Erratum for Tong et al., “Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments”

Vibrio cholerae O1 has caused cholera pandemics. Non-pandemic V. cholerae O1 strains, which are genetically distinctive from the pandemic clones, have been isolated from both human infections and the environment. We aimed to better understand the non-pandemic O1 strains and their pandemic potential. We sequenced 109 non-pandemic O1 isolates from Zhejiang, China (from 1963 to 1996) and compared them with 62 publicly available non-pandemic O1 genomes. The isolates from Zhejiang can be classified into three lineages (L1–L3). All grouped together with L3 sharing the most recent common ancestor with the pandemic clones. L2 and L3 emerged in the 1960s while L1 emerged in the 1970s. L1 and L2 disappeared after the 1990s, but L3 persisted until recently. All isolates contained the type VI secretion system. The Vibrio pathogenicity island was present in all L3 isolates, whereas the type III secretion system was present in all L1 isolates. L2 did not carry any unique virulence genes. An intact CTXφ was present in only two L3 isolates. An intact Vibrio seventh pandemic island 1 was present in only three L3 isolates. The bla CARB-7 gene was identified in 96.3% of L2 isolates. Each of the non-pandemic O1 lineages has unique properties contributing to their capacity to cause disease. Our findings offer new insight into the evolution of O1 V. cholerae for cholera prevention and control. IMPORTANCE It is well recognized that only Vibrio cholerae O1 causes cholera pandemics. However, not all O1 strains cause pandemic-level disease. In this study, we analyzed non-pandemic O1 V. cholerae isolates from the 1960s to the 1990s from China and found that they fell into three lineages, one of which shared the most recent common ancestor with pandemic O1 strains. Each of these non-pandemic O1 lineages has unique properties that contribute to their capacity to cause cholera. The findings of this study enhanced our understanding of the emergence and evolution of both pandemic and non-pandemic O1 V. cholerae .

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Efforts to Minimise the Bacterial Genome as a Free-Living Growing System

Aida,

Ying

2023

Biology

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Exploring the minimal genetic requirements for cells to maintain free living is an exciting topic in biology. Multiple approaches are employed to address the question of the minimal genome. In addition to constructing the synthetic genome in the test tube, reducing the size of the wild-type genome is a practical approach for obtaining the essential genomic sequence for living cells. The well-studied Escherichia coli has been used as a model organism for genome reduction owing to its fast growth and easy manipulation. Extensive studies have reported how to reduce the bacterial genome and the collections of genomic disturbed strains acquired, which were sufficiently reviewed previously. However, the common issue of growth decrease caused by genetic disturbance remains largely unaddressed. This mini-review discusses the considerable efforts made to improve growth fitness, which was decreased due to genome reduction. The proposal and perspective are clarified for further accumulated genetic deletion to minimise the Escherichia coli genome in terms of genome reduction, experimental evolution, medium optimization, and machine learning.

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Erratum for Tong et al., “Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments”

Abstract: that, unexpectedly, phosphoenolpyruvate carboxylase (ppc) was required for robust growth in most carbon sources other than most trichloroacetic acid (TCA) cycle intermediates," "trichloroacetic acid" should be "tricarboxylic acid." This change does not change the conclusions of the paper.

Cited by 3 publications

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sparse-growth-curve: a Computational Pipeline for Parsing Cellular Growth Curves with Low Temporal Resolution

sparse-growth-curve: a Computational Pipeline for Parsing Cellular Growth Curves with Low Temporal Resolution

Emergence and genomic insights of non-pandemic O1 Vibrio cholerae in Zhejiang, China

Efforts to Minimise the Bacterial Genome as a Free-Living Growing System

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