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Cited by 170Evolution and Genetic DynamicsProbiotics and Fermented FoodsGenomics and Phylogenetic Studies

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

Open access
Bachmann, Herwig, Starrenburg, Marjo J.C., Molenaar, Douwe, Kleerebezem, Michiel, van Hylckama Vlieg, Johan E.T.·2012·Genome Research
DOI 10.1101/gr.121285.111PMC PMC3246198
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Abstract

Experimental evolution is a powerful approach to unravel how selective forces shape microbial genotypes and phenotypes. To this date, the available examples focus on the adaptation to conditions specific to the laboratory. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and in dairy environments, and it is proposed that dairy strains originate from the plant niche. Here we investigate the adaptation of a L. lactis strain isolated from a plant to a dairy niche by propagating it for 1000 generations in milk. Two out of three independently evolved strains displayed significantly increased acidification rates and biomass yields in milk. Genome resequencing, revealed six, seven, and 28 mutations in the three strains, including point mutations in loci related to amino acid biosynthesis and transport and in the gene encoding MutL, which is involved in DNA mismatch repair. Two strains lost a conjugative transposon containing genes important in the plant niche but dispensable in milk. A plasmid carrying an extracellular protease was introduced by transformation. Although improving growth rate and growth yield significantly, the plasmid was rapidly lost. Comparative transcriptome and phenotypic analyses confirmed that major physiological changes associated with improved growth in milk relate to nitrogen metabolism and the loss or down-regulation of several pathways involved in the utilization of complex plant polymers. Reproducing the transition from the plant to the dairy niche through experimental evolution revealed several genome, transcriptome, and phenotype signatures that resemble those seen in strains isolated from either niche.

AI snapshot

Written from the paper’s full text.

TL;DR

Propagating the plant isolate *Lactococcus lactis* KF147 in milk for 1000 generations reproduced several genomic, transcriptomic, and phenotypic signatures of dairy domestication, including improved growth and mutations in nitrogen metabolism. Two of three independently evolved strains grew significantly better in milk, and one became a mutator via a *mutL* deletion.

Key findings

  • After 1000 generations, two of three adapted strains had significantly increased acidification and biomass yield in milk: maximum cell density was 2.0-fold higher for NZ5521 (p = 0.006), 2.8-fold for NZ5522 (p < 0.001), and 1.41-fold for NZ5523 (p = 0.31) versus KF147; relative fitness was 1.48, 1.1, and 1.21, respectively.
  • Genome resequencing found 21, 4, and 6 SNPs in NZ5521, NZ5522, and NZ5523, plus 7 and 2 INDELs in NZ5521 and NZ5522; NZ5522 and NZ5523 lost an identical 51.3-kb Tn6098-like conjugative transposon. NZ5521 had a *mutL* deletion and a ~10-fold higher mutation frequency (10.02 vs. 1.34 × 10⁻⁷ mutations/generation for KF147).
  • The protease plasmid pNZ521 improved growth but was rapidly lost; no protease-positive strains were detected after 1000 generations. Transcriptome analysis found 291 of 1850 genes differentially expressed (p < 0.001), with an oligopeptide ABC transporter operon upregulated in NZ5521/NZ5522 via identical *oppD*/*oppC* upstream deletions, and plant-polymer utilization pathways downregulated, converging toward dairy strain IL594.

Methods

  • Experimental evolution: *L. lactis* KF147, a mung-bean sprout isolate carrying pNZ521, was serially propagated in reconstituted skimmed milk in three parallel cultures (SP1–SP3) for 1000 generations (~16.6 generations per transfer; effective population size 1.66 × 10⁶). After 300 generations, protease-positive cells were selected and further propagated.
  • Phenotypic and genomic characterization: acidification, CFU, and competition fitness assays; Illumina whole-genome resequencing with PCR/amplicon validation; fluctuation analysis for mutation rates.
  • Transcriptome analysis: custom Agilent microarrays comparing adapted strains, KF147, KF147_PRT, and dairy isolate IL594 during exponential growth in milk, using 1850 genes covered by 100% matching probes.

Limitations

  • Stated: the 300-generation bottleneck (only ~100 protease-positive colonies per culture) may have lost beneficial mutations; *oppC* probe mismatch may underestimate IL594 expression; averaged P-values are not FDR-corrected; the authors cannot exclude that the GadR homolog regulates additional genes.
  • Evident: the study uses one plant isolate, three evolved lines, and one clone per line under laboratory milk conditions, so it does not directly demonstrate the natural plant-to-dairy transition.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1101/gr.121285.111

Cites

64 of 64 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 34 cited sources checked · 0 supported · 0 flagged

  • Findingcitation

    Competition experiments using KF147, NZ5521, NZ5522, and NZ5523 in coculture with the protease-positive dairy isolate IL594 did not reveal a fitness difference for any tested combination.

    “It should be noted that the competition experiments using the strains KF147, NZ5521, NZ5522, and NZ5523 in coculture with the protease-positive dairy isolate IL594 (Chopin et al. 1984) did not reveal a fitness difference for any of the tested combinations (data not shown).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Chopin et al. 1984

      Not checked in the free run.

  • Findingnone given

    Tn6098 contains the only predicted alpha-galactosidase of the parental KF147 strain.

    “Since Tn6098 contains the only predicted a-galactosidase of the parental KF147 strain”
    Quote in the paperSubstantial claim
  • Findingown data

    Introduction of plasmid pNZ521 encoding the lactococcal extracellular protease PrtP into strain KF147 significantly enhanced growth in milk.

    “Notably, the introduction of a plasmid, pNZ521 (de Vos et al. 1989), encoding the lactococcal extracellular protease (PrtP) in strain KF147 significantly enhanced growth in milk (Fig. 1A).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites de Vos et al. 1989

      Not checked in the free run.

  • Findingcitation

    The majority of mutations (15 out of 21) in strain NZ5521 were A:T to G:C transitions, as expected for a strain with defects in DNA mismatch repair.

    “As expected for a strain with defects in DNA mismatch repair, the majority of mutations (15 out of 21) in strain NZ5521 were A:T 4 G:C transitions (Miller 1996).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Miller 1996

      Not checked in the free run.

  • Findingown data

    Identical single-base deletions were identified in strains NZ5521 and NZ5522 upstream of the fourth gene in the oligopeptide transport operon (oppC).

    “Additionally, identical single-base deletions were identified in strains NZ5521 and NZ5522 upstream of the fourth gene in this operon (oppC).”
    Quote in the paperNot a substantial claim
  • May combine two claims. 30
  • Classified as probably not a substantial claim. 19

  • May combine two claims.

    Findingown data

    The relative fitness of adapted strains in competition with parental KF147 for 3 d was 1.48 (p > 0.000), 1.1 (p = 0.037), and 1.21 (p = 0.009) for NZ5521, NZ5522, and NZ5523, respectively.

    “The relative fitness was 1.48 ( p > 0.000), 1.1 ( p = 0.037), and 1.21 ( p = 0.009) for strains NZ5521, NZ5522, and NZ5523, respectively (Supplemental Fig. 2).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A transcriptional regulator of the RpiR family and a transcriptional regulator involved in fructose/lactose transport were down-regulated in the adapted strains and in IL594.

    “Additionally, a transcriptional regulator of the RpiR family, which has been described to regulate phospho-sugar metabolism in E. coli (Sorensen and Hove-Jensen 1996), as well as a transcriptional regulator involved in fructose/lactose transport were down-regulated in the adapted strains and in IL594.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Sorensen and Hove-Jensen 1996

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    NZ5523 shares loss of Tn6098 with NZ5522, but none of the other mutations occurred in both strains.

    “NZ5523 shares loss of Tn6098 with NZ5522, but none of the other mutations occurred in both strains.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    Genes involved in the utilization of plant polymers like alpha- and beta-glucosides as well as genes involved in uronic acid metabolism display decreased transcription levels in NZ5521, NZ5522, and IL594, which is in agreement with their redundancy in a dairy environment.

    “Furthermore, genes involved in the utilization of plant polymers like a-and b-glucosides as well as genes involved in uronic acid metabolism display decreased transcription levels in NZ5521, NZ5522, and IL594, which is in agreement with their redundancy in a dairy environment.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    NZ5521 and NZ5522 reached their maximum cell density within 24 h of cultivation, while NZ5523 and the parental KF147 took more than 2 d.

    “Notably, the strains NZ5521 and NZ5522 reached their maximum cell density within 24 h of cultivation, while with NZ5523 and the parental KF147, this took more than 2 d (Supplemental Fig. 1).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The acidification rates of NZ5521 and NZ5522 were increased compared with KF147, whereas the acidification rate of NZ5523 was only slightly increased.

    “The acidification rates of NZ5521 and NZ5522 were increased as compared with KF147, whereas the acidification rate of NZ5523 was only slightly increased (Fig. 1C).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Acidification rates were rapid during the initial cultivations and decreased after 300 generations.

    “Acidification rates were rapid during the initial cultivations, whereas they decreased after 300 generations (Fig. 1A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Two point mutations were identified in the NZ5521 genome within the promoter region of a putative transcriptional repressor of the Rgg/GadR/MutR family, one of which was also found in strain NZ5522.

    “Two point mutations were identified in the NZ5521 genome within the promoter region of a putative transcriptional repressor of the Rgg/GadR/MutR family, one of which was also found in strain NZ5522.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The proteolytic trait could not be stabilized in any of the cultures and was lost at a similar rate as observed during the first 300 generations.

    “Further propagation of proteasepositive cells revealed that the proteolytic trait could not be stabilized in any of these cultures, and that it was lost at a similar rate as observed during the first 300 generations.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In NZ5523, affected genes include a truncated phosphonate ABC transporter, an oligopeptide transporter, and a transcriptional regulator of the DeoR family.

    “In addition to truncation of a phosphonate ABC transporter, the other two genes affected in NZ5523 are an oligopeptide transporter and a transcriptional regulator of the DeoR family, which is described to regulate sugar catabolism.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Compared with KF147, the maximum cell density reached by the adapted strains was 2.0-fold (p = 0.006), 2.8-fold (p < 0.001), and 1.41-fold (p = 0.31) higher for NZ5521, NZ5522, and NZ5523, respectively.

    “Compared with KF147, the maximum cell density reached by the adapted strains was 2.0-fold ( p = 0.006), 2.8-fold ( p < 0.001), and 1.41-fold ( p = 0.31) higher for NZ5521, NZ5522, and NZ5523, respectively.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The mutation rate of strain NZ5521 is 10.02 × 10^-7 mutations per generation (95% CI 9.30-10.76).

    “| NZ5521 24 | 10.02 | 9.30 | 10.76 |”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The validation strategy confirmed all except one incorrectly predicted INDEL mutation.

    “This strategy allowed the confirmation of all except one incorrectly predicted INDEL mutation.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The mutation rate of strain NZ5522 is 1.14 × 10^-7 mutations per generation (95% CI 0.96-1.32).

    “| NZ5522 24 | 1.14 | 0.96 | 1.32 |”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    Many of the putative genes not represented on the array were relatively short: 55% had less than 50 amino acids, and 80% had less than 100 amino acids, indicating that not all of them might be coding genes.

    “Many of the putative genes not represented on the array were relatively short: 55% had less than 50 amino acids, and 80% had less than 100 amino acids, indicating that not all of them might be coding genes.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    The mutation rate of strain NZ5523 is 1.06 × 10^-7 mutations per generation (95% CI 0.90-1.22).

    “| NZ5523 24 | 1.06 | 0.90 | 1.22 |”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    The gene with mutations shares 41% protein sequence identity with GadR in L. lactis MG1363, which regulates the gadCB operon involved in glutamate-dependent acid resistance.

    “This gene shares 41% protein sequence identity with GadR in L. lactis MG1363, which has been shown to regulate the expression of the gadCB operon, involved in glutamate-dependent acid resistance (Sanders et al. 1998).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Sanders et al. 1998

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Despite the smaller phenotypic changes detected in NZ5523, the mutations identified in this adapted strain are also related to nitrogen and carbohydrate metabolism, consistent with multiple mutations selected in strains NZ5521 and NZ5522.

    “Therefore, despite the smaller phenotypic changes detected in NZ5523, the mutations identified in this adapted strain are also related to nitrogen and carbohydrate metabolism, which is consistent with multiple mutations selected in strains NZ5521 and NZ5522.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    L. lactis KF147 was isolated from mung-bean sprouts.

    “L. lactis KF147 was isolated from mung-bean sprouts (Kelly et al. 1998;Siezen et al. 2008).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Kelly et al. 1998

      Not checked in the free run.

    • cites Siezen et al. 2008

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The single base-pair deletion identified in NZ5521 and NZ5522 restores the normal full-length oppC gene and probably restores its functionality.

    “The single base-pair deletion identified in NZ5521 and NZ5522 restores the normal full-length oppC gene and thereby probably restores its functionality (Fig. 3; Supplemental Fig. 5).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

    Interpretationreasoning

    The reduced expression of sugar transport systems like the cellobiose-PTS may result from the absence of cellobiose in milk, while this disaccharide can be found in plant-derived materials as a degradation product of cellulose.

    “The reduced expression of sugar transport systems like the cellobiose-PTS may result from the absence of cellobiose in milk, while this disaccharide can be found in plant-derived materials as a degradation product of cellulose.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    The mutL mutation leads to a 200-amino-acid truncation of the encoded protein that most likely renders it non-functional, potentially explaining the increased mutation rate.

    “This mutation leads to a 200-amino-acid truncation of the encoded protein that most likely renders it non-functional, potentially explaining the increased mutation rate.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    The almost simultaneous loss of transposon Tn6098 in cultures SP2 and SP3 indicates that the genes associated with it are dispensable in milk and that its loss confers a fitness advantage.

    “The almost simultaneous loss of transposon Tn6098 in cultures SP2 and SP3 indicates that the genes associated with it are dispensable in milk and that its loss confers a fitness advantage.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

    Interpretationreasoning

    These findings imply that the Leloir Pathway is expressed at a high level during growth on plant material, which may relate to the presence of galactose in typical plant oligosaccharides like stachyose, raffinose, and melibiose.

    “These findings imply that the Leloir Pathway is expressed at a high level during growth on plant material, which may relate to the presence of galactose in typical plant oligosaccharides like stachyose, raffinose, and melibiose.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Only unambiguous SNPs with a sequence coverage of more than 20-fold and a quality score >0.99 were used for further analysis.

    “Only unambiguous SNPs with a sequence coverage of more than 20-fold and a quality score >0.99 were used for further analysis.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductown data

    A rifampicin-resistant strain that showed no growth difference compared with the wild-type strain throughout the growth curve was designated KF147 RIF and used for further experiments.

    “A rifampicin-resistant strain that showed no growth difference compared with the wild-type strain throughout the growth curve was designated KF147 RIF and used for further experiments.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    The BCAA genomic locus was shown to be non-functional in 17 tested dairy isolates, and pseudogenes were identified in the leucine operon of the three sequenced dairy strains IL1403, SK11, and MG1363.

    “The BCAA genomic locus was shown to be non-functional in 17 tested dairy isolates (Godon et al. 1993), and pseudogenes were identified in the leucine operon of the three sequenced dairy strains IL1403, SK11, and MG1363 (Bolotin et al. 2001;Makarova et al. 2006;Wegmann et al. 2007).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites Godon et al. 1993

      Not checked in the free run.

    • cites Bolotin et al. 2001

      Not checked in the free run.

    • cites Makarova et al. 2006

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    The 2721 putative genes were represented on the microarray by one (5.4%), two (6.7%), three to six (68%), or seven or more probes (11.7%).

    “The 2721 putative genes were represented by one (5.4%),two (6.7%), three to six (68%), or seven or more probes (11.7%).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    Such an increase in fitness might be limited to lactococci isolated from the plant environment, which have additional genes that allow them to grow in nutritionally poorer and more dynamic environments than milk.

    “Alternatively, such an increase in fitness might be limited to lactococci isolated from the plant environment, which have been described to harbor additional genes that allow them to grow in nutritionally poorer and more dynamic environments than milk (van Hylckama Vlieg et al. 2006;Siezen et al. 2008).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites van Hylckama Vlieg et al. 2006

      Not checked in the free run.

    • cites Siezen et al. 2008

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    These carbon sources are particularly abundant in plant-associated niches, and their loss or down-regulation is expected and consistent with earlier descriptions of genomic and phenotypic traits of dairy lactococci.

    “These carbon sources are particularly abundant in plant-associated niches, and their loss or down-regulation is expected and consistent with earlier descriptions of genomic and phenotypic traits of dairy lactococci (Siezen et al. 2008).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Siezen et al. 2008

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Despite the positive effects on growth rate and growth yield, the rapid loss of the protease-encoding plasmid suggests that it imposes a high burden on the cell.

    “Despite the positive effects on growth rate and growth yield, the rapid loss of the protease-encoding plasmid suggests that it imposes a high burden on the cell.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    Microarray probes designed to detect oppC are not 100% matching to the sequence of strain IL594, so the actual expression level of oppC in strain IL594 might be higher than indicated.

    “(*) Microarray probes designed to detect oppC are not 100% matching to the sequence of strain IL594-the actual expression level of oppC in strain IL594 might therefore be higher than indicated.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    The reference genome of KF147 was resequenced with the same technology and confirmed the previously published sequence.

    “To increase the accuracy of Single Nucleotide Polymorphism (SNP) and INsertion/DELETion (INDEL) identification, the reference genome was also resequenced with the same technology and confirmed the sequence previously published for this strain (Siezen et al. 2010).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Siezen et al. 2010

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Our finding that strain NZ5522 performs well in milk despite the low expression of the BCAA biosynthesis operon appears to falsify the first explanation and strongly favors the second explanation.

    “Our finding that strain NZ5522 performs well in milk despite the low expression of the BCAA biosynthesis operon appears to falsify the first and strongly favors the second explanation.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    A total of 218 putative genes were not represented on the array because no unique probe satisfying the selection criteria could be selected.

    “A total of 218 putative genes were not represented on the array because no unique probe satisfying the selection criteria could be selected.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Since the protease is located extracellularly, peptides produced by it will also be consumed by protease-negative cheater variants, allowing these to invade the culture.

    “Since the protease is located extracellularly, peptides produced by it will also be consumed by protease-negative cheater variants, allowing these to invade the culture.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Premiseown data

    The coagulation of milk is an indicator of fully grown cultures because lactococcal growth in milk is tightly coupled to lactic acid production and ceases after milk coagulation.

    “The coagulation of milk was considered an indicator of fully grown cultures since lactococcal growth in milk is tightly coupled to lactic acid production and ceases after milk coagulation (Supplemental Fig. 7).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Supplemental Fig. 7

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationown data

    The observation that niche-specific adaptations occurring in environmental isolates can be reproduced by experimental evolution opens possibilities for the investigation of evolutionary strategies as they occur in complex environmental samples.

    “The observation that niche-specific adaptations occurring in environmental isolates can be reproduced by experimental evolution opens exciting possibilities for the investigation of evolutionary strategies as they occur in complex environmental samples.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Although the averaged P-values do not represent an FDR-corrected P-value, low average P-values for a gene are still indicative of highly significant regulation ratios and likely underestimate the significance of the observed regulation.

    “Although clearly the averaged P-values do not represent an FDR-corrected P-value anymore, low average P-values for a gene are still indicative of highly significant regulation ratios, and, in fact, they are likely to underestimate the significance of the observed regulation.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Dairy adapted strains of Streptococcus thermophilus and Lactobacillus bulgaricus show high proportions of pseudogenes related to carbohydrate metabolism.

    “Notably, also dairy adapted strains of Streptococcus thermophilus and Lactobacillus bulgaricus show high proportions of pseudogenes related to carbohydrate metabolism (Bolotin et al. 2004;van de Guchte et al. 2006).”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites Bolotin et al. 2004

      Not checked in the free run.

    • cites van de Guchte et al. 2006

      Not checked in the free run.

40 of 40

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • We cannot clearly predict the scale at which improved phenotypes emerge during laboratory evolution, although recent literature indicates that such predictions are possible in certain growth contexts such as carbon source adaptation.

    “In this context, we cannot clearly predict the scale at which improved phenotypes emerge during laboratory evolution, although recent literature indicates that such predictions are possible in certain growth contexts such as carbon source adaptation [65].”

    From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [65]

  • Suboptimal growth on glycerol can approach its theoretical maximum during laboratory evolution.

    “Subsequently, it was shown that suboptimal growth on glycerol can approach its theoretical maximum during laboratory evolution [65].”

    From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [65]

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.

  • OppC and oppD deletions are assigned inconsistently

    Major

    The text and Table 2 assign the adenine deletion 48 bases upstream to oppD and the thymidine deletion 64 bases upstream to oppC. Figure 3 reverses those assignments, attributing the thymidine deletion to oppD and the adenine deletion to oppC; this changes which mutation is proposed to explain increased expression.

1 of 1

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. Sambrook J , Fritsch EF , Maniatis T . 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

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Related

Authors
Bachmann, H., Starrenburg, M. J. C., Molenaar, D., Kleerebezem, M., & van Hylckama Vlieg, J. E. T.
Affiliations
Nederlands Instituut Voor Zuivel Oonderzoek (NL)
ORCID
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2011-11-11
Volume
22
Issue
1
Pages
115-124
ISSN
1088-9051 (ISSN-L)
DOI
10.1101/gr.121285.111
PMC
PMC3246198
OpenAlex
W2037362492
Semantic Scholar
17f0bb98eba2f0b6aa5dde7979c0ef4add070073
Cited by
170
References
63
Citations by year
2026: 6 · 2025: 9 · 2024: 12 · 2023: 7 · 2022: 12 · 2021: 15 · 2020: 9 · 2019: 17 · 2018: 10 · 2017: 13 · 2016: 10 · 2015: 16 · 2014: 14 · 2013: 11 · 2012: 8
Type
posted content
Language
en
Open access
Locations
  • Genome Research (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • VU Research Portal (publishedVersion)
  • Socio-Environmental Systems Modeling (acceptedVersion)
  • HighWire Press Open Archive (submittedVersion)
  • Data Archiving and Networked Services (DANS) (submittedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
  • Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
Lactococcus lactis, experimental evolution, niche adaptation, milk acidification, nitrogen metabolism, amino acid biosynthesis, genome resequencing, transcriptome, lactic acid bacteria
MeSH terms
Dairy Products, Lactococcus lactis, Transcription, Genetic, Gene Expression Regulation, Bacterial, Genome, Bacterial, Point Mutation, Evolution, Molecular, Genetic Loci

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