Skip to main content
SpringerLink
Log in

BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies

  • Methods
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Recent advances in science and technology are leading to a revision and re-orientation of methodologies, addressing old and current issues under a new perspective. Advances in next generation sequencing (NGS) are allowing comparative analysis of the abundance and diversity of whole microbial communities, generating a large amount of data and findings at a systems level. The current limitation for biologists has been the increasing demand for computational power and training required for processing of NGS data. Here, we describe the deployment of the Brazilian Microbiome Project Operating System (BMPOS), a flexible and user-friendly Linux distribution dedicated to microbiome studies. The Brazilian Microbiome Project (BMP) has developed data analyses pipelines for metagenomic studies (phylogenetic marker genes), conducted using the two main high-throughput sequencing platforms (Ion Torrent and Illumina MiSeq). The BMPOS is freely available and possesses the entire requirement of bioinformatics packages and databases to perform all the pipelines suggested by the BMP team. The BMPOS may be used as a bootable live USB stick or installed in any computer with at least 1 GHz CPU and 512 MB RAM, independent of the operating system previously installed. The BMPOS has proved to be effective for sequences processing, sequences clustering, alignment, taxonomic annotation, statistical analysis, and plotting of metagenomic data. The BMPOS has been used during several metagenomic analyses courses, being valuable as a tool for training, and an excellent starting point to anyone interested in performing metagenomic studies. The BMPOS and its documentation are available at http://www.brmicrobiome.org.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C (2015) Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat Rev Microbiol 13(6):360–372

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Siqueira JF Jr, Fouad AF, Rôças (2012) Pyrosequencing as a tool for better understanding of human microbiomes. J Oral Microbiol 4:10. doi:10.3402/jom.v4i0.10743

    Article  PubMed Central  Google Scholar 

  3. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AK, Kent AD, Daroub SH, Camargo FA, Farmerie WG, Triplett EW (2015) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1(4):283–290

    Google Scholar 

  4. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6(8):1621–1624

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C (2014) Ten years of next-generation sequencing technology. Trends Genet 30(9):418–426

    Article  PubMed  Google Scholar 

  6. Schulthess TC (2015) Programming revisited. Nat Phys 11(5):369–373

    Article  Google Scholar 

  7. NERC Environmental Bioinformatics Centre. Bio-Linux. 2009. [http://environmentalomics.org/bio-linux/]

  8. Anjar U (2006) Scibuntu: Ubuntu Linux for scientists. [http://scibuntu.sourceforge.net/]

  9. Thomson RC (2009) phyLIs: a simple GnU/Linux distribution for phylogenetics and phyloinformatics. Evol Bioinforma 5:91–95

    CAS  Google Scholar 

  10. Yu G, Wang LG, Meng XH, He QY (2012) LXtoo: an integrated live Linux distribution for the bioinformatics community. BMC Res Notes 5(1):360

    Article  PubMed  PubMed Central  Google Scholar 

  11. Liao YC, Lin HH, Sabharwal A, Haase EM, Scannapieco FA (2015) MyPro: a seamless pipeline for automated prokaryotic genome assembly and annotation. J Microbiol Methods 113:72–74

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Pylro VS, Roesch LF, Ortega JM, do Amaral AM, Tótola MR, Hirsch PR, Rosado AS, Góes-Neto A, da Costa da Silva AL, Rosa CA, Morais DK, Andreote FD, Duarte GF, de Melo IS, Seldin L, Lambais MR, Hungria M, Peixoto RS, Kruger RH, Tsai SM, Azevedo V, Melo IS, Seldin L, Lambais MR, Hungria M, Peixoto RS, Kruger RH, Tsai SM, Azevedo V, Brazilian Microbiome Project Organization Committee (2014) Brazilian Microbiome Project: revealing the unexplored microbial diversity—challenges and prospects. Microb Ecol 67(2):237–241

    Article  PubMed  Google Scholar 

  13. Pylro VS, Roesch LF, Morais DK, Clark IM, Hirsch PR, Tótola MR (2014) Data analysis for 16S microbial profiling from different benchtop sequencing platforms. J Microbiol Methods 107:30–37

    Article  CAS  PubMed  Google Scholar 

  14. Goecks J, Nekrutenko A, Taylor J (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11(8):R86. doi:10.1186/gb-2010-11-8-r86

    Article  PubMed  PubMed Central  Google Scholar 

  15. Pylro VS (2014) BMP standards and protocols. http://www.brmicrobiome.org/#!standardsand-protocols/cpbw. Accessed 10 March 2016

  16. Pylro VS (2014) BMP What is Included? http://www.brmicrobiome.org/#!what-is-included/c1for. Accessed 10 March 2016

  17. Rognes T, Mahé F, Flouri T, Ijaz UZ, Nichols B, Quince C (2015) VSEARCH. https://zenodo.org/record/16153#.VfBYchFViko. Accessed 15 Dec 2015

  18. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461

    Article  CAS  PubMed  Google Scholar 

  19. R Development Core Team. R (2008) A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna ISBN 3-900051-07-0. http://www.R-project.org. Accessed 15 Dec 2015

  20. Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Sousa F, Amend A, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson H (2013) Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol 4(10):914–919

    Google Scholar 

  21. Johnson LS, Eddy SR, Portugaly E (2010) Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinf 11(1):431–439

    Article  Google Scholar 

  22. Gordon A, Hannon GJ (2010) Fastx-toolkit. FASTQ/A short-reads preprocessing tools. http://hannonlab.cshl.edu/fastx_toolkit. Accessed 15 Dec 2015

  23. McDonald D, Clemente JC, Kuczynski J, Rideout JR, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG (2012) The biological observation matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaSci 1(1):7–13

    Article  Google Scholar 

  24. Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML (2013) Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol 4(12):1111–1119

    Article  PubMed Central  Google Scholar 

  25. Parks DH, Beiko RG (2010) Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26(6):715–721

    Article  CAS  PubMed  Google Scholar 

  26. Bastian M, Heymann S, Jacomy M (2008) Gephi: an open source software for exploring and manipulating networks. ICWSM 8:361–362

    Google Scholar 

  27. Friedman J, Alm EJ (2012) Inferring correlation networks from genomic survey data. PLoS Comput Biol 8(9):e1002687

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498–2504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VA, Nikolenko SI, Pham S, Prjibelski AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8):1072–1075

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Wu YW, Tang YH, Tringe SG, Simmons BA, Singer SW (2014) MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2(1):1–18

    Article  Google Scholar 

  32. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72(7):5069–5072

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Maidak BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR (1996) The ribosomal database project (RDP). Nucleic Acids Res 24(1):82–85

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns TD, Bengtsson-Palme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Dueñas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lücking R, Martín MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, Peterson M, Põldmaa K, Saag L, Saar I, Schüßler A, Scott JA, Senés C, Smith ME, Suija A, Taylor DL, Telleria MT, Weiß M, Larsson K-H (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22(21):5271–5277

    Article  PubMed  Google Scholar 

  35. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, The Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21(3):494–504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Article  CAS  PubMed  Google Scholar 

  37. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Nilakanta H, Drews KL, Firrell S, Foulkes MA, Jablonski KA (2014) A review of software for analyzing molecular sequences. BMC Res Notes 7(1):830

    Article  PubMed  PubMed Central  Google Scholar 

  39. Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

Download references

Acknowledgments

We would like to thank Alysson Silvano and Thermo Fisher/Brazil, for providing the USB flash drives used to freely distribute the BMPOS (under request or during training). CNPq, FAPEMIG (PACCSS program), and CAPES (PROEX program) funded this work. LN Lemos receive research fellowship from the FAPESP (process number 13/05325-5). We also thank Melline Fontes Noronha for helping with editing some BMP scripts and Dr. Marc Redmile-Gordon (Centre for Sustainable Soils and Grassland Systems, Rothamsted Research, UK) for critical comments and review of the written English in the manuscript.

Authors Contributions

VSP, FSO, LNL, and LFWR conceived the BMPOS and wrote the manuscript with contributions from DKM, FGS, and GO. FSO and FGS were responsible to install, implement, and test all packages and scripts in the BMPOS. VSP, FSO, and LNL wrote/edited the BMP scripts. FSO implemented the BMP desktop application (Java). All authors read and approved the final manuscript.

Author information

Authors and Affiliations

  1. Genomics and Computational Biology Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, MG, 30190-002, Brazil

    Victor S. Pylro, Daniel K. Morais, Francislon S. de Oliveira & Fausto G. dos Santos

  2. Programa de Pós-graduação Interunidades em Bioinformática, Instituto de Química - IQ, Universidade de São Paulo - USP, São Paulo, SP, Brazil

    Leandro N. Lemos

  3. Vale Institute of Technology – ITV, Belém, PA, Brazil

    Guilherme Oliveira

  4. Universidade Federal do Pampa - UNIPAMPA, São Gabriel, RS, Brazil

    Luiz F. W. Roesch

Authors
  1. Victor S. Pylro
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Daniel K. Morais
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Francislon S. de Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Fausto G. dos Santos
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Leandro N. Lemos
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Guilherme Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Luiz F. W. Roesch
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Victor S. Pylro.

Ethics declarations

Competing Interests

The authors declare that they have no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Pylro, V.S., Morais, D.K., de Oliveira, F.S. et al. BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies. Microb Ecol 72, 443–447 (2016). https://doi.org/10.1007/s00248-016-0785-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-016-0785-x

Keywords

Search

Navigation