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Forthcoming changes in Lactobacillus taxonomy

Mary Ellen Sanders PhD, Executive Science Officer, ISAPP

I was privileged to be included in a small meeting of scientists, both academic and industry, who met last week in Verona to discuss changes in Lactobacillus taxonomy. The first objectives of the meeting were to clarify with industry the need for the proposed changes and to clarify the methodology that will be used. The second objectives were to discuss at large potential consequences and approaches to address them.

Changes to the Lactobacillus genus

Experts from the Taxonomic Subcommittee for Lactobacilli, Bifidobacteria and Related Organisms agreed that the genus Lactobacillus is too heterogeneous and dividing this genus into several genera is inevitable. The need for this taxonomic ‘correction’ has been known for a long time, but until recently, the methodologies needed to reliably group the current Lactobacillus species into new genera were not available. But earlier this year, a paper by Salvetti et al (2018) analyzed 269 Lactobacillus and related (e.g., Pediococcus, Leuconostoc, Fructobacillus, Oenococcus) species and showed that the Lactobacillus genus comprises 10 phylogroups (see box). Each of these phylogroups represents at least one new genus. These same 10 phylogroups were observed using three separate approaches [phylogenetic analysis of 16S ribosomal DNA sequences, whole genome sequence analysis, leading to the comparison of 72 shared housekeeping genes (the core genome), and the comparison of average amino acid identity and percentage of conserved proteins], providing strong evidence that these groupings are robust. Commercially important Lactobacillus probiotic strains span at least 7 of those newly defined phylogroups; food fermentation lactobacilli cover even more.

lactobacillus_info

Although these 10 phylogroups were identified by this study, the current genus Lactobacillus could ultimately be resolved into 10 or up to 23 genera, depending on the cut-off values used for the different approaches. If researchers choose to split the genus into fewer new genera, it increases the chance that taxonomic changes will be needed in the nearer future. If they split the genus into more genera, it increases the chance that nomenclature will remain stable.

The names of the new genera are not decided. New names must be published (or validated) in the International Journal of Systematic and Evolutionary Microbiology. The authors of the publication will propose the new genus names. All species will be retained and their species names will not change. To minimize disruption, researchers will try to propose new genera names that begin with the letter “L”. Because “Lactobacillus” is a masculine Latin noun, the new genus names must be masculine for the species names to be retained.

A silver lining

Critics of these changes may suppose that adhering to taxonomic convention is their only purpose. But a classification system that better reflects genetic relatedness of the species may reap other benefits. As evidence for clinical benefits accumulates (summarized in open access review “Probiotics for Human Use”, 2018) and investigations provide insight into probiotic mechanisms of action, a clearer image of mechanisms and functions associated with particular taxonomic groups may emerge. The concept of core, shared benefits that were not strain-specific but linked to higher taxonomic groupings was explored in two ISAPP publications [Hill et al. (2014) and more in depth in Sanders et al. (2018)]. Reconsideration of clinical evidence and its relationship to new genera might prove enlightening.

What can be done to minimize confusion?

The meeting attendees brainstormed potential complications that might result from changing genus names. Company representatives in general considered that internal changes could be managed, although resources would be required to update names on all different paperwork and labels associated with commercial products (for example, marketing materials, product information, certificates of analysis, labeling, import/export certificates). The 2002 WHO/FAO probiotic guidelines, as well as the 2017 CRN/IPA guidelines, indicate that the genus, species and strain designation should be included on product labels. Further, the name used should reflect current nomenclature. This requirement is reflected in some national regulations. Therefore, genus name changes will necessitate label changes.

Further, it was emphasized that a clear document should be prepared and endorsed by reputable organizations (EFSA, NIH, FDA, medical organizations, and others). The document should: (a) indicate the name changes, (b) provide a clear, concise statement of why the changes were needed, and (c) emphasize that only the names, not the strains, would be different. This could be leveraged by companies to communicate with all stakeholders. End-users of probiotic products would likely not be a significant communication challenge. Authorities involved with probiotic safety (FDA with GRAS and EFSA with QPS) likely will manage these changes, as they are science-based. More of a concern was communication with other regulators, both at the level of national agencies responsible for probiotic-specific regulations (including countries with positive lists of species that are acceptable as probiotics) as well as authorities involved in import/export of product. Some potential issue with intellectual property may be envisaged, especially in a transition period during which the new names are not routinely used yet.

The bottom line: Name will change but the strains will stay the same 

The current Lactobacillus genus will be split into at least 10, and perhaps as many as 23, genera. No species names will change, but many species – including commercially important ones – will have a different genus names, hopefully beginning with the letter “L”.  Because of the tremendous heterogeneity of the current Lactobacillus genus, Prof. Paul O’Toole concluded his presentation saying “the status quo is not an option.” Some disruptions can be expected from this massive change, but the probiotic field would benefit from embracing these changes and developing strategies to minimize any difficulties resulting from them.

 

Additional information:

The International Committee on Systematics of Prokaryotes (ICSP) and the International Code of Nomenclature of Bacteria are responsible for the naming of bacteria. The subcommittee of the ICSP responsible for naming lactobacilli is the Taxonomic Subcommittee for Lactobacilli, Bifidobacteria and Related Organisms.

The meeting was convened by the Lactic Acid Bacteria Industrial Platform and chaired by Esben Laulund of Chr Hansens, who also chairs IPA Europe. A full report of meeting conclusions is expected to be published in a scientific journal by the end of 2018. Abstracts and program will to be posted on the LABIP website in due time.

The taxonomic hierarchy for Lactobacillus currently is: Domain: Bacteria; Division/Phylum: Firmicutes; Class: Bacilli; Order Lactobacillales; Family: Lactobacillaceae; Genus: Lactobacillus. The lowest order of taxonomy is the subspecies; the strain designation has no official standing in nomenclature. There are currently over 230 recognized species of Lactobacillus, and approximately 10 new species are added each year.

clinician_guides

Guides for use of probiotics in the clinic – some recent ISAPP initiatives

By Mary Ellen Sanders, PhD

At the ISAPP meeting earlier this month, Prof. Dan Merenstein, MD, presented a summary of recent ISAPP initiatives focused on helping translate the evidence of probiotics and prebiotics into clinical action.

A 2013 paper reported that 87% of hospital formularies surveyed in the United States carried at least one probiotic. Yet when Merenstein looked at the names of the products tested, many were not supported by evidence for such uses. This highlights the need for clinicians to have access to clear, evidence-based probiotic use guidelines.

ISAPP has worked through a variety of avenues to get information into the hands of clinicians. It has supported continuing education credit activities, webinars, collaboration with clinical organizations to develop guidelines, publications in clinical journals, presentations at clinical meetings, and simplified summaries using infographics and videos. Some examples include the following.

 

World Gastroenterology Organisation Global Guidelines – Probiotics and Prebiotics

This document is the most visited and downloaded of all WGO guidelines. In 2017, under the leadership of Prof. Francisco Guarner, MD PhD, this document was updated. Three current ISAPP board members were part of the process and ISAPP provided funding. See here.

 

Petitions

ISAPP petitioned the United States Preventive Services Task Force to examine the role of probiotics in preventing antibiotic-associated diarrhea. They considered the petition, but didn’t feel it fit their mission.

ISAPP petitioned American Academy of Family Physicians to consider reviewing the evidence for probiotics for AAD to include in their evidence-based guidelines. This is under consideration.

After attending 2017 ISAPP, Dr. Claire Merrifield BSc MBBS PhD led an effort to have NICE Clinical Knowledge Summaries mention probiotics for AAD in an effort to get local groups to adopt guidelines. This has met with limited success. See here.

 

CME or CE activities

On April 17, 2018, Merenstein and Mary Ellen Sanders PhD served as faculty for a CME-eligible webinar sponsored by Medscape on “Navigating the World of Probiotics. Helping Patients Make Good Choices”. The activity is available on Medscape’s website here.

In February 2018, Merenstein published a CE activity with the Pharmacy Times titled “The Expanding Health Benefits of Prebiotics and Probiotics”. See here

Upcoming in October 2018, Merenstein will present “Probiotics and the GI Tract. What Should a Busy Clinician Know” at the American Academy of Family Physicians Annual Conference. This conference is attended by over 4,000 physicians and is focused on clinical practice. The event, eligible for CME, will be recorded and made available after the live presentation.

ISAPP co-founder, Prof. Glenn Gibson has or will present 6 lectures over 2017 and 2018 on the topic of “The Learning Curve for Probiotics and Prebiotics.” These lectures are available for CME credit and are targeted to family doctors, gastroenterologists, pediatricians, and dieticians in the UK.

Numerous CME presentations over 2017-2018 have been given by ISAPP board members:

M.D. Cabana:

  • “Probiotics: Friend or Folly?”  American Academy of Pediatrics National Conference and Exhibition. Chicago, IL. September 17, 2017.  The audience was about 450-500 clinicians.
  • “Probiotics in Primary Care Pediatrics: Diarrhea, Colic & Eczema.” American Academy of Pediatrics California Chapter 1 Meeting. 300 clinicians
  • “Probiotics for Colic?” Zuckerberg San Francisco General Hospital. Department of Pediatrics Grand Rounds. San Francisco, CA.
  • “Probiotic Interventions for Colic” UCSF Benioff Children’s Hospital, Oakland.
  1. Reid:
  • “Effects and importance of microbiota on urogenital health in women.” 16th Annual Congress of Gynecology and Obstetrics, Antalya, Turkey. 300 obstetricians and gynecologists.
  • “Probiotics to whom for what?” Health World Ltd International Congress Natural Medicine 2017, Hunter Valley, New South Wales, Australia,.601 healthcare practitioners and naturopaths.
  • “The microbiome and how it relates to maternal/newborn care.” The Graham Chance Lectureship, Perinatal Research Day, London, ON. 100 neonatologists and pediatric experts.
  • “Microbes and the brain.” Integrative Healthcare Symposium, New York City. 500 naturopaths and various specialists.
  • “Probiotics and detoxification.” Environmental Health Symposium, Scottsdale, Arizona, 8th April. 500 naturopaths and various specialists.

 

Webinars

On June 28, ISAPP co-founder, Prof. Glenn Gibson, will present a webinar along with Profs. Ted Dinan and Ian Rowland titled “Why is everybody talking about gut microbiota?” Sponsored by the British Nutrition Foundation, this webinar will target healthcare professionals in the UK and Europe. See here.

 

Publications in clinical journals

Several ISAPP board members

  • Evidence-Based Probiotic Use in Family Medicine. Submitted, Journal of Family Practice. Merenstein/Sanders/Tancredi
  • Probiotics for Human Use. In press, Nutrition Bulletin. Sanders/Merenstein/Hutkins/Merrifield
  • Probiotics and prebiotics in intestinal health and disease: from biology to the clinic. Invited review in preparation, Nature Reviews Gastroenterology and Hepatology. Gibson/Reid/Sanders/Merenstein
  • Clinical perspectives of prebiotics and synbiotics. In preparation, Gastroenterology. Gibson/Quigley

 

Featured on ISAPPscience.org

Infographics

 

Videos

  • What is a probiotic?
  • Health benefits of probiotics
  • Are all probiotics the same?
  • How to choose a probiotic

 

General guidelines for choosing probiotics and prebiotics

Some initiatives that Merenstein championed were a direct result of ideas generated during the discussion group he led during the 2017 ISAPP meeting in Chicago.

 

Image courtesy of nursingschoolsnearme.com/