   Ahmed, Giasuddin ^b   Jeyaram, Kumaraswamy ^a  

^a INSTITUTE OF BIORESOURCES AND SUSTAINABLE DEVELOPMENT   (India)

^b GAUHATI UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ACETOBACTERACEAE; AMPLICON; BACILLACEAE; BAMBOO; CLOSTRIDIACEAE; CYTOLYSIS; DNA EXTRACTION; ECOLOGICAL NICHE; ECOLOGY; FERMENTED PRODUCT; FISH; LACTIC ACID BACTERIUM; METAGENOME; METAGENOMICS; MICROBIAL COMMUNITY; MILK; MINING; NONHUMAN; POLYMERASE CHAIN REACTION; QUANTITATIVE STUDY; SOYBEAN; YEAST;

EID: 84989257100     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep34155     Document Type: Article

References (55)

1. Rantsiou, K. et al. Culture-dependent and-independent methods to investigate the microbial ecology of Italian fermented sausages. Appl. Environ. Microbiol. 71, 1977-1986 (2005).
2. Delbes, C., Ali-Mandjee, L., Montel, M. C. Monitoring bacterial communities in raw milk and cheese by culture-dependent and-independent 16S rRNA gene-based analyses. Appl. Environ. Microbiol. 73, 1882-1891 (2007).
3. Quail, M. A. et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13, 341 (2012).
4. Ercolini, D. High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology. Appl. Environ. Microbiol. 79, 3148-3155 (2013).
5. Polka, J., Rebecchi, A., Pisacane, V., Morelli, L., Puglisi, E. Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons. Food Microbiol. 46, 342-356 (2015).
6. Romi, W., Ahmed, G., Jeyaram, K. Three-phase succession of autochthonous lactic acid bacteria to reach a stable ecosystem within 7 days of natural bamboo shoot fermentation as revealed by different molecular approaches. Mol. Ecol. 24, 3372-3389 (2015).
7. Liu, Z., Lozupone, C., Hamady, M., Bushman, F. D., Knight, R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 35, e120 (2007).
8. Cai, L., Zhang, T. Detecting human bacterial pathogens in wastewater treatment plants by a high-throughput shotgun sequencing technique. Environ. Sci. Technol. 47, 5433-5441 (2013).
9. Lozupone, C. A. et al. Meta-analyses of studies of the human microbiota. Genome Res. 23, 1704-1714 (2013).
10. Hurt, R. A. et al. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67, 4495-4503 (2001).
11. Martin-Laurent, F. et al. DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl. Environ. Microbiol. 67, 2354-2359 (2001).
12. Luna, G. M., Dell'Anno, A., Danovaro, R. DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environ. Microbiol. 8, 308-320 (2006).
13. Kostic, T. et al. A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of nonpathogens. Anal. Biochem. 360, 244-254 (2007).
14. Courtois, S. et al. Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ. Microbiol. 3, 431-439 (2001).
15. Roose-Amsaleg, C., Garnier-Sillam, E., Harry, M. Extraction and purification of microbial DNA from soil and sediment samples. Appl. Soil Ecol. 18, 47-60 (2001).
16. Abriouel, H. et al. Culture-independent analysis of the microbial composition of the African traditional fermented foods poto poto and degue by using three different DNA extraction methods. Int. J. Food Microbiol. 111, 228-233 (2006).
17. Salonen, A. et al. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J. Microbiol. Methods. 81, 127-134 (2010).
18. Delmont, T. O., Simonet, P., Vogel, T. M. Describing microbial communities and performing global comparisons in the 'omic era. ISME J. 6, 1625-1628 (2012).
19. Flórez, A. B., Mayo, B. Microbial diversity and succession during the manufacture and ripening of traditional, Spanish, blue-veined Cabrales cheese, as determined by PCR-DGGE. Int. J. Food Microbiol. 110, 165-171 (2006).
20. Garcia-Armisen, T. et al. Diversity of the total bacterial community associated with Ghanaian and Brazilian cocoa bean fermentation samples as revealed by a 16S rRNA gene clone library. Appl. Microbiol. Biotechnol. 87, 2281-2292 (2010).
21. Quigley, L. et al. A comparison of methods used to extract bacterial DNA from raw milk and raw milk cheese. J. Appl. Microbiol. 113, 96-105 (2012).
22. Hazen, T. C., Rocha, A. M., Techtmann, S. M. Advances in monitoring environmental microbes. Curr. Opin. Biotechnol. 24, 526-533 (2013).
23. Forney, L. J., Zhou, X., Brown, C. J. Molecular microbial ecology: land of the one-eyed king. Curr. Opin. Microbiol. 7, 210-220 (2004).
24. Stach, J. E., Bathe, S., Clapp, J. P., Burns, R. G. PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods. FEMS Microbiol. Ecol. 36, 139-151 (2001).
25. Ning, J. et al. Different influences of DNA purity indices and quantity on PCR-based DGGE and functional gene microarray in soil microbial community study. Appl. Microbiol. Biotechnol. 82, 983-993 (2009).
26. Wagner, A. O., Praeg, N., Reitschuler, C., Illmer, P. Effect of DNA extraction procedure, repeated extraction and ethidium monoazide (EMA)/propidium monoazide (PMA) treatment on overall DNA yield and impact on microbial fingerprints for bacteria, fungi and archaea in a reference soil. Appl. Soil Ecol. 93, 56-64 (2015).
27. Devi, K. R., Deka, M., Jeyaram, K. Bacterial dynamics during yearlong spontaneous fermentation for production of ngari, a dry fermented fish product of Northeast India. Int. J. Food Microbiol. 199, 62-71 (2015).
28. Chaillou, S. et al. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage. ISME J. 9, 1105-1118 (2015).
29. Guo, F., Zhang, T. Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing. Appl. Microbiol. Biotechnol. 97, 4607-4616 (2013).
30. Starke, I. C., Vahjen, W., Pieper, R., Zentek, J. The influence of DNA extraction procedure and primer set on the bacterial community analysis by pyrosequencing of barcoded 16S rRNA gene amplicons. Mol. Biol. Int. 2014, 548683 (2014).
31. Mackenzie, B. W., Waite, D. W., Taylor, M. W. Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences. Front. Microbiol. 6, 130 (2015).
32. Lazarevic, V., Gaia, N., Girard, M., Francois, P., Schrenzel, J. Comparison of DNA extraction methods in analysis of salivary bacterial communities. PLoS One 8, e67699 (2013).
33. Abusleme, L., Hong, B.-Y., Dupuy, A. K., Strausbaugh, L. D., Diaz, P. I. Influence of DNA extraction on oral microbial profiles obtained via 16S rRNA gene sequencing. J. Oral Microbiol. 6 (2014).
34. Henderson, G. et al. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One 8, e74787 (2013).
35. Terrat, S. et al. Molecular biomass and MetaTaxogenomic assessment of soil microbial communities as influenced by soil DNA extraction procedure. Microb Biotechnol 5, 135-141 (2012).
36. Vandeventer, P. E. et al. Mechanical disruption of lysis-resistant bacterial cells by use of a miniature, low-power, disposable device. J. Clin. Microbiol. 49, 2533-2539 (2011).
37. Maukonen, J., Simões, C., Saarela, M. The currently used commercial DNA-extraction methods give different results of Clostridial and Actinobacterial populations derived from human fecal samples. FEMS Microbiol. Ecol. 79, 697-708 (2012).
38. Sohrabi, M. et al. The yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodology. J Microbiol Methods 122, 64-72 (2016).
39. Yuan, S., Cohen, D. B., Ravel, J., Abdo, Z., Forney, L. J. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One 7, e33865 (2012).
40. Gajer, P. et al. Temporal dynamics of the human vaginal microbiota. Sci Transl Med 4, 132-152 (2012).
41. Kennedy, K., Hall, M. W., Lynch, M. D., Moreno-Hagelsieb, G., Neufeld, J. D. Evaluating bias of illumina-based bacterial 16S rRNA gene profiles. Appl Environ Microbiol 80, 5717-5722 (2014).
42. Delmont, T. O. et al. Accessing the soil metagenome for studies of microbial diversity. Appl. Environ. Microbiol. 77, 1315-1324 (2011).
43. Brooks, J. P. et al. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol. 15, 66 (2015).
44. Rubin, B. E. et al. DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure. Microbiol. Open 3, 910-921 (2014).
45. Zhou, J. et al. Random sampling process leads to overestimation of beta-diversity of microbial communities. MBio 4, e00324-00313 (2013).
46. Soergel, D. A., Dey, N., Knight, R., Brenner, S. E. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. ISME J. 6, 1440-1444 (2012).
47. Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencingbased diversity studies. Nucleic Acids Res. 41, e1 (2013).
48. Ercolini, D., Hill, P. J., Dodd, C. E. Bacterial community structure and location in Stilton cheese. Appl. Environ. Microbiol. 69, 3540-3548 (2003).
49. Ritalahti, K. M. et al. Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Appl. Environ. Miicrobiol. 72, 2765-2774 (2006).
50. Hammer, ∅., Harper, D., Ryan, P. Paleontological Statistics Software Package for education and data analysis. Palaeontologia Electronica 4, 1-9 (2001).
51. Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621-1624 (2012).
52. Meyer, F. et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386 (2008).
53. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336 (2010).
54. Hulsen, T., de Vlieg, J., Alkema, W. BioVenn-a web application for the comparison and visualization of biological lists using areaproportional Venn diagrams. BMC Genomics 9, 488 (2008).
55. Spitzer, M., Wildenhain, J., Rappsilber, J., Tyers, M. BoxPlotR: a web tool for generation of box plots. Nat. Methods 11, 121-122 (2014).