Fleming’s penicillin producing strain is not Penicillium chrysogenum but P. rubens
Open accessAbstract
Penicillium chrysogenum is a commonly occurring mould in indoor environments and foods, and has gained much attention for its use in the production of the antibiotic penicillin. Phylogenetic analysis of the most important penicillin producing P. chrysogenum isolates revealed the presence of two highly supported clades, and we show here that these two clades represent two species, P. chrysogenum and P. rubens. These species are phenotypically similar, but extrolite analysis shows that P. chrysogenum produces secalonic acid D and F and/or a metabolite related to lumpidin, while P. rubens does not produce these metabolites. Fleming's original penicillin producing strain and the full genome sequenced strain of P. chrysogenum are re-identified as P. rubens. Furthermore, the well-known claim that Alexander Fleming misidentified the original penicillin producing strain as P. rubrum is discussed.
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Written from the paper’s full text.
TL;DR
Phylogenetic and extrolite analyses show that *Penicillium chrysogenum* sensu lato comprises two species, *P. chrysogenum* and *P. rubens*. Fleming’s original penicillin-producing strain, the Wisconsin wild-type strain, and the full genome-sequenced strain are all re-identified as *P. rubens*.
Key findings
- Combined β-tubulin, calmodulin, and RPB2 data resolve two highly supported clades: one around the ex-type of *P. chrysogenum* (CBS 306.48), the other around the ex-type of *P. rubens* (NRRL 792).
- Fleming’s original penicillin strain (CBS 205.57), the wild-type Wisconsin strain (CBS 307.48 = NRRL 1951), the full genome-sequenced strain Wisconsin 54-1255, and the submerged-production strain CBS 197.46 = NRRL 832 all fall in the *P. rubens* clade.
- *P. chrysogenum* produces secalonic acid D and F and/or a lumpidin-related metabolite, whereas *P. rubens* does not produce these metabolites.
- Phenotypic macro- and microscopic characters did not clearly separate the two species; three strains showed deviating growth: CBS 355.48 had smaller colonies, while NRRL 792 and CBS 307.48 had reduced sporulation on most agar media.
Methods
- Morphology: strains from Table 1 were inoculated on CYA, YES, CREA, and MEA, incubated 7 d at 25 °C, and examined macro- and microscopically.
- Molecular analysis: partial β-tubulin, calmodulin, and RPB2 were sequenced; maximum likelihood used RAxML v. 7.2.8 with GTR and separate partitions, and maximum parsimony used MEGA5 with 500 bootstrap replicates; *P. griseofulvum* CBS 185.27 was the outgroup. The calmodulin partition was 506 bp with 90 distinct alignment patterns, RPB2 was 981 characters with 91 distinct patterns, and β-tubulin was 434 bp with 62 distinct patterns; parsimony analysis found 118 parsimony-informative sites (3150 MP trees, length = 400, CI 0.69, RI 0.83).
- Extrolite analysis: strains were grown 7–14 d at 25 °C on YES, CYA, and MEA, then extracted and analyzed by HPLC-DAD against characterized compounds.
Limitations
- Stated in the paper: the status of Scott et al. lineage 3 remains under investigation; a more detailed molecular or extrolite analysis is needed to place additional synonyms within *P. chrysogenum*, *P. rubens*, or other unrecognized species; and the suggestion that *P. rubens* has a competitive advantage in indoor niches requires investigation of distribution patterns in other geographic regions.
- Evident from the text: phenotypic examination did not reveal clear differences between the two species, so separation depends on molecular and extrolite data; the study focuses on historically important penicillin-producing strains rather than a comprehensive population sample.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
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Cites
Statistics
Claims the paper makes
1 of 7 cited sources checked · 0 supported · 0 flagged · accuracy not yet measured
- Interpretationown data
The full genome sequenced strain of P. chrysogenum (Wisconsin 54-1255, derived from NRRL 1951) is P. rubens.
“the full genome sequenced strain of P. chrysogenum are re-identified as P. rubens”
- Also stated in: § Phylogenetic analysis · plain
“Fleming’s original penicillin producing strain (CBS 205.57), the wild-type Wisconsin strain isolated from a mouldy cantaloupe (CBS 307.48 = NRRL 1951), the full genome sequenced strain derived from NRRL 1951 (Wisconsin 54-1255) (van den Berg et al. 2008), the strain first found to produce satisfactory yields of penicillin when grown submerged (CBS 197.46 = NRRL 832), are accommodated in this clade”
- Also stated in: § Current taxonomy and implications · plain
“The full genome sequenced strain derived from NRRL 1951 (van den Berg 2008) is also a P. rubens”
Quote in the paperSubstantial claim1 of 1 sources checked- cites van den Berg et al. 2008 source
The Abstract and Methods identify Wisconsin 54-1255 as the P. chrysogenum strain whose genome was sequenced; the Abstract also says industrial strains derive from NRRL1951. Neither passage, nor the additional passages searched, says Wisconsin 54-1255 was re-identified as P. rubens. That central taxonomic claim is therefore unsupported by this source. (LLM, conf=0.86)
Experimental — accuracy not yet measured
- Also stated in: § Phylogenetic analysis · plain
- Findingown data
The wild-type Wisconsin strain NRRL 1951 is P. rubens.
“Fleming’s original penicillin producing strain (CBS 205.57), the wild-type Wisconsin strain isolated from a mouldy cantaloupe (CBS 307.48 = NRRL 1951), the full genome sequenced strain derived from NRRL 1951 (Wisconsin 54-1255) (van den Berg et al. 2008), the strain first found to produce satisfactory yields of penicillin when grown submerged (CBS 197.46 = NRRL 832), are accommodated in this clade”
Quote in the paperSubstantial claim- Rests on an assumption: The wild-type Wisconsin strain isolated from a mouldy cantaloupe is CBS 307.48 = NRRL 1951.
- Findingown data
The strain first found to produce satisfactory yields of penicillin when grown submerged (CBS 197.46 = NRRL 832) is P. rubens.
“Fleming’s original penicillin producing strain (CBS 205.57), the wild-type Wisconsin strain isolated from a mouldy cantaloupe (CBS 307.48 = NRRL 1951), the full genome sequenced strain derived from NRRL 1951 (Wisconsin 54-1255) (van den Berg et al. 2008), the strain first found to produce satisfactory yields of penicillin when grown submerged (CBS 197.46 = NRRL 832), are accommodated in this clade”
Quote in the paperSubstantial claim- Rests on an assumption: The strain first found to produce satisfactory yields of penicillin when grown submerged is CBS 197.46 = NRRL 832.
- Findingown data
Phylogenetic analysis of the combined partial β-tubulin, calmodulin and RPB2 datasets revealed two highly supported clades in Penicillium chrysogenum sensu lato.
“Phylogenetic analysis of the most important penicillin producing P. chrysogenum isolates revealed the presence of two highly supported clades”
- Also stated in: § Phylogenetic analysis · plain
“Phylogenetic analysis of the combined partial β-tubulin, calmodulin and RPB2 datasets revealed two highly supported clades in Penicillium chrysogenum sensu lato.”
Quote in the paperSubstantial claim - Also stated in: § Phylogenetic analysis · plain
- Findingown data
Extrolite analysis differentiated the P. chrysogenum and P. rubens clades.
“Extrolite analysis differentiated the P. chrysogenum and P. rubens clades.”
Quote in the paperSubstantial claim
- Findingown data
Penicillium rubens does not produce secalonic acid D and F or a metabolite related to lumpidin.
“while P. rubens does not produce these metabolites”
- Also stated in: § Phenotypic and extrolite analysis · plain
“while P. rubens does not produce these metabolites”
Quote in the paperSubstantial claim - Also stated in: § Phenotypic and extrolite analysis · plain
- Findingown data
The majority of examined strains of P. chrysogenum and P. rubens showed similar growth characteristics: good growth and sporulation on YES agar, weak or moderate growth on CREA with poor acid production, and large clear or yellow exudate droplets on MEA and/or CYA.
“The majority of the examined strains showed similar growth characteristics, such as good growth and sporulation on YES agar, weak or moderate growth on CREA with poor acid production and large clear or yellow coloured exudate droplets on MEA and/or CYA (Fig. 2).”
Quote in the paperNot a substantial claim - Interpretationreasoning
La Touche, not Fleming, identified the original penicillin-producing strain as Penicillium rubrum.
“However, it was the mycologist, Charles J La Touche (1904–1981), working in a room on the floor below that occupied by Fleming, who actually identified the strain as Penicillium rubrum.”
Quote in the paperSubstantial claim - Interpretationown data
Fleming's original penicillin producing strain (CBS 205.57) is P. rubens.
“Fleming’s original penicillin producing strain and the full genome sequenced strain of P. chrysogenum are re-identified as P. rubens.”
- Also stated in: § Phylogenetic analysis · plain
“Fleming’s original penicillin producing strain (CBS 205.57), the wild-type Wisconsin strain isolated from a mouldy cantaloupe (CBS 307.48 = NRRL 1951), the full genome sequenced strain derived from NRRL 1951 (Wisconsin 54-1255) (van den Berg et al. 2008), the strain first found to produce satisfactory yields of penicillin when grown submerged (CBS 197.46 = NRRL 832), are accommodated in this clade”
- Also stated in: § Identity of Fleming’s original penicillin-producing strain · boosted
“Our current study shows that the correct name of this strain is P. rubens.”
Quote in the paperSubstantial claim- Rests on an assumption: Fleming’s original penicillin producing strain is CBS 205.57.
- Also stated in: § Phylogenetic analysis · plain
- Interpretationown data
The two highly supported clades in Penicillium chrysogenum sensu lato represent two species, P. chrysogenum and P. rubens.
“we show here that these two clades represent two species, P. chrysogenum and P. rubens.”
- Also stated in: § Phylogenetic analysis · boosted
“These two clades evidently represent two different species, P. chrysogenum and P. rubens.”
Quote in the paperSubstantial claim - Also stated in: § Phylogenetic analysis · boosted
- Interpretationreasoning
There is as yet no strain of P. chrysogenum sensu stricto full genome sequenced.
“this shows that there is as yet no strain of P. chrysogenum sensu stricto full genome sequenced.”
Quote in the paperSubstantial claim
- May combine two claims. 7
May combine two claims.
Findingown dataPenicillium chrysogenum and P. rubens are phenotypically similar; macro- and microscopical examination did not reveal clear differences.
“These species are phenotypically similar”
- Also stated in: § Phenotypic and extrolite analysis · plain
“Phenotypic examination using macro- and microscopical characters of strains of the Penicillium rubens and P. chrysogenum clades did not reveal clear differences.”
Quote in the paperSubstantial claim- Also stated in: § Phenotypic and extrolite analysis · plain
May combine two claims.
FindingcitationPenicillium chrysogenum produces secalonic acid D and F and/or a metabolite related to lumpidin.
“P. chrysogenum produces secalonic acid D and F and/or a metabolite related to lumpidin”
- Also stated in: § Phenotypic and extrolite analysis · plain
“P. chrysogenum produces secalonic acid D and F and/or a metabolite related to lumpidin (Larsen et al. 2001)”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Larsen et al. 2001 source
- Also stated in: § Phenotypic and extrolite analysis · plain
May combine two claims.
Findingown dataThree strains (CBS 355.48, NRRL 792, and CBS 307.48) had deviating growth characteristics: CBS 355.48 had smaller colonies on all tested agar media, and NRRL 792 and CBS 307.48 had reduced sporulation on most agar media.
“Three strains had deviating growth characteristics: CBS 355.48 (ex-type culture of P. notatum) had smaller colonies on all tested agar media, and NRRL 792 (ex-type culture of P. rubens; Fig. 3), and CBS 307.48 ( = NRRL 1951, wild-type full genome-sequenced strain) deviated in having reduced sporulation on most agar media.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingnone givenThe historically important penicillin producers (Wisconsin strain NRRL 1951, Fleming's strain CBS 205.57, and CBS 197.46) all proved to be P. rubens.
“It is noticeable that the historical important penicillin producers (Wisconsin strain NRRL 1951, Fleming’s strain CBS 205.57 = NRRL 824 = IMI 015378, and the strain first used for producing penicillin in submerged conditions CBS 197.46), all proved to be P. rubens.”
Quote in the paperSubstantial claim- Rests on an assumption: Fleming’s original penicillin producing strain is CBS 205.57.
- Rests on an assumption: The wild-type Wisconsin strain isolated from a mouldy cantaloupe is CBS 307.48 = NRRL 1951.
- Rests on an assumption: The strain first found to produce satisfactory yields of penicillin when grown submerged is CBS 197.46 = NRRL 832.
May combine two claims.
PremisecitationBoth P. rubens and P. chrysogenum produce penicillin.
“Both P. rubens and P. chrysogenum produce penicillin”
- Also stated in: § INTRODUCTION · plain
“all species produce penicillin (Frisvad et al. 1987, Andersen & Frisvad 1994, Banke et al. 1997, Färber & Geisen 1994)”
Quote in the paperNot a substantial claim0 of 3 sources checked- Also stated in: § INTRODUCTION · plain
May combine two claims.
InterpretationcitationScott's lineages 1 and 2 are P. chrysogenum, and lineage 4 corresponds to P. rubens.
“Scott’s lineages 1 and 2 are P. chrysogenum, and lineage 4 corresponds to P. rubens.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Scott et al. 2004 source
May combine two claims.
InterpretationcitationLa Touche's identification of Fleming's strain as P. rubrum Grassberger-Stoll (as defined by Biourge) was accurate at that time and not incorrect as claimed in literature.
“In conclusion, La Touche used Biourge’s taxonomic scheme and identified Fleming’s strain as P. rubrum Grassberger-Stoll (as defined by Biourge) and this identification was accurate at that time and not incorrect as claimed in literature (Thom 1945, Raper & Thom 1949, Lax 2005).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Biourge 1923
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
The paper relies on this without support.
Fleming’s original penicillin producing strain is CBS 205.57.
“Fleming’s original penicillin producing strain (CBS 205.57)”
The paper relies on this without support.
The wild-type Wisconsin strain isolated from a mouldy cantaloupe is CBS 307.48 = NRRL 1951.
“the wild-type Wisconsin strain isolated from a mouldy cantaloupe (CBS 307.48 = NRRL 1951)”
The paper relies on this without support.
The strain first found to produce satisfactory yields of penicillin when grown submerged is CBS 197.46 = NRRL 832.
“the strain first found to produce satisfactory yields of penicillin when grown submerged (CBS 197.46 = NRRL 832)”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Wild-type Wisconsin strain is also called the genome-sequenced strain
MinorThe paper identifies CBS 307.48 (NRRL 1951) as the wild-type strain and says the genome-sequenced strain was derived from it. Elsewhere, it calls CBS 307.48 itself the "wild-type full genome-sequenced strain."
“CBS 307.48 ( = NRRL 1951, wild-type full genome-sequenced strain)”
“the full genome sequenced strain derived from NRRL 1951 (Wisconsin 54-1255)”
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- Authors
- Houbraken, J., Frisvad, J. C., & Samson, R. A.
- Affiliations
- Westerdijk Fungal Biodiversity Institute (NL)
- Technical University of Denmark (DK)
- Corresponding author
- Houbraken, Jos
- Venue
- IMA Fungus
- Publisher
- Pensoft Publishers
- Published
- 2011-06
- Volume
- 2
- Issue
- 1
- Pages
- 87-95
- ISSN
- 2210-6340 (ISSN-L)
- 2210-6359
- PMC
- PMC3317369
- OpenAlex
- W2149410962
- Semantic Scholar
- e6db8d20571d3de7cbf7141caba340c28a6f3f58
- Cited by
- 262
- References
- 32
- Citations by year
- 2026: 9 · 2025: 14 · 2024: 13 · 2023: 45 · 2022: 26 · 2021: 24 · 2020: 21 · 2019: 10 · 2018: 13 · 2017: 18 · 2016: 15 · 2015: 17 · 2014: 15 · 2013: 11 · 2012: 7
- FWCI
- 8.67
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- IMA Fungus (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (publishedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, cc-by-nc-nd)
- KNAW research portal (Royal Academy of Art and Sciences (KNAW)) (submittedVersion, other-oa)
- Topics
- Health Sciences › Medicine › Pharmacology › Microbial Natural Products and Biosynthesis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Plant Pathogens and Fungal Diseases
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Mycotoxins in Agriculture and Food
- Keywords
- Penicillium chrysogenum, Penicillium rubens, penicillin production, phylogenetic analysis, secalonic acid D, Alexander Fleming, Penicillium rubrum, fungal taxonomy
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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