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   https://doi.org/10.1021/acs.chemrev.8b00285  

   Chao, Alex; Sieminski, Paul J.; Owens, Cedric P.; Goulding, Celia W. (September 2018, Chemical Reviews)
2. Zinc limitation triggers anticipatory adaptations in Mycobacterium tuberculosis

   https://doi.org/10.1371/journal.ppat.1009570  

   Dow, Allexa; Sule, Preeti; O’Donnell, Timothy J.; Burger, Andrew; Mattila, Joshua T.; Antonio, Brandi; Vergara, Kevin; Marcantonio, Endrei; Adams, L. Garry; James, Nicholas; et al (May 2021, PLOS Pathogens)

   Sassetti, Christopher M. (Ed.)

   Mycobacterium tuberculosis ( Mtb ) has complex and dynamic interactions with the human host, and subpopulations of Mtb that emerge during infection can influence disease outcomes. This study implicates zinc ion (Zn 2+ ) availability as a likely driver of bacterial phenotypic heterogeneity in vivo . Zn 2+ sequestration is part of “nutritional immunity”, where the immune system limits micronutrients to control pathogen growth, but this defense mechanism seems to be ineffective in controlling Mtb infection. Nonetheless, Zn 2+ -limitation is an environmental cue sensed by Mtb , as calprotectin triggers the zinc uptake regulator (Zur) regulon response in vitro and co-localizes with Zn 2+ -limited Mtb in vivo . Prolonged Zn 2+ limitation leads to numerous physiological changes in vitro , including differential expression of certain antigens, alterations in lipid metabolism and distinct cell surface morphology. Furthermore, Mtb enduring limited Zn 2+ employ defensive measures to fight oxidative stress, by increasing expression of proteins involved in DNA repair and antioxidant activity, including well described virulence factors KatG and AhpC, along with altered utilization of redox cofactors. Here, we propose a model in which prolonged Zn 2+ limitation defines a population of Mtb with anticipatory adaptations against impending immune attack, based on the evidence that Zn 2+ -limited Mtb are more resistant to oxidative stress and exhibit increased survival and induce more severe pulmonary granulomas in mice. Considering that extracellular Mtb may transit through the Zn 2+ -limited caseum before infecting naïve immune cells or upon host-to-host transmission, the resulting phenotypic heterogeneity driven by varied Zn 2+ availability likely plays a key role during early interactions with host cells. 

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3. Mycobacterium avium Infection in a C3HeB/FeJ Mouse Model

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4. Mycobacterium abscessus persistence in the face of Pseudomonas aeruginosa antagonism

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   Gupta, Rashmi; Schuster, Martin; Rohde, Kyle H (May 2025, Frontiers in Cellular and Infection Microbiology)
5. The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis

   https://doi.org/10.1093/g3journal/jkac055  

   Sabin, Susanna; Morales-Arce, Ana Y; Pfeifer, Susanne P; Jensen, Jeffrey D (March 2022, G3 Genes|Genomes|Genetics)

   Wong, A (Ed.)

   Abstract Mycobacterium canettii is a causative agent of tuberculosis in humans, along with the members of the Mycobacterium tuberculosis complex. Frequently used as an outgroup to the M. tuberculosis complex in phylogenetic analyses, M. canettii is thought to offer the best proxy for the progenitor species that gave rise to the complex. Here, we leverage whole-genome sequencing data and biologically relevant population genomic models to compare the evolutionary dynamics driving variation in the recombining M. canettii with that in the nonrecombining M. tuberculosis complex, and discuss differences in observed genomic diversity in the light of expected levels of Hill–Robertson interference. In doing so, we highlight the methodological challenges of estimating recombination rates through traditional population genetic approaches using sequences called from populations of microorganisms and evaluate the likely mis-inference that arises owing to a neglect of common model violations including purifying selection, background selection, progeny skew, and population size change. In addition, we compare performance when full within-host polymorphism data are utilized, versus the more common approach of basing analyses on within-host consensus sequences. 

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