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Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution
Open accessAbstract
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.
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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.
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In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Increased growth rate, yield, and fitness of mutants in milk
What the sources say
- Not checked yetcites Chopin et al. 1984
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In the paper
“Since Tn6098 contains the only predicted a-galactosidase of the parental KF147 strain”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Adaptation resulted in the loss of mobile elements and generation of a mutator strain
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“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Results
What the sources say
- Not checked yetcites de Vos et al. 1989
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“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
What the sources say
- Not checked yetcites Miller 1996
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In the paper
“Additionally, identical single-base deletions were identified in strains NZ5521 and NZ5522 upstream of the fourth gene in this operon (oppC).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“It grows poorly in milk as compared to typical dairy L. lactis strains.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Results
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In the paper
“It was also expressed at a significantly increased level in strains NZ5521 and NZ5522 (Fig. 2, cluster 7).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“In the ancestral strain KF147, oppC is annotated as a pseudogene, which due to a frameshift encodes an N-terminally truncated version of the conserved OppC protein, the permease subunit of the oligopeptide ABC transporter.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“The transcription level of a locus encoding genes involved in Branched Chain Amino Acid (BCAA) (leucine, valine, isoleucine) biosynthesis was significantly increased in strains NZ5521 and NZ5523.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“In contrast, the same locus was transcribed at slightly lower levels in strains NZ5522 and in KF147_PRT (Supplemental Fig. 6).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“Furthermore, strains NZ5522 and NZ5523 had lost an identical 51.3-kb genomic fragment that is similar to a lactococcal sucrose transposon, designated Tn6098 (Kelly et al. 2000;Machielsen et al. 2011).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Adaptation resulted in the loss of mobile elements and generation of a mutator strain
What the sources say
- Not checked yetcites Kelly et al. 2000
- Not checked yetcites Machielsen et al. 2011
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In the paper
“In addition to the Tn6098-mediated loss of genes associated with the utilization of a-galactosides, the transcriptome analysis revealed the down-regulation of genes involved in cellobiose, galactose, and uronic-acid metabolism.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Genes associated with plant-polymer utilization are down-regulated in milk-adapted strains
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In the paper
“This locus is also highly expressed in the dairy isolate IL594 (Fig. 2, cluster 6).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“Compared with KF147, the transcription level of 291 genes (out of 1850 genes measured) appeared to be significantly ( p < 0.001) differentially expressed in at least one of the adapted strains, or in KF147_PRT or IL594.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
Load-bearingStrength:hedged· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Fluctuation analysis (Luria and Delbruck 1943) revealed that the mutation frequency of NZ5521 is ;10-fold increased as compared with strains KF147, NZ5522, and NZ5523 (Table 3).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
What the sources say
- Not checked yetcites Luria and Delbruck 1943
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In the paper
“Whole genome resequencing of the adapted strains NZ5521, NZ5522, and NZ5523 revealed 21, four, and six single-nucleotide polymorphisms (SNPs), respectively (Table 1)”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Adaptation resulted in the loss of mobile elements and generation of a mutator strain
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In the paper
“An operon encoding an ABC-type oligopeptide transport system displayed the highest differential expression level (;350-fold higher) in strain IL594 as compared with strain KF147.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“Other SNPs and INDELs were found within and around genes coding for transport functions (Tables 1, 2).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
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In the paper
“and seven and two single-base INsertions/DELetions (INDEL) in strains NZ5521 and NZ5522, respectively (Table 2).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Adaptation resulted in the loss of mobile elements and generation of a mutator strain
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In the paper
“Despite the loss of the proteolytic trait, adapted cultures displayed an increased acidification rate as compared with the parental KF147 strain.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Results
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“The final cell densities in milk cultures of the strains NZ5521 and NZ5522 (;2 3 10 9 CFU/mL) were similar to those typically reached by dairy strains grown in milk ( Juillard et al. 1995).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Increased growth rate, yield, and fitness of mutants in milk
What the sources say
- Not checked yetcites Juillard et al. 1995
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In the paper
“Remarkably, in strains NZ5521 and NZ5522, an identical single base-pair deletion of an adenine residue was identified 48 bases up-stream of the first gene in this operon (oppD) (Fig. 3; Table 2).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“Interestingly, the genome of NZ5521 harbors a singlebase deletion in a gene involved in DNA mismatch repair, mutL (Table 2).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
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In the paper
“Cluster 3 and cluster 4 (Fig. 2) represent transcript levels of ABC-type sugar transporters, cellobiose phospho-transferase systems (PTS), and galactose metabolism, which are expressed at a lower level in IL594 as well as in the adapted strains NZ5521 and NZ5522.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“Simultaneously, the fraction of protease-positive cells in the culture decreased drastically in all three experiments (Fig. 1B).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Results
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“With the exception of one deletion in a stretch of three adenine residues, all INDELs identified were located in mononucleotide stretches of at least 8 nt, which is consistent with the majority of mutations found in dairy-adapted streptococci (Table 2; Bolotin et al. 2004).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Adaptation resulted in the loss of mobile elements and generation of a mutator strain
What the sources say
- Not checked yetcites Bolotin et al. 2004
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In the paper
“Strain NZ5523 shows fewer transcriptional changes than the other two adapted isolates.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
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In the paper
“After 1000 generations of serial propagation, no protease-positive strains could be detected in any of the parallel cultures.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Results
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In the paper
“No significant differences between isolates from each culture were found, and subsequently one isolate of each independently evolved culture was chosen for further evaluation.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Phenotypic characterization
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In the paper
“However, compared with KF147, this operon is expressed at a higher level in strains NZ5521, NZ5523, and IL594.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Down-regulation of BCAA biosynthesis is consistent with genome decay of dairy isolates
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In the paper
“A point mutation upstream of a genomic locus involved in the biosynthesis of branched-chain amino acids coincides with a reduced expression level in NZ5522.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Down-regulation of BCAA biosynthesis is consistent with genome decay of dairy isolates
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In the paper
“The deletion of the transposon Tn6098 was confirmed by the amplification across the deletion junction using genomic DNA as a template in combination with primers HB03delFW (59-gtcatttaagaagcctttcgcatagag-39) and HB03delREV (59-gaacatag aactccctgctcttggag-39), and the resulting amplicon was subjected to sequence determination, confirming the anticipated transposon excision site.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Genotypic characterization
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In the paper
“Nevertheless, we were able to select mutants that thrive in milk even without an extracellular protease.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Extracellular protease could not be stabilized by host-plasmid coevolution
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In the paper
“| KF147 | 24 | 1.34 | 1.14 | 1.55 |”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Array data analysis
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In the paper
“Overall, transcriptome changes occurring in NZ5521 and NZ5522 reflect a convergence toward the transcriptome of IL594 (Fig. 2).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
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In the paper
“The fact that two identical mutations were found in two independently evolved strains indicates that they confer an important selective advantage during growth in milk.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“This emphasizes the importance of nitrogen metabolism as a key performance determinant for the dairy environment.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Increased growth rate, yield, and fitness of mutants in milk
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Clonal interference most likely explains the observations for culture SP1, where 8% a-galactosidasenegative cells were detected after 650 generations, which then vanished during subsequent propagations (Supplemental Fig. 4; Hegreness et al. 2006).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
What the sources say
- Not checked yetcites Hegreness et al. 2006
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In the paper
“This mutation could be responsible for the increased expression level.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Among the mutations identified in NZ5521 was a single base deletion in the open reading frame of mutL, which is likely to have hitchhiked along with beneficial mutations (Shaver et al. 2002).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Mutators can play a role in bacterial domestication
What the sources say
- Not checked yetcites Shaver et al. 2002
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In the paper
“This is probably due to the generation of high amounts of peptides by the protease-positive IL594 strain, which allow high growth rates of both populations.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Increased growth rate, yield, and fitness of mutants in milk
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In the paper
“Moreover, the rapid loss of Tn6098 in cultures SP2 and SP3 indicates that maintenance of this transposon poses a burden on fitness under the propagation conditions used in this study.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
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In the paper
“The higher number of SNPs identified in the genome of strain NZ5521 suggest an increased mutation rate as compared with the other adapted strains.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
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In the paper
“Many of the mutations identified in the adapted strains are located within the coding regions of genes and therefore may affect the functional properties of the encoded proteins rather than their expression levels.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
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In the paper
“A point mutation that is located within the regulatory terminator/antiterminator region of this operon and that may explain the observed decreased expression level in strain NZ5522 was identified in strain NZ5522 (Supplemental Fig. 6; Table 1).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
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In the paper
“Several of these, such as ABC-type amino acid and oligopeptide transporters, are likely to influence growth in milk.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The identification of SNPs and INDELs, as well as transcriptome analysis in milk, established the importance of changes in nitrogen metabolism and the utilization of typical plant polymers.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Discussion
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“The reduced expression level of this locus in strain KF147_PRT is most probably a consequence of the protease-mediated supply of peptides and free amino acids in that culture (Guedon et al. 2005).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
What the sources say
- Not checked yetcites Guedon et al. 2005
Tests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIn the paper
“We demonstrated that population composition and cell density play a crucial role in the stabilization of the proteolytic trait (Bachmann et al. 2011).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Extracellular protease could not be stabilized by host-plasmid coevolution
What the sources say
- Not checked yetcites Bachmann et al. 2011
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“This oligopeptide transport system has been shown to be indispensable for the transport of casein-derived peptides (Kunji et al. 1995).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Oligo-peptide transport plays a key role during the adaptation to growth in milk
What the sources say
- Not checked yetcites Kunji et al. 1995
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“The IL1403 BCAA biosynthesis genes were described to be expressed in a regulated manner, despite BCAA auxotrophy (Godon et al. 1993).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Down-regulation of BCAA biosynthesis is consistent with genome decay of dairy isolates
What the sources say
- Not checked yetcites Godon et al. 1993
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIn the paper
“Analogous to the instability of the extracellular protease in L. lactis, yeast cells expressing the extracellular sucrose-degrading enzyme invertase and cheating invertase-negative mutants show comparable population dynamics (Gore et al. 2009).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Extracellular protease could not be stabilized by host-plasmid coevolution
What the sources say
- Not checked yetcites Gore et al. 2009
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesNone of the sources cited for this claim have been checked yet.
In the paper
“Moreover, several genes involved in nitrogen metabolism and peptide transport were induced after transition to a dairy environment (Gitton et al. 2005;Bachmann et al. 2010).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Oligo-peptide transport plays a key role during the adaptation to growth in milk
What the sources say
- Not checked yetcites Gitton et al. 2005
- Not checked yetcites Bachmann et al. 2010
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These observations, in combination with the stimulation of growth in milk of the plant isolate KF147 by the addition of amino acids (Supplemental Fig. 3), are consistent with the notion that the elevated expression of the oligopeptide transport system is an important adaptation to the dairy niche.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Oligo-peptide transport plays a key role during the adaptation to growth in milk
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The deletion of a thymidine residue 64 bases upstream of the GTG-start codon of oppD in strains NZ5521 and NZ5522 is likely to explain the higher expression levels in these strains.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Array data analysis
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our results indicate that protease-negative derivatives should be able to enhance their growth rate and overall performance almost to the level of protease-positive strains by adaptive evolution.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Extracellular protease could not be stabilized by host-plasmid coevolution
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The observation that protease stability could not be increased through host-plasmid coevolution demonstrates the complex dynamics associated with the expression of extracellular substratedegrading enzymes.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Extracellular protease could not be stabilized by host-plasmid coevolution
Strength:boosted· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Overall, numerous aspects of our findings are in agreement with an evolutionary process that is proposed to have occurred naturally.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Conclusion
Tests✓ Asserted: passes? Checkable: unclear✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In the same two strains, the deletion of an adenine residue (blue) in the upstream region of the truncated oppC gene generates an (alternative) start codon (purple), which is located 78 bases upstream of the native oppC start codon (green) and is preceded by a typical lactococcal ribosome binding site (red) that appears to be absent upstream of the native start codon.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Array data analysis
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The identical mutations in the promoter region of a highly upregulated oligopeptide transport system in two adapted strains represent an astonishing parallel to dairy L. lactis isolates.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Oligo-peptide transport plays a key role during the adaptation to growth in milk
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesA conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The inability to degrade extracellular proteins into utilizable peptides is most likely overcome by a more efficient uptake of free peptides in milk combined with amino acid biosynthesis.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Extracellular protease could not be stabilized by host-plasmid coevolution
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesNone of the sources cited for this claim have been checked yet.
In the paper
“Comparative genomics has revealed that the acquisition of genes related to amino acid degradation and transport, as well as the loss of genes involved in the utilization of carbohydrates that do not occur in milk, are prominent dairy-specific adaptations (Siezen et al. 2005;Makarova et al. 2006;Makarova and Koonin 2007).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Oligo-peptide transport plays a key role during the adaptation to growth in milk
What the sources say
- Not checked yetcites Siezen et al. 2005
- Not checked yetcites Makarova et al. 2006
- Not checked yetcites Makarova and Koonin 2007
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passes
- It may state two separate claims as one. 30
- Probably not a substantial claim. 19
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Increased growth rate, yield, and fitness of mutants in milk
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
What the sources say
- Not checked yetcites Sorensen and Hove-Jensen 1996
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“NZ5523 shares loss of Tn6098 with NZ5522, but none of the other mutations occurred in both strains.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Increased growth rate, yield, and fitness of mutants in milk
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Increased growth rate, yield, and fitness of mutants in milk
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Acidification rates were rapid during the initial cultivations, whereas they decreased after 300 generations (Fig. 1A).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Results
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Results
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
Strength:plain· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Increased growth rate, yield, and fitness of mutants in milk
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“| NZ5521 24 | 10.02 | 9.30 | 10.76 |”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Array data analysis
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This strategy allowed the confirmation of all except one incorrectly predicted INDEL mutation.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Genotypic characterization
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“| NZ5522 24 | 1.14 | 0.96 | 1.32 |”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Array data analysis
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Design of microarrays
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“| NZ5523 24 | 1.06 | 0.90 | 1.22 |”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Array data analysis
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
What the sources say
- Not checked yetcites Sanders et al. 1998
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“L. lactis KF147 was isolated from mung-bean sprouts (Kelly et al. 1998;Siezen et al. 2008).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Results
What the sources say
- Not checked yetcites Kelly et al. 1998
- Not checked yetcites Siezen et al. 2008
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Transcriptome of two adapted strains converges toward that of a dairy strain
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✗ Based: failsProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Mobile elements facilitate genome reduction
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution of dairy lactococci
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✗ Based: failsProbably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Only unambiguous SNPs with a sequence coverage of more than 20-fold and a quality score >0.99 were used for further analysis.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Genotypic characterization
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Determination of relative fitness
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Down-regulation of BCAA biosynthesis is consistent with genome decay of dairy isolates
What the sources say
- Not checked yetcites Godon et al. 1993
- Not checked yetcites Bolotin et al. 2001
- Not checked yetcites Makarova et al. 2006
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The 2721 putative genes were represented by one (5.4%),two (6.7%), three to six (68%), or seven or more probes (11.7%).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Design of microarrays
Strength:plain· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Extracellular protease could not be stabilized by host-plasmid coevolution
What the sources say
- Not checked yetcites van Hylckama Vlieg et al. 2006
- Not checked yetcites Siezen et al. 2008
Strength:hedged· not yet calibratedCausal:conditional· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Genes associated with plant-polymer utilization are down-regulated in milk-adapted strains
What the sources say
- Not checked yetcites Siezen et al. 2008
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes? Load-bearing: unclear✓ Based: passesIt may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Extracellular protease could not be stabilized by host-plasmid coevolution
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“(*) 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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Array data analysis
Tests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Genotypic characterization
What the sources say
- Not checked yetcites Siezen et al. 2010
Strength:plain· not yet calibratedSingle caseTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Down-regulation of BCAA biosynthesis is consistent with genome decay of dairy isolates
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“A total of 218 putative genes were not represented on the array because no unique probe satisfying the selection criteria could be selected.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Design of microarrays
Strength:plain· not yet calibratedCausal:direct· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Extracellular protease could not be stabilized by host-plasmid coevolution
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesIt may state two separate claims as one.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Experimental evolution
What the sources say
- Not checked yetcites Supplemental Fig. 7
Tests✓ Asserted: passes✓ Checkable: passes✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Conclusion
Load-bearingStrength:plain· not yet calibratedTests✓ Asserted: passes✗ Checkable: fails✓ Load-bearing: passes✓ Based: passesProbably not a substantial claim. It may be too vague to check against evidence.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“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.”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Array data analysis
Strength:hedged· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“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).”
§ Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution > Genes associated with plant-polymer utilization are down-regulated in milk-adapted strains
What the sources say
- Not checked yetcites Bolotin et al. 2004
- Not checked yetcites van de Guchte et al. 2006
Strength:plain· not yet calibratedCausal:correlational· not yet calibratedTests✓ Asserted: passes✓ Checkable: passes✗ Load-bearing: fails✓ Based: passesProbably not a substantial claim. The paper’s conclusions may not depend on it.
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?
In the citing paper
“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]
In the citing paper
“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
MajorThe 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.
“Remarkably, in strains NZ5521 and NZ5522, an identical single base-pair deletion of an adenine residue was identified 48 bases up-stream of the first gene in this operon (oppD) (Fig. 3; Table 2).”
“The deletion of a thymidine residue 64 bases upstream of the GTG-start codon of oppD in strains NZ5521 and NZ5522 is likely to explain the higher expression levels in these strains.In the same two strains, the deletion of an adenine residue (blue) in the upstream region of the truncated oppC gene generates an (alternative) start codon (purple)”
Citations
Cites
Mutations of bacteria from virus sensitivity to virus resistance
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Comparative genomics of the lactic acid bacteria.
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Genome evolution and adaptation in a long-term experiment with Escherichia coli
Barrick, J. E., Yu, D. S., Yoon, S. H., Jeong, H., Oh, T. K., Schneider, D., Lenski, R. E., & Kim, J. F. (2009) · Nature · doi:10.1038/nature08480 · Cited by 1,184
The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403Preprint
Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., Ehrlich, S. D., & Sorokin, A. (2001) · Genome Research · doi:10.1101/gr.169701 · Cited by 1,161
The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403
Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., Ehrlich, S. D., & Sorokin, A. (2001) · Genome Research · doi:10.1101/gr.gr-1697r · Cited by 1,139
Evolution of high mutation rates in experimental populations of E. coli
Sniegowski, P. D., Gerrish, P. J., & Lenski, R. E. (1997) · Nature · doi:10.1038/42701 · Cited by 879
The proteotytic systems of lactic acid bacteria
Kunji, E. R. S., Mierau, I., Hagting, A., Poolman, B., & Konings, W. N. (1996) · Antonie van Leeuwenhoek · doi:10.1007/bf00395933 · Cited by 724
Role of mutator alleles in adaptive evolution
Taddéi, F., Radman, M., Smith, J. M., Toupance, B., Gouyon, P. H., & Godelle, B. (1997) · Nature · doi:10.1038/42696 · Cited by 678
Flagged first, then by citations
Research works printed but not linked: 1
- Sambrook J , Fritsch EF , Maniatis T . 1989. Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
Cited by
Sorted by citations
Marco, M. L., Sanders, M. E., Gänzle, M., Arrieta, M. C., Cotter, P. D., De Vuyst, L., Hill, C., Holzapfel, W., Lebeer, S., Merenstein, D., et al. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-00390-5 · Cited by 937
Stress Physiology of Lactic Acid Bacteria.
Papadimitriou, K., Alegría, Á., Bron, P. A., de Angelis, M., Gobbetti, M., Kleerebezem, M., Lemos, J. A., Linares, D. M., Ross, P., Stanton, C., et al. (2016) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00076-15 · Cited by 914
Self-citationAdaptive laboratory evolution—Principles and applications for biotechnology
Dragosits, M., & Mattanovich, D. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-64 · Cited by 827
Traditional Cheeses: Rich and Diverse Microbiota with Associated Benefits
Montel, M.-C., Buchin, S., Mallet, A., Delbes-Paus, C., Vuitton, D. A., Desmasures, N., & Berthier, F. (2014) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2014.02.019 · Cited by 665
Fate, activity, and impact of ingested bacteria within the human gut microbiota
Derrien, M., & van Hylckama Vlieg, J. E. T. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.03.002 · Cited by 605
Metadata
- Authors
- Bachmann, H., Starrenburg, M. J. C., Molenaar, D., Kleerebezem, M., & van Hylckama Vlieg, J. E. T.
- Affiliations
- Nederlands Instituut Voor Zuivel Oonderzoek (NL)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-11-11
- Volume
- 22
- Issue
- 1
- Pages
- 115-124
- ISSN
- 1088-9051 (ISSN-L)
- 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
- bronze
- doi.org
- 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
About these checks
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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A second model labelled each claim on 2026-10-10 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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