Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Applied and Environmental Microbiology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Archive
    • Minireviews
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About AEM
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Letter to the Editor

Towards a Genome-Based Reclassification of the Genus Lactobacillus

Stijn Wittouck, Sander Wuyts, Sarah Lebeer
Johanna Björkroth, Editor
Stijn Wittouck
aResearch Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Stijn Wittouck
Sander Wuyts
aResearch Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sander Wuyts
Sarah Lebeer
aResearch Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sarah Lebeer
Johanna Björkroth
University of Helsinki
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/AEM.02155-18
  • Article
  • Info & Metrics
  • PDF
Loading

Ed. Note: The authors of the published article did not feel that a response was necessary.

LETTER

Since the advent of the genomic era, it has become clear that the genus Lactobacillus is as large as a typical bacterial family (1). In addition, it has been shown several times that this genus is polyphyletic, as it encompasses at least five other genera. Attempts to define smaller genus-sized phylogroups within Lactobacillus have been undertaken, e.g., by Zheng et al. (2) and by Sun et al. (1). In a more recent paper published in this journal, Salvetti et al. (3) propose ten phylogroups and (i) assess the robust monophyly of these phylogroups, (ii) check the within-phylogroup diversity, and (iii) search for gene presence/absence signatures that are able to discriminate between the phylogroups. We believe that this effort to define phylogroups that are robustly monophyletic and of consistent diversity is an important step in the right direction toward the reclassification of the genus Lactobacillus. Nonetheless, we feel that several of the proposed phylogroups are not adequate to form new genera and believe that alternatives should first be explored.

The authors convincingly showed that their ten phylogroups are robustly monophyletic. However, four of these ten groups do not meet the commonly cited requirement that genomes of the same genus should share >50% of conserved proteins (POCP) (4). For three of those, the authors report that the POCP values without “peripheral species” are >50%, but we feel that this is somewhat arbitrary. A second point for further improvement and discussion is that these proposed phylogroups, as defined now, do not seem to be uniquely identifiable using their proposed gene signatures: several species, such as Lactobacillus floricola, Lactobacillus mellifer, and Lactobacillus brevis (see Tables 1 and 3 in reference 3), do not fully conform to the gene signature found for the phylogroup to which they belong.

We believe that some of these issues with the newly proposed phylogroups could be overcome if a less ad hoc strategy to find phylogroups is used. For example, we understand that the fourteen phylogroups that Salvetti et al. (3) used as a reference have been circulating and validated in the literature (see reference 5 for an overview). However, in the new article, some of those 14 groups were merged to form 10, while it is at present unclear why those mergers were performed and not others or, conversely, why the splitting of phylogroups was not considered. Therefore, we would like to propose that future efforts to define new phylogroups and genera follow an explorative and transparent approach—explorative in the sense that each clade within the Lactobacillus genus tree is assessed as a potential phylogroup, and transparent in the sense that explicit criteria are applied. An excellent example of a more generalized approach applicable to all bacterial genera/taxonomy is the recent proposal by Parks et al. (6), who constructed a revised bacterial taxonomy based solely on genomics. Of interest, with their approach, the Lactobacillus genus was split into sixteen smaller genera, indicating that there is still a need for further open discussion about the exact number and nature of the Lactobacillus phylogroups.

In order to form new phylogroups, we are in favor of applying three criteria, two of which are already used by Salvetti et al. (3): robust monophyly and consistent diversity. For the third criterion, we propose determining the total number of common and exclusive genes of each clade (marker genes) and selecting phylogroups that have a large common number of such genes. This final criterion ensures that phylogroups have biological meaning, even if we do not yet know the function of all these marker genes.

Thus, to conclude, bacterial taxonomy—in particular, that of the Lactobacillus genus—is under strong pressure, as evidenced by the above-mentioned publications and our recent comparative genomics work on the Lactobacillus casei group (7). As mentioned by Salvetti et al. (3), this is an important issue, since reclassification of the Lactobacillus genus could have large implications not only for the scientific community but also for legislative bodies, regulatory agencies, manufacturers of Lactobacillus-containing products, and microbial safety assessors. However, as an alternative to the polyphasic approach proposed by Salvetti et al. (3), we believe that a monophasic approach, based solely on genomics, is feasible, but only when executed in an explorative way based on explicit criteria for what constitutes a proper genus.

  • Copyright © 2019 American Society for Microbiology.

All Rights Reserved.

REFERENCES

  1. 1.↵
    1. Sun Z,
    2. Harris HM,
    3. McCann A,
    4. Guo C,
    5. Argimón S,
    6. Zhang W,
    7. Yang X,
    8. Jeffery IB,
    9. Cooney JC,
    10. Kagawa TF,
    11. Liu W,
    12. Song Y,
    13. Salvetti E,
    14. Wrobel A,
    15. Rasinkangas P,
    16. Parkhill J,
    17. Rea MC,
    18. O’Sullivan O,
    19. Ritari J,
    20. Douillard FP,
    21. Ross RP,
    22. Yang R,
    23. Briner AE,
    24. Felis GE,
    25. de Vos WM,
    26. Barrangou R,
    27. Klaenhammer TR,
    28. Caufield PW,
    29. Cui Y,
    30. Zhang H,
    31. O’Toole PW
    . 2015. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun 6:8322. doi:10.1038/ncomms9322.
    OpenUrlCrossRefPubMed
  2. 2.↵
    1. Zheng J,
    2. Ruan L,
    3. Sun M,
    4. Gänzle M
    . 2015. A genomic view of lactobacilli and pediococci demonstrates that phylogeny matches ecology and physiology. Appl Environ Microbiol 81:7233–7243. doi:10.1128/AEM.02116-15.
    OpenUrlAbstract/FREE Full Text
  3. 3.↵
    1. Salvetti E,
    2. Harris HM,
    3. Felis GE,
    4. O'Toole PW
    . 2018. Comparative genomics of the genus Lactobacillus reveals robust phylogroups that provide the basis for reclassification. Appl Environ Microbiol 84:e00993-18. doi:10.1128/AEM.00993-18.
    OpenUrlAbstract/FREE Full Text
  4. 4.↵
    1. Qin Q-L,
    2. Xie B-B,
    3. Zhang X-Y,
    4. Chen X-L,
    5. Zhou B-C,
    6. Zhou J,
    7. Oren A,
    8. Zhang Y-Z
    . 2014. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 196:2210–2215. doi:10.1128/JB.01688-14.
    OpenUrlAbstract/FREE Full Text
  5. 5.↵
    1. Salvetti E,
    2. Torriani S,
    3. Felis GE
    . 2012. The genus Lactobacillus: a taxonomic update. Probiotics Antimicrob Proteins 4:217–226. doi:10.1007/s12602-012-9117-8.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Parks DH,
    2. Chuvochina M,
    3. Waite DW,
    4. Rinke C,
    5. Skarshewski A,
    6. Chaumeil P-A,
    7. Hugenholtz P
    . 2018. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36:996–1004. doi:10.1038/nbt.4229.
    OpenUrlCrossRef
  7. 7.↵
    1. Wuyts S,
    2. Wittouck S,
    3. De Boeck I,
    4. Allonsius CN,
    5. Pasolli E,
    6. Segata N,
    7. Lebeer S
    . 2017. Large-scale phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and reveals novel clade-associated features. mSystems 2:e00061-17. doi:10.1128/mSystems.00061-17.
    OpenUrlAbstract/FREE Full Text
PreviousNext
Back to top
Download PDF
Citation Tools
Towards a Genome-Based Reclassification of the Genus Lactobacillus
Stijn Wittouck, Sander Wuyts, Sarah Lebeer
Applied and Environmental Microbiology Jan 2019, 85 (3) e02155-18; DOI: 10.1128/AEM.02155-18

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Applied and Environmental Microbiology article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Towards a Genome-Based Reclassification of the Genus Lactobacillus
(Your Name) has forwarded a page to you from Applied and Environmental Microbiology
(Your Name) thought you would be interested in this article in Applied and Environmental Microbiology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Towards a Genome-Based Reclassification of the Genus Lactobacillus
Stijn Wittouck, Sander Wuyts, Sarah Lebeer
Applied and Environmental Microbiology Jan 2019, 85 (3) e02155-18; DOI: 10.1128/AEM.02155-18
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • LETTER
    • REFERENCES
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About AEM
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #AppEnvMicro

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

 

Print ISSN: 0099-2240; Online ISSN: 1098-5336