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Zappa S, Berne C, Morton Iii RI, Whitfield GB, De Stercke J, Brun YV. The HmrABCX pathway regulates the transition between motile and sessile lifestyles in Caulobacter crescentus by a mechanism independent of hfiA transcription. mBio 2024:e0100224. [PMID: 39230277 DOI: 10.1128/mbio.01002-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/03/2024] [Indexed: 09/05/2024] Open
Abstract
During its cell cycle, the bacterium Caulobacter crescentus switches from a motile, free-living state, to a sessile surface-attached cell. During this coordinated process, cells undergo irreversible morphological changes, such as shedding of their polar flagellum and synthesis of an adhesive holdfast at the same pole. In this work, we used genetic screens to identify genes involved in the regulation of the transition from the motile to the sessile lifestyle. We identified a predicted hybrid histidine kinase that inhibits biofilm formation and promotes the motile lifestyle: HmrA (holdfast and motility regulator A). Genetic screens and genomic localization led to the identification of additional genes that form a putative phosphorelay pathway with HmrA. We postulate that the Hmr pathway acts as a rheostat to control the proportion of cells harboring a flagellum or a holdfast in the population. Further genetic analysis suggests that the Hmr pathway impacts c-di-GMP synthesis through the diguanylate cyclase DgcB pathway. Our results also indicate that the Hmr pathway is involved in the regulation of motile to sessile lifestyle transition as a function of various environmental factors: biofilm formation is repressed when excess copper is present and derepressed under non-optimal temperatures. Finally, we provide evidence that the Hmr pathway regulates motility and adhesion without modulating the transcription of the holdfast synthesis regulator HfiA. IMPORTANCE Complex communities attached to a surface, or biofilms, represent the major lifestyle of bacteria in the environment. Such a sessile state enables the inhabitants to be more resistant to adverse environmental conditions. Thus, having a deeper understanding of the underlying mechanisms that regulate the transition between the motile and the sessile states could help design strategies to improve biofilms when they are beneficial or impede them when they are detrimental. For Caulobacter crescentus motile cells, the transition to the sessile lifestyle is irreversible, and this decision is regulated at several levels. In this work, we describe a putative phosphorelay that promotes the motile lifestyle and inhibits biofilm formation, providing new insights into the control of adhesin production that leads to the formation of biofilms.
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Affiliation(s)
- Sébastien Zappa
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Cécile Berne
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | | | - Gregory B Whitfield
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Jonathan De Stercke
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Yves V Brun
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Quebec, Canada
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Salemi RI, Cruz AK, Hershey DM. A flagellar accessory protein links chemotaxis to surface sensing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599946. [PMID: 38948737 PMCID: PMC11212940 DOI: 10.1101/2024.06.20.599946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Bacteria find suitable locations for colonization by sensing and responding to surfaces. Complex signaling repertoires control surface colonization, and surface contact sensing by the flagellum plays a central role in activating colonization programs. Caulobacter crescentus adheres to surfaces using a polysaccharide adhesin called the holdfast. In C. crescentus, disruption of the flagellum through interactions with a surface or mutation of flagellar genes increases holdfast production. Our group previously identified several C. crescentus genes involved in flagellar surface sensing. One of these, called fssF, codes for a protein with homology to the flagellar C-ring protein FliN. We show here that a fluorescently tagged FssF protein localizes to the flagellated pole of the cell and requires all components of the flagellar C-ring for proper localization, supporting the model that FssF associates with the C-ring. Deleting fssF results in a severe motility defect that we show is due to a disruption of chemotaxis. Epistasis experiments demonstrate that fssF promotes adhesion through a stator-dependent pathway when late-stage flagellar mutants are disrupted. Separately, we find that disruption of chemotaxis through deletion of fssF or other chemotaxis genes results in a hyperadhesion phenotype. Key genes in the surface sensing network (pleD, motB, and dgcB) contribute to both ∆flgH-dependent and ∆fssF-dependent hyperadhesion, but these genes affect adhesion differently in the two hyperadhesive backgrounds. Our results support a model in which the stator subunits of the flagella incorporate both mechanical and chemical signals to regulate adhesion.
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Affiliation(s)
- Rachel I. Salemi
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ana K. Cruz
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David M. Hershey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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3
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Liu X, Lertsethtakarn P, Mariscal VT, Yildiz F, Ottemann KM. Counterclockwise rotation of the flagellum promotes biofilm initiation in Helicobacter pylori. mBio 2024; 15:e0044024. [PMID: 38700325 PMCID: PMC11237671 DOI: 10.1128/mbio.00440-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/26/2024] [Indexed: 05/05/2024] Open
Abstract
Motility promotes biofilm initiation during the early steps of this process: microbial surface association and attachment. Motility is controlled in part by chemotaxis signaling, so it seems reasonable that chemotaxis may also affect biofilm formation. There is a gap, however, in our understanding of the interactions between chemotaxis and biofilm formation, partly because most studies analyzed the phenotype of only a single chemotaxis signaling mutant, e.g., cheA. Here, we addressed the role of chemotaxis in biofilm formation using a full set of chemotaxis signaling mutants in Helicobacter pylori, a class I carcinogen that infects more than half the world's population and forms biofilms. Using mutants that lack each chemotaxis signaling protein, we found that chemotaxis signaling affected the biofilm initiation stage, but not mature biofilm formation. Surprisingly, some chemotaxis mutants elevated biofilm initiation, while others inhibited it in a manner that was not tied to chemotaxis ability or ligand input. Instead, the biofilm phenotype correlated with flagellar rotational bias. Specifically, mutants with a counterclockwise bias promoted biofilm initiation, e.g., ∆cheA, ∆cheW, or ∆cheV1; in contrast, those with a clockwise bias inhibited it, e.g., ∆cheZ, ∆chePep, or ∆cheV3. We tested this correlation using a counterclockwise bias-locked flagellum, which induced biofilm formation independent of the chemotaxis system. These CCW flagella, however, were not sufficient to induce biofilm formation, suggesting there are downstream players. Overall, our work highlights the new finding that flagellar rotational direction promotes biofilm initiation, with the chemotaxis signaling system operating as one mechanism to control flagellar rotation. IMPORTANCE Chemotaxis signaling systems have been reported to contribute to biofilm formation in many bacteria; however, how they regulate biofilm formation remains largely unknown. Chemotaxis systems are composed of many distinct kinds of proteins, but most previous work analyzed the biofilm effect of loss of only a few. Here, we explored chemotaxis' role during biofilm formation in the human-associated pathogenic bacterium Helicobacter pylori. We found that chemotaxis proteins are involved in biofilm initiation in a manner that correlated with how they affected flagellar rotation. Biofilm initiation was high in mutants with counterclockwise (CCW) flagellar bias and low in those with clockwise bias. We supported the idea that a major driver of biofilm formation is flagellar rotational direction using a CCW-locked flagellar mutant, which stays CCW independent of chemotaxis input and showed elevated biofilm initiation. Our data suggest that CCW-rotating flagella, independent of chemotaxis inputs, are a biofilm-promoting signal.
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Affiliation(s)
- Xiaolin Liu
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Paphavee Lertsethtakarn
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Vanessa T. Mariscal
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Fitnat Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
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Nisha FA, Tagoe JNA, Pease AB, Horne SM, Ugrinov A, Geddes BA, Prüß BM. Plant seedlings of peas, tomatoes, and cucumbers exude compounds that are needed for growth and chemoattraction of Rhizobium leguminosarum bv. viciae 3841 and Azospirillum brasilense Sp7. Can J Microbiol 2024; 70:150-162. [PMID: 38427979 DOI: 10.1139/cjm-2023-0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
This study characterizes seedling exudates of peas, tomatoes, and cucumbers at the level of chemical composition and functionality. A plant experiment confirmed that Rhizobium leguminosarum bv. viciae 3841 enhanced growth of pea shoots, while Azospirillum brasilense Sp7 supported growth of pea, tomato, and cucumber roots. Chemical analysis of exudates after 1 day of seedling incubation in water yielded differences between the exudates of the three plants. Most remarkably, cucumber seedling exudate did not contain detectable sugars. All exudates contained amino acids, nucleobases/nucleosides, and organic acids, among other compounds. Cucumber seedling exudate contained reduced glutathione. Migration on semi solid agar plates containing individual exudate compounds as putative chemoattractants revealed that R. leguminosarum bv. viciae was more selective than A. brasilense, which migrated towards any of the compounds tested. Migration on semi solid agar plates containing 1:1 dilutions of seedling exudate was observed for each of the combinations of bacteria and exudates tested. Likewise, R. leguminosarum bv. viciae and A. brasilense grew on each of the three seedling exudates, though at varying growth rates. We conclude that the seedling exudates of peas, tomatoes, and cucumbers contain everything that is needed for their symbiotic bacteria to migrate and grow on.
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Affiliation(s)
- Fatema A Nisha
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Janice N A Tagoe
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Amanda B Pease
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Shelley M Horne
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Barney A Geddes
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - Birgit M Prüß
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA
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Sagoo J, Abedrabbo S, Liu X, Ottemann KM. Helicobacter pylori cheV1 mutants recover semisolid agar migration due to loss of a previously uncharacterized Type IV filament membrane alignment complex homolog. J Bacteriol 2024; 206:e0040623. [PMID: 38446058 PMCID: PMC11025336 DOI: 10.1128/jb.00406-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
The bacterial chemotaxis system is a well-understood signaling pathway that promotes bacterial success. Chemotaxis systems comprise chemoreceptors and the CheA kinase, linked by CheW or CheV scaffold proteins. Scaffold proteins provide connections between chemoreceptors and CheA and also between chemoreceptors to create macromolecular arrays. Chemotaxis is required for host colonization by many microbes, including the stomach pathogen Helicobacter pylori. This bacterium builds chemoreceptor-CheA contacts with two distinct scaffold proteins, CheW and CheV1. H. pylori cheW or cheV1 deletion mutants both lose chemoreceptor array formation, but show differing semisolid agar chemotaxis assay behaviors: ∆cheW mutants exhibit total migration failure, whereas ∆cheV1::cat mutants display a 50% reduction. On investigating these varied responses, we found that both mutants initially struggle with migration. However, over time, ∆cheV1::cat mutants develop a stable, enhanced migration capability, termed "migration-able" (Mig+). Whole-genome sequencing analysis of four distinct ∆cheV1::cat Mig+ strains identified single-nucleotide polymorphisms (SNPs) in hpg27_252 (hp0273) that were predicted to truncate the encoded protein. Computational analysis of the hpg27_252-encoded protein revealed it encoded a hypothetical protein that was a remote homolog of the PilO Type IV filament membrane alignment complex protein. Although H. pylori lacks Type IV filaments, our analysis showed it retains an operon of genes for homologs of PilO, PilN, and PilM. Deleting hpg27_252 in the ∆cheV1::cat or wild type strain resulted in enhanced migration in semisolid agar. Our study thus reveals that while cheV1 mutants initially have significant migration defects, they can recover the migration ability through genetic suppressors, highlighting a complex regulatory mechanism in bacterial migration. IMPORTANCE Chemotactic motility, present in over half of bacteria, depends on chemotaxis signaling systems comprising receptors, kinases, and scaffold proteins. In Helicobacter pylori, a stomach pathogen, chemotaxis is crucial for colonization, with CheV1 and CheW as key scaffold proteins. While both scaffolds are essential for building chemoreceptor complexes, their roles vary in other assays. Our research reexamines cheV1 mutants' behavior in semisolid agar, a standard chemotaxis test. Initially, cheV1 mutants exhibited defects similar to those of cheW mutants, but they evolved genetic suppressors that enhanced migration. These suppressors involve mutations in a previously uncharacterized gene, unknown in motility behavior. Our findings highlight the significant chemotaxis defects in cheV1 mutants and identify new elements influencing bacterial motility.
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Affiliation(s)
- Jashwin Sagoo
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
| | - Samar Abedrabbo
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
| | - Xiaolin Liu
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology, UC Santa Cruz, Santa Cruz, California, USA
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Bao R, Guo H, Liang Y, Tang K, Feng F, Meng J. Terrihabitans rhizophilus sp. nov., isolated from the rhizosphere soil of plant in temperate semi-arid steppe. Antonie Van Leeuwenhoek 2024; 117:67. [PMID: 38607451 DOI: 10.1007/s10482-024-01966-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
A bacterial strain PJ23T was isolated from the rhizosphere soil of Elymus dahuricus Turcz. sampled from a temperate semi-arid steppe in the northern of Inner Mongolia Autonomous Region, China. The strain is Gram-stain-negative, aerobic, light-pink, short rod-shaped, and non-spore-forming. Cell growth could be observed at 4-29℃ (optimal at 24℃), pH 6.0-8.6 (optimal at 8.0) and in the presence of 0-5.0% (w/v) NaCl (optimal at 2.5%). The major cellular fatty acids of strain PJ23T were Summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) (39.42%) and C16:0 (9.60%). The polar lipids were phosphatidylcholine, two unidentified glycolipids, one unidentified aminophospholipid, and two other unidentified polar lipids. The major respiratory quinone was ubiquinone-10. Phylogeny analysis based on 16S rRNA gene sequences retrieved from the genomes showed that, the strain was closely related to the species Terrihabitans soli IZ6T and Flaviflagellibacter deserti SYSU D60017T, with the sequence similarities of 96.79% and 96.15%, respectively. The G + C content was 65.23 mol% calculated on draft genome sequencing. Between the strains PJ23T and Terrihabitans soli IZ6T, the average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) was 73.39%,71.12% and 15.7%, these values were lower than the proposed and generally accepted species boundaries of ANI, AAI and dDDH, respectively. Based on phenotypic, chemotaxonomic, and phylogenetic characteristics, strain PJ23T represents a novel species of Terrihabitans, for which the name Terrihabitans rhizophilus sp. nov. is proposed. The type strain is PJ23T (= KCTC 92977 T = CGMCC 1.61577 T).
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Affiliation(s)
- Runze Bao
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Huiling Guo
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Yungang Liang
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Kai Tang
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Fuying Feng
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China
| | - Jianyu Meng
- Laboratory of Environmental Microbiology and Biotechnology in Arid and Cold Regions, College of Life Science, Inner Mongolia Agricultural University, Huhhot, 010018, PR, China.
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Behringer MG, Ho WC, Miller SF, Worthan SB, Cen Z, Stikeleather R, Lynch M. Trade-offs, trade-ups, and high mutational parallelism underlie microbial adaptation during extreme cycles of feast and famine. Curr Biol 2024; 34:1403-1413.e5. [PMID: 38460514 PMCID: PMC11066936 DOI: 10.1016/j.cub.2024.02.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/12/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024]
Abstract
Microbes are evolutionarily robust organisms capable of rapid adaptation to complex stress, which enables them to colonize harsh environments. In nature, microbes are regularly challenged by starvation, which is a particularly complex stress because resource limitation often co-occurs with changes in pH, osmolarity, and toxin accumulation created by metabolic waste. Often overlooked are the additional complications introduced by eventual resource replenishment, as successful microbes must withstand rapid environmental shifts before swiftly capitalizing on replenished resources to avoid invasion by competing species. To understand how microbes navigate trade-offs between growth and survival, ultimately adapting to thrive in environments with extreme fluctuations, we experimentally evolved 16 Escherichia coli populations for 900 days in repeated feast/famine conditions with cycles of 100-day starvation before resource replenishment. Using longitudinal population-genomic analysis, we found that evolution in response to extreme feast/famine is characterized by narrow adaptive trajectories with high mutational parallelism and notable mutational order. Genetic reconstructions reveal that early mutations result in trade-offs for biofilm and motility but trade-ups for growth and survival, as these mutations conferred positively correlated advantages during both short-term and long-term culture. Our results demonstrate how microbes can navigate the adaptive landscapes of regularly fluctuating conditions and ultimately follow mutational trajectories that confer benefits across diverse environments.
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Affiliation(s)
- Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA; Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, 21st Avenue S, Nashville, TN 37232, USA.
| | - Wei-Chin Ho
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA; Department of Biology, University of Texas at Tyler, University Blvd., Tyler, TX 75799, USA.
| | - Samuel F Miller
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Zeer Cen
- Department of Biological Sciences, Vanderbilt University, 21st Avenue S, Nashville, TN 37232, USA
| | - Ryan Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, S McAllister Ave., Tempe, AZ 85281, USA
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Jakuszeit T, Croze OA. Role of tumbling in bacterial scattering at convex obstacles. Phys Rev E 2024; 109:044405. [PMID: 38755868 DOI: 10.1103/physreve.109.044405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/15/2024] [Indexed: 05/18/2024]
Abstract
Active propulsion, as performed by bacteria and Janus particles, in combination with hydrodynamic interaction results in the accumulation of bacteria at a flat wall. However, in microfluidic devices with cylindrical pillars of sufficiently small radius, self-propelled particles can slide along and scatter off the surface of a pillar, without becoming trapped over long times. This nonequilibrium scattering process has been predicted to result in large diffusivities, even at high obstacle density, unlike particles that undergo classical specular reflection. Here, we test this prediction by experimentally studying the nonequilibrium scattering of pusherlike swimmers in microfluidic obstacle lattices. To explore the role of tumbles in the scattering process, we microscopically tracked wild-type (run and tumble) and smooth-swimming (run only) mutants of the bacterium Escherichia coli scattering off microfluidic pillars. We quantified key scattering parameters and related them to previously proposed models that included a prediction for the diffusivity, discussing their relevance. Finally, we discuss potential interpretations of the role of tumbles in the scattering process and connect our work to the broader study of swimmers in porous media.
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Affiliation(s)
- Theresa Jakuszeit
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS UMR 144, 75005 Paris, France
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ottavio A Croze
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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Jin C, Sengupta A. Microbes in porous environments: from active interactions to emergent feedback. Biophys Rev 2024; 16:173-188. [PMID: 38737203 PMCID: PMC11078916 DOI: 10.1007/s12551-024-01185-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024] Open
Abstract
Microbes thrive in diverse porous environments-from soil and riverbeds to human lungs and cancer tissues-spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal heterogeneities, often leading to physiologically stressful settings. How microbes respond and adapt to such biophysical constraints is an active field of research where considerable insight has been gained over the last decades. With a focus on bacteria, here we review recent advances in self-organization and dispersal in inorganic and organic porous settings, highlighting the role of active interactions and feedback that mediates microbial survival and fitness. We discuss open questions and opportunities for using integrative approaches to advance our understanding of the biophysical strategies which microbes employ at various scales to make porous settings habitable.
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Affiliation(s)
- Chenyu Jin
- Physics of Living Matter Group, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, Luxembourg City, L-1511 Luxembourg
| | - Anupam Sengupta
- Physics of Living Matter Group, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, Luxembourg City, L-1511 Luxembourg
- Institute for Advanced Studies, University of Luxembourg, 2 Avenue de l’Université, Esch-sur-Alzette, L-4365 Luxembourg
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Mukhopadhyay S, Bishayi R, Shaji A, Lee AH, Gupta R, Mohajeri M, Katiyar A, McKee B, Schmitz IR, Shin R, Lele TP, Lele PP. Dynamic Adaptation in Extant Porins Facilitates Antibiotic Tolerance in Energetic Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583920. [PMID: 38496420 PMCID: PMC10942424 DOI: 10.1101/2024.03.07.583920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Bacteria can tolerate antibiotics despite lacking the genetic components for resistance. The prevailing notion is that tolerance results from depleted cellular energy or cell dormancy. In contrast to this view, many cells in the tolerant population of Escherichia coli can exhibit motility - a phenomenon that requires cellular energy, specifically, the proton-motive force (PMF). As these motile-tolerant cells are challenging to isolate from the heterogeneous tolerant population, their survival mechanism is unknown. Here, we discovered that motile bacteria segregate themselves from the tolerant population under micro-confinement, owing to their unique ability to penetrate micron-sized channels. Single-cell measurements on the motile-tolerant population showed that the cells retained a high PMF, but they did not survive through active efflux alone. By utilizing growth assays, single-cell fluorescence studies, and chemotaxis assays, we showed that the cells survived by dynamically inhibiting the function of existing porins in the outer membrane. A drug transport model for porin-mediated intake and efflux pump-mediated expulsion suggested that energetic tolerant cells withstand antibiotics by constricting their porins. The novel porin adaptation we have uncovered is independent of gene expression changes and may involve electrostatic modifications within individual porins to prevent extracellular ligand entry.
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Phan TV, Mattingly HH, Vo L, Marvin JS, Looger LL, Emonet T. Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model. Proc Natl Acad Sci U S A 2024; 121:e2309251121. [PMID: 38194458 PMCID: PMC10801886 DOI: 10.1073/pnas.2309251121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.
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Affiliation(s)
- Trung V. Phan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | | | - Lam Vo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | - Jonathan S. Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA20147
| | - Loren L. Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA20147
- HHMI, University of California, San Diego, CA92093
- Department of Neurosciences, University of California, San Diego, CA92093
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Department of Physics, Yale University, New Haven, CT06511
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Vo L, Avgidis F, Mattingly HH, Balasubramanian R, Shimizu TS, Kazmierczak BI, Emonet T. Non-genetic adaptation by collective migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.02.573956. [PMID: 38260286 PMCID: PMC10802332 DOI: 10.1101/2024.01.02.573956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Collective behaviors require coordination of individuals. Thus, a population must adjust its phenotypic distribution to adapt to changing environments. How can a population regulate its phenotypic distribution? One strategy is to utilize specialized networks for gene regulation and maintaining distinct phenotypic subsets. Another involves genetic mutations, which can be augmented by stress-response pathways. Here, we studied how a migrating bacterial population regulates its phenotypic distribution to traverse across diverse environments. We generated isogenic Escherichia coli populations with varying distributions of swimming behaviors and observed their phenotype distributions during migration in liquid and porous environments. Surprisingly, we found that during collective migration, the distributions of swimming phenotypes adapt to the environment without mutations or gene regulation. Instead, adaptation is caused by the dynamic and reversible enrichment of high-performing swimming phenotypes within each environment. This adaptation mechanism is supported by a recent theoretical study, which proposed that the phenotypic composition of a migrating population results from a balance between cell growth generating diversity and collective migration eliminating the phenotypes that are unable to keep up with the migrating group. Furthermore, by examining chemoreceptor abundance distributions during migration towards different attractants, we found that this mechanism acts on multiple chemotaxis-related traits simultaneously. Our findings reveal that collective migration itself can enable cell populations with continuous, multi-dimensional phenotypes to flexibly and rapidly adapt their phenotypic composition to diverse environmental conditions. Significance statement Conventional cell adaptation mechanisms, like gene regulation and random phenotypic switching, act swiftly but are limited to a few traits, while mutation-driven adaptations unfold slowly. By quantifying phenotypic diversity during bacterial collective migration, we discovered an adaptation mechanism that rapidly and reversibly adjusts multiple traits simultaneously. By dynamically balancing the elimination of phenotypes unable to keep pace with generation of diversity through growth, this process enables populations to tune their phenotypic composition based on the environment, without the need for gene regulation or mutations. Given the prevalence of collective migration in microbes, cancers, and embryonic development, non-genetic adaptation through collective migration may be a universal mechanism for populations to navigate diverse environments, offering insights into broader applications across various fields.
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Couceiro JF, Marques M, Silva SG, Keller-Costa T, Costa R. Aquimarina aquimarini sp. nov. and Aquimarina spinulae sp. nov., novel bacterial species with versatile natural product biosynthesis potential isolated from marine sponges. Int J Syst Evol Microbiol 2024; 74. [PMID: 38240740 DOI: 10.1099/ijsem.0.006228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
This study describes two Gram-negative, flexirubin-producing, biofilm-forming, motile-by-gliding and rod-shaped bacteria, isolated from the marine sponges Ircinia variabilis and Sarcotragus spinosulus collected off the coast of Algarve, Portugal. Both strains, designated Aq135T and Aq349T, were classified into the genus Aquimarina by means of 16S rRNA gene sequencing. We then performed phylogenetic, phylogenomic and biochemical analyses to determine whether these strains represent novel Aquimarina species. Whereas the closest 16S rRNA gene relatives to strain Aq135T were Aquimarina macrocephali JAMB N27T (97.8 %) and Aquimarina sediminis w01T (97.1 %), strain Aq349T was more closely related to Aquimarina megaterium XH134T (99.2 %) and Aquimarina atlantica 22II-S11-z7T (98.1 %). Both strains showed genome-wide average nucleotide identity scores below the species level cut-off (95 %) with all Aquimarina type strains with publicly available genomes, including their closest relatives. Digital DNA-DNA hybridization further suggested a novel species status for both strains since values lower than 70 % hybridization level with other Aquimarina type strains were obtained. Strains Aq135T and Aq349T grew from 4 to 30°C and with between 1-5 % (w/v) NaCl in marine broth. The most abundant fatty acids were iso-C17 : 03-OH and iso-C15 : 0 and the only respiratory quinone was MK-6. Strain Aq135T was catalase-positive and β-galactosidase-negative, while Aq349T was catalase-negative and β-galactosidase-positive. These strains hold unique sets of secondary metabolite biosynthetic gene clusters and are known to produce the peptide antibiotics aquimarins (Aq135T) and the trans-AT polyketide cuniculene (Aq349T), respectively. Based on the polyphasic approach employed in this study, we propose the novel species names Aquimarina aquimarini sp. nov. (type strain Aq135T=DSM 115833T=UCCCB 169T=ATCC TSD-360T) and Aquimarina spinulae sp. nov. (type strain Aq349T=DSM 115834T=UCCCB 170T=ATCC TSD-361T).
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Affiliation(s)
- Joana F Couceiro
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Matilde Marques
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Sandra G Silva
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Tina Keller-Costa
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Rodrigo Costa
- iBB-Institute for Bioengineering and Biosciences and i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengeneering, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
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14
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Zappa S, Berne C, Morton RI, De Stercke J, Brun YV. The HmrABCX pathway regulates the transition between motile and sessile lifestyles in Caulobacter crescentus by a HfiA-independent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571505. [PMID: 38168291 PMCID: PMC10760086 DOI: 10.1101/2023.12.13.571505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Through its cell cycle, the bacterium Caulobacter crescentus switches from a motile, free-living state, to a sessile surface-attached cell. During this coordinated process, cells undergo irreversible morphological changes, such as shedding of their polar flagellum and synthesis of an adhesive holdfast at the same pole. In this work, we used genetic screens to identify genes involved in the regulation of the motile to sessile lifestyle transition. We identified a predicted hybrid histidine kinase that inhibits biofilm formation and activates the motile lifestyle: HmrA (Holdfast and motility regulator A). Genetic screens and genomic localization led to the identification of additional genes that regulate the proportion of cells harboring an active flagellum or a holdfast and that form a putative phosphorelay pathway with HmrA. Further genetic analysis indicates that the Hmr pathway is independent of the holdfast synthesis regulator HfiA and may impact c-di-GMP synthesis through the diguanylate cyclase DgcB pathway. Finally, we provide evidence that the Hmr pathway is involved in the regulation of sessile-to-motile lifestyle as a function of environmental stresses, namely excess copper and non-optimal temperatures.
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Affiliation(s)
- Sébastien Zappa
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
| | - Cecile Berne
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
| | - Robert I. Morton
- Department of Biology, Indiana University, Bloomington, IN, USA
- Present address: Boston Scientific, Yokneam, Northern, ISRAEL
| | - Jonathan De Stercke
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
- Present address: Unité de Recherche en Biologie des Micro-organismes, Université de Namur, 61 rue de Bruxelles, B-5000 Namur, BELGIUM
| | - Yves V. Brun
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Québec, CANADA
- Department of Biology, Indiana University, Bloomington, IN, USA
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15
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Ren WT, Guo LL, Bu YX, Han CH, Zhou P, Wu YH. Rheinheimera oceanensis sp. nov., a novel member of the genus Rheinheimera, isolated from the West Pacific Ocean. Int J Syst Evol Microbiol 2023; 73. [PMID: 37861399 DOI: 10.1099/ijsem.0.006054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023] Open
Abstract
Two Gram-stain-negative, aerobic, non-motile and short-rod-shaped bacteria, designated as strains GL-53T and GL-15-2-5, were isolated from the seamount area of the West Pacific Ocean and identified using a polyphasic taxonomic approach. The growth of strains GL-53ᵀ and GL-15-2-5 occurred at pH 5.5-10.0, 4-40 °C (optimum at 28 °C) and 0-10.0 % NaCl concentrations (optimum at 0-5.0 %). On the basis of 16S rRNA gene sequence analysis, strains GL-53ᵀ and GL-15-2-5 exhibited the highest similarity to Rheinheimera lutimaris YQF-2T (98.4 %), followed by Rheinheimera pacifica KMM 1406T (98.1 %), Rheinheimera nanhaiensis E407-8T (97.4 %), Rheinheimera aestuarii H29T (97.4 %), Rheinheimera hassiensis E48T (97.2 %) and Rheinheimera aquimaris SW-353T (97.2 %). Phylogenetic analysis revealed that the isolates were affiliated with the genus Rheinheimera and represented an independent lineage. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The sole isoprenoid quinone was ubiquinone 8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid (and one unidentified glycolipid. The DNA G+C content was 48.5 mol%. The average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization values among the genomes of strain GL-53ᵀ and the related strains in the genus Rheinheimera were 75.5-90.1 %, 67.5-93.9 % and 21.4-41.4 %, respectively. Based on their phenotypic, chemotaxonomic and genotypic properties, the two strains were identified as representing a novel species of the genus Rheinheimera, for which the name Rheinheimera oceanensis sp. nov. is proposed. The type strain is GL-53T (=KCTC 82651T=MCCC M20598T).
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Affiliation(s)
- Wen-Ting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Li-Li Guo
- College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, PR China
| | - Yu-Xin Bu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Chen-Hua Han
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, PR China
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16
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Grognot M, Nam JW, Elson LE, Taute KM. Physiological adaptation in flagellar architecture improves Vibrio alginolyticus chemotaxis in complex environments. Proc Natl Acad Sci U S A 2023; 120:e2301873120. [PMID: 37579142 PMCID: PMC10450658 DOI: 10.1073/pnas.2301873120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/10/2023] [Indexed: 08/16/2023] Open
Abstract
Bacteria navigate natural habitats with a wide range of mechanical properties, from the ocean to the digestive tract and soil, by rotating helical flagella like propellers. Species differ in the number, position, and shape of their flagella, but the adaptive value of these flagellar architectures is unclear. Many species traverse multiple types of environments, such as pathogens inside and outside a host. We investigate the hypothesis that flagellar architectures mediate environment-specific benefits in the marine pathogen Vibrio alginolyticus which exhibits physiological adaptation to the mechanical environment. In addition to its single polar flagellum, the bacterium produces lateral flagella in environments that differ mechanically from water. These are known to facilitate surface motility and attachment. We use high-throughput 3D bacterial tracking to quantify chemotactic performance of both flagellar architectures in three archetypes of mechanical environments relevant to the bacterium's native habitats: water, polymer solutions, and hydrogels. We reveal that lateral flagella impede chemotaxis in water by lowering the swimming speed but improve chemotaxis in both types of complex environments. Statistical trajectory analysis reveals two distinct underlying behavioral mechanisms: In viscous solutions of the polymer PVP K90, lateral flagella increase the swimming speed. In agar hydrogels, lateral flagella improve overall chemotactic performance, despite lowering the swimming speed, by preventing trapping in pores. Our findings show that lateral flagella are multipurpose tools with a wide range of applications beyond surfaces. They implicate flagellar architecture as a mediator of environment-specific benefits and point to a rich space of bacterial navigation behaviors in complex environments.
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Affiliation(s)
- Marianne Grognot
- Rowland Institute, Harvard University, Cambridge, MA02142
- Institute of Medical Microbiology, Rheinisch-Westfälische Technische Hochschule University Hospital Aachen, Rheinisch-Westfälische Technische Hochschule University, Aachen52074, Germany
| | - Jong Woo Nam
- Rowland Institute, Harvard University, Cambridge, MA02142
| | | | - Katja M. Taute
- Rowland Institute, Harvard University, Cambridge, MA02142
- Biozentrum, Ludwig-Maximilians-Universität München, Martinsried82152, Germany
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17
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Frantz R, Gwozdzinski K, Gisch N, Doijad SP, Hudel M, Wille M, Abu Mraheil M, Schwudke D, Imirzalioglu C, Falgenhauer L, Ehrmann M, Chakraborty T. A Single Residue within the MCR-1 Protein Confers Anticipatory Resilience. Microbiol Spectr 2023; 11:e0359222. [PMID: 37071007 PMCID: PMC10269488 DOI: 10.1128/spectrum.03592-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
The envelope stress response (ESR) of Gram-negative enteric bacteria senses fluctuations in nutrient availability and environmental changes to avert damage and promote survival. It has a protective role toward antimicrobials, but direct interactions between ESR components and antibiotic resistance genes have not been demonstrated. Here, we report interactions between a central regulator of ESR viz., the two-component signal transduction system CpxRA (conjugative pilus expression), and the recently described mobile colistin resistance protein (MCR-1). Purified MCR-1 is specifically cleaved within its highly conserved periplasmic bridge element, which links its N-terminal transmembrane domain with the C-terminal active-site periplasmic domain, by the CpxRA-regulated serine endoprotease DegP. Recombinant strains harboring cleavage site mutations in MCR-1 are either protease resistant or degradation susceptible, with widely differing consequences for colistin resistance. Transfer of the gene encoding a degradation-susceptible mutant to strains that lack either DegP or its regulator CpxRA restores expression and colistin resistance. MCR-1 production in Escherichia coli imposes growth restriction in strains lacking either DegP or CpxRA, effects that are reversed by transactive expression of DegP. Excipient allosteric activation of the DegP protease specifically inhibits growth of isolates carrying mcr-1 plasmids. As CpxRA directly senses acidification, growth of strains at moderately low pH dramatically increases both MCR-1-dependent phosphoethanolamine (PEA) modification of lipid A and colistin resistance levels. Strains expressing MCR-1 are also more resistant to antimicrobial peptides and bile acids. Thus, a single residue external to its active site induces ESR activity to confer resilience in MCR-1-expressing strains to commonly encountered environmental stimuli, such as changes in acidity and antimicrobial peptides. Targeted activation of the nonessential protease DegP can lead to the elimination of transferable colistin resistance in Gram-negative bacteria. IMPORTANCE The global presence of transferable mcr genes in a wide range of Gram-negative bacteria from clinical, veterinary, food, and aquaculture environments is disconcerting. Its success as a transmissible resistance factor remains enigmatic, because its expression imposes fitness costs and imparts only moderate levels of colistin resistance. Here, we show that MCR-1 triggers regulatory components of the envelope stress response, a system that senses fluctuations in nutrient availability and environmental changes, to promote bacterial survival in low pH environments. We identify a single residue within a highly conserved structural element of mcr-1 distal to its catalytic site that modulates resistance activity and triggers the ESR. Using mutational analysis, quantitative lipid A profiling and biochemical assays, we determined that growth in low pH environments dramatically increases colistin resistance levels and promotes resistance to bile acids and antimicrobial peptides. We exploited these findings to develop a targeted approach that eliminates mcr-1 and its plasmid carriers.
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Affiliation(s)
- Renate Frantz
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Konrad Gwozdzinski
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Swapnil Prakash Doijad
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Martina Hudel
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Maria Wille
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Mobarak Abu Mraheil
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site: Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Airway Research Center North, Partner Site: Research Center Borstel, Borstel, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
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18
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Kinosita Y, Sowa Y. Flagellar polymorphism-dependent bacterial swimming motility in a structured environment. Biophys Physicobiol 2023; 20:e200024. [PMID: 37867560 PMCID: PMC10587448 DOI: 10.2142/biophysico.bppb-v20.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/29/2023] [Indexed: 10/24/2023] Open
Abstract
Most motile bacteria use supramolecular motility machinery called bacterial flagellum, which converts the chemical energy gained from ion flux into mechanical rotation. Bacterial cells sense their external environment through a two-component regulatory system consisting of a histidine kinase and response regulator. Combining these systems allows the cells to move toward favorable environments and away from their repellents. A representative example of flagellar motility is run-and-tumble swimming in Escherichia coli, where the counter-clockwise (CCW) rotation of a flagellar bundle propels the cell forward, and the clockwise (CW) rotation undergoes cell re-orientation (tumbling) upon switching the direction of flagellar motor rotation from CCW to CW. In this mini review, we focus on several types of chemotactic behaviors that respond to changes in flagellar shape and direction of rotation. Moreover, our single-cell analysis demonstrated back-and-forth swimming motility of an original E. coli strain. We propose that polymorphic flagellar changes are required to enhance bacterial movement in a structured environment as a colony spread on an agar plate.
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Affiliation(s)
| | - Yoshiyuki Sowa
- Department of Frontier Bioscience, Hosei University, Tokyo 184-8584, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo 184-8584, Japan
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19
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Phan TV, Mattingly HH, Vo L, Marvin JS, Looger LL, Emonet T. Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543315. [PMID: 37333331 PMCID: PMC10274659 DOI: 10.1101/2023.06.01.543315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering new insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.
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Affiliation(s)
- Trung V. Phan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
| | | | - Lam Vo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
| | | | - Loren L. Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
- Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
- Quantitative Biology Institute, Yale University, New Haven, CT
- Department of Physics, Yale University, New Haven, CT
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20
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Sagoo J, Abedrabbo S, Liu X, Ottemann KM. Discovery of Type IV filament membrane alignment complex homologs in H. pylori that promote soft-agar migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.537399. [PMID: 37163056 PMCID: PMC10168365 DOI: 10.1101/2023.04.27.537399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The stomach pathogen Helicobacter pylori utilizes two scaffold proteins, CheW and CheV1, to build critical chemotaxis arrays. Chemotaxis helps bacteria establish and maintain infection. Mutants lacking either of these chemotaxis proteins have different soft agar phenotypes: deletion of cheW creates non-chemotactic strains, while deletion of cheV1 results in 50% loss of chemotaxis. In this work, we characterized the cheV1 deletion mutant phenotype in detail. cheV1 deletion mutants had poor soft-agar migration initially, but regained migration ability over time. This improved bacterial migration was stable, suggesting a genetic suppressor phenotype, termed Che+. Whole-genome sequencing analysis of four distinct cheV1 Che+ strains revealed single nucleotide polymorphisms (SNPs) in a common gene, HPG27_252 (HP0273). These SNPs were predicted to truncate the encoded protein. To confirm the role of HPG27_252 in the cheV1 phenotype, we created a targeted deletion of HPG27_252 and found that loss of HPG27_252 enhanced soft-agar migration. HPG27_252 and CheV1 appear to interact directly, based on bacterial two-hybrid analysis. HPG27_252 is predicted to encode a 179 amino acid, 21 kDa protein annotated as a hypothetical protein. Computational analysis revealed this protein to be a remote homolog of the PilO Type IV filament membrane alignment complex protein. Although H. pylori is not known to possess Type IV filaments, our analysis showed it retains an operon of genes for homologs of PilO, PilN, and PilM, but does not possess other Type IV pili genes. Our data suggest the PilO homolog plays a role in regulating H. pylori chemotaxis and motility, suggesting new ideas about evolutionary steps for controlling migration through semi-solid media.
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21
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Lim S, Yadunandan A, Khalid Jawed M. Bacteria-inspired robotic propulsion from bundling of soft helical filaments at low Reynolds number. SOFT MATTER 2023; 19:2254-2264. [PMID: 36916641 DOI: 10.1039/d2sm01398c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The bundling of flagella is known to create a "run" phase, where the bacteria moves in a nearly straight line rather than making changes in direction. Historically, mechanical explanations for the bundling phenomenon intrigued many researchers, and significant advances were made in physical models and experimental methods. Contributing to the field of research, we present a bacteria-inspired centimeter-scale soft robotic hardware platform and a computational framework for a physically plausible simulation model of the multi-flagellated robot under low Reynolds number (∼10-1). The fluid-structure interaction simulation couples the discrete elastic rods algorithm with the method of regularized Stokeslet segments. Contact between two flagella is handled by a penalty-based method. We present a comparison between our experimental and simulation results and verify that the simulation tool can capture the essential physics of this problem. Preliminary findings on robustness to buckling provided by the bundling phenomenon and the efficiency of a multi-flagellated soft robot are compared with the single-flagellated counterparts. Observations were made on the coupling between geometry and elasticity, which manifests itself in the propulsion of the robot by nonlinear dependency on the rotational speed of the flagella.
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Affiliation(s)
- Sangmin Lim
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California, 90095, USA.
| | - Achyuta Yadunandan
- Department of Electrical and Computer Engineering, University of California, Los Angeles, California, 90095, USA
| | - M Khalid Jawed
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, California, 90095, USA.
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22
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Windes P, Tafti DK, Behkam B. A computational framework for investigating bacteria transport in microvasculature. Comput Methods Biomech Biomed Engin 2023; 26:438-449. [PMID: 35486738 DOI: 10.1080/10255842.2022.2066473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Blood-borne bacteria disseminate in tissue through microvasculature or capillaries. Capillary size, presence of red blood cells (RBCs), and bacteria motility affect bacteria intracapillary transport, an important yet largely unexplored phenomenon. Computational description of the system comprising interactions between plasma, RBCs, and motile bacteria in 5-10 μm diameter capillaries pose several challenges. The Immersed Boundary Method (IBM) was used to resolve the capillary, deformed RBCs, and bacteria. The challenge of disparate coupled time scales of flow and bacteria motion are reconciled by a temporal multiscale simulation method. Bacterium-wall and bacterium-RBC collisions were detected using a hierarchical contact- detection algorithm. Motile bacteria showed a net outward radial velocity of 2.8 µm/s compared to -0.5 µm/s inward for non-motile bacteria; thus, exhibiting a greater propensity to escape the bolus flow region between RBCs and marginate for potential extravasation, suggesting motility enhances extravasation of bacteria from capillaries.
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Affiliation(s)
- Peter Windes
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Danesh K Tafti
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Bahareh Behkam
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, USA.,School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, VA, USA
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Hong M, Luo X, Fan R, An L, Li Q, Zhang X, Xu M, Lan Y, Shi H, Li M. Croceibacterium selenioxidans sp. nov. , isolated from seleniferous soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 36920984 DOI: 10.1099/ijsem.0.005726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
A Gram-negative, aerobic bacterial strain, designated LX-88T, was isolated from seleniferous soil in Enshi, Hubei Province, PR China. Strain LX-88Toxidized elemental selenium to selenite, and produced carotenoids but not bacteriochlorophyll. The isolate grew optimally at 28 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Phylogenetic analysies of the organism's 16S rRNA and bacterial core gene set sequences indicated that LX-88T belongs to the genus Croceibacterium, and has the highest degree of 16S rRNA gene sequence similarity to Croceibacterium soli MN-1T (97.4 %). The LX-88T genome was 3.4 Mbp and had a G+C content of 63.6 mol%. The average nucleotide identity and digital DNA-DNA hybridization values showed low relatedness (below 95 and 70 %, respectively) between strain LX-88T and other strains in the genus Croceibacterium. Ubiquinone-10 was the predominant quinone. The polar lipid profile was dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. The major fatty acid was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). These physiological and biochemical tests facilitated the differentiation of strain LX-88T from other members of the genus Croceibacterium. The results of this multifaceted taxonomic study indicate that strain LX-88T represents a novel species in the genus Croceibacterium, for which the name Croceibacterium selenioxidans sp. nov. is proposed. The type strain is LX-88T (=MCCC 1K08007T=LMG 32570T).
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Affiliation(s)
- Mengjuan Hong
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiong Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Rongrong Fan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lijin An
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Qiushi Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiaoyan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mingzhu Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yan Lan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Heli Shi
- Enshi Tobacco Company of Hubei Province, Enshi, Hubei 445000, PR China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes. Appl Environ Microbiol 2023; 89:e0172722. [PMID: 36695629 PMCID: PMC9972950 DOI: 10.1128/aem.01727-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This study investigates migration phenotypes of 265 Escherichia coli soil isolates from the Buffalo River basin in Minnesota, USA. Migration rates on semisolid tryptone swim plates ranged from nonmotile to 190% of the migration rate of a highly motile E. coli K-12 strain. The nonmotile isolate, LGE0550, had mutations in flagellar and chemotaxis genes, including two IS3 elements in the flagellin-encoding gene fliC. A genome-wide association study (GWAS), associating the migration rates with genetic variants in specific genes, yielded two metabolic variants (rygD-serA and metR-metE) with previous implications in chemotaxis. As a novel way of confirming GWAS results, we used minimal medium swim plates to confirm the associations. Other variants in metabolic genes and genes that are associated with biofilm were positively or negatively associated with migration rates. A determination of growth phenotypes on Biolog EcoPlates yielded differential growth for the 10 tested isolates on d-malic acid, putrescine, and d-xylose, all of which are important in the soil environment. IMPORTANCE E. coli is a Gram-negative, facultative anaerobic bacterium whose life cycle includes extra host environments in addition to human, animal, and plant hosts. The bacterium has the genomic capability of being motile. In this context, the significance of this study is severalfold: (i) the great diversity of migration phenotypes that we observed within our isolate collection supports previous (G. NandaKafle, A. A. Christie, S. Vilain, and V. S. Brözel, Front Microbiol 9:762, 2018, https://doi.org/10.3389/fmicb.2018.00762; Y. Somorin, F. Abram, F. Brennan, and C. O'Byrne, Appl Environ Microbiol 82:4628-4640, 2016, https://doi.org/10.1128/AEM.01175-16) ideas of soil promoting phenotypic heterogeneity, (ii) such heterogeneity may facilitate bacterial growth in the many different soil niches, and (iii) such heterogeneity may enable the bacteria to interact with human, animal, and plant hosts.
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Kurniyati K, Chang Y, Guo W, Liu J, Malkowski MG, Li C. Anti-σ 28 Factor FlgM Regulates Flagellin Gene Expression and Flagellar Polarity of Treponema denticola. J Bacteriol 2023; 205:e0046322. [PMID: 36715541 PMCID: PMC9945498 DOI: 10.1128/jb.00463-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/07/2023] [Indexed: 01/31/2023] Open
Abstract
FlgM, an antagonist of FliA (also known as σ28), inhibits transcription of bacterial class 3 flagellar genes. It does so primarily through binding to free σ28 to prevent it from forming a complex with core RNA polymerase. We recently identified an FliA homolog (FliATd) in the oral spirochete Treponema denticola; however, its antagonist FlgM remained uncharacterized. Herein, we provide several lines of evidence that TDE0201 functions as an antagonist of FliATd. TDE0201 is structurally similar to FlgM proteins, although its sequence is not conserved. Heterologous expression of TDE0201 in Escherichia coli inhibits its flagellin gene expression and motility. Biochemical and mutational analyses demonstrate that TDE0201 binds to FliATd and prevents it from binding to the σ28-dependent promoter. Deletions of flgM genes typically enhance bacterial class 3 flagellar gene expression; however, deletion of TDE0201 has an opposite effect (e.g., the mutant has a reduced level of flagellins). Follow-up studies revealed that deletion of TDE0201 leads to FliATd turnover, which in turn impairs the expression of flagellin genes. Swimming plate, cell tracking, and cryo-electron tomography analyses further disclosed that deletion of TDE0201 impairs spirochete motility and alters flagellar number and polarity: i.e., instead of having bipolar flagella, the mutant has flagella only at one end of cells. Collectively, these results indicate that TDE0201 is a FlgM homolog but acts differently from its counterparts in other bacteria. IMPORTANCE Spirochetes are a group of bacteria that cause several human diseases. A unique aspect of spirochetes is that they have bipolar periplasmic flagella (PFs), which bestow on the spirochetes a unique spiral shape and distinct swimming behaviors. While the structure and function of PFs have been extensively studied in spirochetes, the molecular mechanism that regulates the PFs' morphogenesis and assembly is poorly understood. In this report, FlgM, an anti-σ28 factor, is identified and functionally characterized in the oral spirochete Treponema denticola. Our results show that FlgM regulates the number and polarity of PFs via a unique mechanism. Identification of FliA and FlgM in T. denticola sets a benchmark to investigate their roles in other spirochetes.
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Affiliation(s)
- Kurni Kurniyati
- Department of Oral Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Yunjie Chang
- Department of Microbial Pathogenesis, Yale University, School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, School of Medicine, New Haven, Connecticut, USA
| | - Wangbiao Guo
- Department of Microbial Pathogenesis, Yale University, School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, School of Medicine, New Haven, Connecticut, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University, School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, School of Medicine, New Haven, Connecticut, USA
| | - Michael G. Malkowski
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, New York, USA
| | - Chunhao Li
- Department of Oral Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA
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26
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Barak-Gavish N, Dassa B, Kuhlisch C, Nussbaum I, Brandis A, Rosenberg G, Avraham R, Vardi A. Bacterial lifestyle switch in response to algal metabolites. eLife 2023; 12:e84400. [PMID: 36691727 PMCID: PMC9873259 DOI: 10.7554/elife.84400] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in the biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly recognized that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during its interaction with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. To unravel the bacterial lifestyle switch, we analyzed bacterial transcriptomes in response to exudates derived from algae in exponential growth and stationary phase, which supported the Sulfitobacter D7 coexistence and pathogenicity lifestyles, respectively. In pathogenic mode, Sulfitobacter D7 upregulated flagellar motility and diverse transport systems, presumably to maximize assimilation of E. huxleyi-derived metabolites released by algal cells upon cell death. Algal dimethylsulfoniopropionate (DMSP) was a pivotal signaling molecule that mediated the transition between the lifestyles, supporting our previous findings. However, the coexisting and pathogenic lifestyles were evident only in the presence of additional algal metabolites. Specifically, we discovered that algae-produced benzoate promoted the growth of Sulfitobacter D7 and hindered the DMSP-induced lifestyle switch to pathogenicity, demonstrating that benzoate is important for maintaining the coexistence of algae and bacteria. We propose that bacteria can sense the physiological state of the algal host through changes in the metabolic composition, which will determine the bacterial lifestyle during interaction.
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Affiliation(s)
- Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Bareket Dassa
- Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Inbal Nussbaum
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Gili Rosenberg
- Department of Biological Regulation, Weizmann Institute of ScienceRehovotIsrael
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of ScienceRehovotIsrael
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
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27
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Role of the Two Flagellar Stators in Swimming Motility of Pseudomonas putida. mBio 2022; 13:e0218222. [PMID: 36409076 PMCID: PMC9765564 DOI: 10.1128/mbio.02182-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In the soil bacterium Pseudomonas putida, the motor torque for flagellar rotation is generated by the two stators MotAB and MotCD. Here, we construct mutant strains in which one or both stators are knocked out and investigate their swimming motility in fluids of different viscosity and in heterogeneous structured environments (semisolid agar). Besides phase-contrast imaging of single-cell trajectories and spreading cultures, dual-color fluorescence microscopy allows us to quantify the role of the stators in enabling P. putida's three different swimming modes, where the flagellar bundle pushes, pulls, or wraps around the cell body. The MotAB stator is essential for swimming motility in liquids, while spreading in semisolid agar is not affected. Moreover, if the MotAB stator is knocked out, wrapped mode formation under low-viscosity conditions is strongly impaired and only partly restored for increased viscosity and in semisolid agar. In contrast, when the MotCD stator is missing, cells are indistinguishable from the wild type in fluid experiments but spread much more slowly in semisolid agar. Analysis of the microscopic trajectories reveals that the MotCD knockout strain forms sessile clusters, thereby reducing the number of motile cells, while the swimming speed is unaffected. Together, both stators ensure a robust wild type that swims efficiently under different environmental conditions. IMPORTANCE Because of its heterogeneous habitat, the soil bacterium Pseudomonas putida needs to swim efficiently under very different environmental conditions. In this paper, we knocked out the stators MotAB and MotCD to investigate their impact on the swimming motility of P. putida. While the MotAB stator is crucial for swimming in fluids, in semisolid agar, both stators are sufficient to sustain a fast-swimming phenotype and increased frequencies of the wrapped mode, which is known to be beneficial for escaping mechanical traps. However, in contrast to the MotAB knockout, a culture of MotCD knockout cells spreads much more slowly in the agar, as it forms nonmotile clusters that reduce the number of motile cells.
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28
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Lim S, Du Y, Lee Y, Panda SK, Tong D, Khalid Jawed M. Fabrication, control, and modeling of robots inspired by flagella and cilia. BIOINSPIRATION & BIOMIMETICS 2022; 18:011003. [PMID: 36533860 DOI: 10.1088/1748-3190/aca63d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Flagella and cilia are slender structures that serve important functionalities in the microscopic world through their locomotion induced by fluid and structure interaction. With recent developments in microscopy, fabrication, biology, and modeling capability, robots inspired by the locomotion of these organelles in low Reynolds number flow have been manufactured and tested on the micro-and macro-scale, ranging from medicalin vivomicrobots, microfluidics to macro prototypes. We present a collection of modeling theories, control principles, and fabrication methods for flagellated and ciliary robots.
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Affiliation(s)
- Sangmin Lim
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Yayun Du
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Yongkyu Lee
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Shivam Kumar Panda
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - Dezhong Tong
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
| | - M Khalid Jawed
- Department of Mechanical & Aerospace Engineering, Westwood Plaza, University of California, Los Angeles, CA 90095, United States of America
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29
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Ni C, Lu T. Individual-Based Modeling of Spatial Dynamics of Chemotactic Microbial Populations. ACS Synth Biol 2022; 11:3714-3723. [PMID: 36336839 PMCID: PMC10129442 DOI: 10.1021/acssynbio.2c00322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
One important direction of synthetic biology is to establish desired spatial structures from microbial populations. Underlying this structural development process are different driving factors, among which bacterial motility and chemotaxis serve as a major force. Here, we present an individual-based, biophysical computational framework for mechanistic and multiscale simulation of the spatiotemporal dynamics of motile and chemotactic microbial populations. The framework integrates cellular movement with spatial population growth, mechanical and chemical cellular interactions, and intracellular molecular kinetics. It is validated by a statistical comparison of single-cell chemotaxis simulations with reported experiments. The framework successfully captures colony range expansion of growing isogenic populations and also reveals chemotaxis-modulated, spatial patterns of a two-species amensal community. Partial differential equation-based models subsequently validate these simulation findings. This study provides a versatile computational tool to uncover the fundamentals of microbial spatial ecology as well as to facilitate the design of synthetic consortia for desired spatial patterns.
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Affiliation(s)
- Congjian Ni
- Center of Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ting Lu
- Center of Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,National Center for Supercomputing Applications, Urbana, Illinois 61801, United States
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30
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Identification and Characterization of the Alternative σ 28 Factor in Treponema denticola. J Bacteriol 2022; 204:e0024822. [PMID: 36043861 PMCID: PMC9487585 DOI: 10.1128/jb.00248-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
FliA (also known as σ28), a member of the bacterial σ70 family of transcription factors, directs RNA polymerase to flagellar late (class 3) promoters and initiates transcription. FliA has been studied in several bacteria, yet its role in spirochetes has not been established. In this report, we identify and functionally characterize a FliA homolog (TDE2683) in the oral spirochete Treponema denticola. Computational, genetic, and biochemical analyses demonstrated that TDE2683 has a structure similar to that of the σ28 of Escherichia coli, binds to σ28-dependent promoters, and can functionally replace the σ28 of E. coli. However, unlike its counterparts from other bacteria, TDE2683 cannot be deleted, suggesting its essential role in the survival of T. denticola. In vitro site-directed mutagenesis revealed that E221 and V231, two conserved residues in the σ4 region of σ28, are indispensable for the binding activity of TDE2683 to the σ28-dependent promoter. We then mutated these two residues in T. denticola and found that the mutations impair the expression of flagellin and chemotaxis genes and bacterial motility as well. Cryo-electron tomography analysis further revealed that the mutations disrupt the flagellar symmetry (i.e., number and placement) of T. denticola. Collectively, these results indicate that TDE2683 is a σ28 transcription factor that regulates the class 3 gene expression and controls the flagellar symmetry of T. denticola. To the best of our knowledge, this is the first report establishing the functionality of FliA in spirochetes. IMPORTANCE Spirochetes are a group of medically important but understudied bacteria. One of the unique aspects of spirochetes is that they have periplasmic flagella (PF, also known as endoflagella) which give rise to their unique spiral shape and distinct swimming behaviors and play a critical role in the pathophysiology of spirochetes. PF are structurally similar to external flagella, but the underpinning mechanism that regulates PF biosynthesis and assembly remains largely unknown. By using the oral spirochete Treponema denticola as a model, this report provides several lines of evidence that FliA, a σ28 transcriptional factor, regulates the late flagellin gene (class 3) expression, PF assembly, and flagellar symmetry as well, which provides insights into flagellar regulation and opens an avenue to investigate the role of σ28 in spirochetes.
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Martin CS, Jubelin G, Darsonval M, Leroy S, Leneveu-Jenvrin C, Hmidene G, Omhover L, Stahl V, Guillier L, Briandet R, Desvaux M, Dubois-Brissonnet F. Genetic, physiological, and cellular heterogeneities of bacterial pathogens in food matrices: Consequences for food safety. Compr Rev Food Sci Food Saf 2022; 21:4294-4326. [PMID: 36018457 DOI: 10.1111/1541-4337.13020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 01/28/2023]
Abstract
In complex food systems, bacteria live in heterogeneous microstructures, and the population displays phenotypic heterogeneities at the single-cell level. This review provides an overview of spatiotemporal drivers of phenotypic heterogeneity of bacterial pathogens in food matrices at three levels. The first level is the genotypic heterogeneity due to the possibility for various strains of a given species to contaminate food, each of them having specific genetic features. Then, physiological heterogeneities are induced within the same strain, due to specific microenvironments and heterogeneous adaptative responses to the food microstructure. The third level of phenotypic heterogeneity is related to cellular heterogeneity of the same strain in a specific microenvironment. Finally, we consider how these phenotypic heterogeneities at the single-cell level could be implemented in mathematical models to predict bacterial behavior and help ensure microbiological food safety.
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Affiliation(s)
- Cédric Saint Martin
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France.,Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Grégory Jubelin
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Maud Darsonval
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
| | - Charlène Leneveu-Jenvrin
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France.,Association pour le Développement de l'Industrie de la Viande (ADIV), Clermont-Ferrand, France
| | - Ghaya Hmidene
- Risk Assessment Department, ANSES, Maisons-Alfort, France
| | - Lysiane Omhover
- Aerial, Technical Institute of Agro-Industry, Illkirch, France
| | - Valérie Stahl
- Aerial, Technical Institute of Agro-Industry, Illkirch, France
| | | | - Romain Briandet
- MICALIS Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, UMR454 MEDIS, Clermont-Ferrand, France
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Collective behavior and nongenetic inheritance allow bacterial populations to adapt to changing environments. Proc Natl Acad Sci U S A 2022; 119:e2117377119. [PMID: 35727978 DOI: 10.1073/pnas.2117377119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Collective behaviors require coordination among a group of individuals. As a result, individuals that are too phenotypically different from the rest of the group can be left out, reducing heterogeneity, but increasing coordination. If individuals also reproduce, the offspring can have different phenotypes from their parent(s). This raises the question of how these two opposing processes-loss of diversity by collective behaviors and generation of it through growth and inheritance-dynamically shape the phenotypic composition of an isogenic population. We examine this question theoretically using collective migration of chemotactic bacteria as a model system, where cells of different swimming phenotypes are better suited to navigate in different environments. We find that the differential loss of phenotypes caused by collective migration is environment-dependent. With cell growth, this differential loss enables migrating populations to dynamically adapt their phenotype compositions to the environment, enhancing migration through multiple environments. Which phenotypes are produced upon cell division depends on the level of nongenetic inheritance, and higher inheritance leads to larger composition adaptation and faster migration at steady state. However, this comes at the cost of slower responses to new environments. Due to this trade-off, there is an optimal level of inheritance that maximizes migration speed through changing environments, which enables a diverse population to outperform a nondiverse one. Growing populations might generally leverage the selection-like effects provided by collective behaviors to dynamically shape their own phenotype compositions, without mutations.
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Müller J, Jäkel AC, Richter J, Eder M, Falgenhauer E, Simmel FC. Bacterial Growth, Communication, and Guided Chemotaxis in 3D-Bioprinted Hydrogel Environments. ACS APPLIED MATERIALS & INTERFACES 2022; 14:15871-15880. [PMID: 35349260 PMCID: PMC9012179 DOI: 10.1021/acsami.1c20836] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/14/2022] [Indexed: 06/06/2023]
Abstract
Bioprinting of engineered bacteria is of great interest for applications of synthetic biology in the context of living biomaterials, but so far, only a few viable approaches are available for the printing of gels hosting live Escherichia coli bacteria. Here, we develop a gentle extrusion-based bioprinting method based on an inexpensive alginate/agarose ink mixture that enables printing of E. coli into three-dimensional hydrogel structures up to 10 mm in height. We first characterize the rheological properties of the gel ink and then study the growth of the bacteria inside printed structures. We show that the maturation of fluorescent proteins deep within the printed structures can be facilitated by the addition of a calcium peroxide-based oxygen generation system. We then utilize the bioprinter to control different types of interactions between bacteria that depend on their spatial position. We next show quorum-sensing-based chemical communication between the engineered sender and receiver bacteria placed at different positions inside the bioprinted structure and finally demonstrate the fabrication of barrier structures defined by nonmotile bacteria that can guide the movement of chemotactic bacteria inside a gel. We anticipate that a combination of 3D bioprinting and synthetic biological approaches will lead to the development of living biomaterials containing engineered bacteria as dynamic functional units.
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Irani E, Mokhtari Z, Zippelius A. Dynamics of Bacteria Scanning a Porous Environment. PHYSICAL REVIEW LETTERS 2022; 128:144501. [PMID: 35476466 DOI: 10.1103/physrevlett.128.144501] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
It has recently been reported that bacteria, such as Escherichia coli Bhattacharjee and Datta, Nat. Commun. 10, 2075 (2019).NCAOBW2041-172310.1038/s41467-019-10115-1 and Pseudomonas putida Alirezaeizanjani et al., Sci. Adv. 6, eaaz6153 (2020).SACDAF2375-254810.1126/sciadv.aaz6153, perform distinct modes of motion when placed in porous media as compared to dilute regions or free space. This has led us to suggest an efficient strategy for active particles in a disordered environment: reorientations are suppressed in locally dilute regions and intensified in locally dense ones. Thereby the local geometry determines the optimal path of the active agent and substantially accelerates the dynamics for up to 2 orders of magnitude. We observe a nonmonotonic behavior of the diffusion coefficient in dependence on the tumbling rate and identify a localization transition, either by increasing the density of obstacles or by decreasing the reorientation rate.
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Affiliation(s)
- Ehsan Irani
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), The Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany
| | - Zahra Mokhtari
- Freie Universität Berlin, Department of Mathematics and Computer Science, Institute of Mathematics, Arnimallee 9, 14195 Berlin, Germany
| | - Annette Zippelius
- Georg-August-Universität Göttingen, Institut für Theoretische Physik, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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35
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Wölflingseder M, Tutz S, Fengler VH, Schild S, Reidl J. Regulatory Interplay of RpoS and RssB Controls Motility and Colonization in Vibrio cholerae. Int J Med Microbiol 2022; 312:151555. [DOI: 10.1016/j.ijmm.2022.151555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/27/2022] [Accepted: 04/12/2022] [Indexed: 11/28/2022] Open
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Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XW. Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (GL-11-2T and ZH2-Y79) were isolated from the seawater collected from the West Pacific Ocean and the East China Sea, respectively. Cells were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Cells grew in the medium containing 0.5–7.5 % NaCl (w/v, optimum, 1.0–3.0 %), at pH 6.0–8.0 (optimum, pH 6.5–7.0) and at 4–40 °C (optimum, 30 °C). H2S production occurred in marine broth supplemented with sodium thiosulphate. The almost-complete 16S rRNA gene sequences of the two isolates were identical, and exhibited the highest similarity to
Pseudoruegeria aquimaris
JCM 13603T (97.5 %), followed by
Ruegeria conchae
TW15T (97.2%),
Shimia aestuarii
DSM 15283T (97.1 %) and
Ruegeria lacuscaerulensis
ITI-1157T (97.0 %). Phylogenetic analysis revealed that the isolates were affiliated with the family
Roseobacteraceae
and represented an independent lineage. The sole isoprenoid quinone was ubiquinone 10. The principal fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and cyclo-C19 : 0
ω8c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content was 62.3 mol%. The orthologous average nucleotide identity, in silico DNA–DNA hybridization and average amino acid identity values among the genomes of strain GL-11-2T and the reference strains were 73.2–79.0, 20.3–22.5 and 66.0–80.8 %, respectively. Strains GL-11-2ᵀ and ZH2-Y79 possessed complete metabolic pathways for thiosulphate oxidation, dissimilatory nitrate reduction and denitrification. Phylogenetic distinctiveness, chemotaxonomic differences and phenotypic properties revealed that the isolates represent a novel genus and species of the family
Roseobacteraceae
, belonging to the class
Alphaproteobacteria
, for which the name Thiosulfatihalobacter marinus gen. nov., sp. nov. (type strain, GL-11–2T=KCTC 82723T=MCCC M20691T) is proposed.
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Affiliation(s)
- Yuehong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Wen-Ting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Ying-Wen Zhong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Li-Li Guo
- College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
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Bhattacharjee T, Amchin DB, Alert R, Ott JA, Datta SS. Chemotactic smoothing of collective migration. eLife 2022; 11:e71226. [PMID: 35257660 PMCID: PMC8903832 DOI: 10.7554/elife.71226] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/24/2022] [Indexed: 12/24/2022] Open
Abstract
Collective migration-the directed, coordinated motion of many self-propelled agents-is a fascinating emergent behavior exhibited by active matter with functional implications for biological systems. However, how migration can persist when a population is confronted with perturbations is poorly understood. Here, we address this gap in knowledge through studies of bacteria that migrate via directed motion, or chemotaxis, in response to a self-generated nutrient gradient. We find that bacterial populations autonomously smooth out large-scale perturbations in their overall morphology, enabling the cells to continue to migrate together. This smoothing process arises from spatial variations in the ability of cells to sense and respond to the local nutrient gradient-revealing a population-scale consequence of the manner in which individual cells transduce external signals. Altogether, our work provides insights to predict, and potentially control, the collective migration and morphology of cellular populations and diverse other forms of active matter.
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Affiliation(s)
- Tapomoy Bhattacharjee
- The Andlinger Center for Energy and the Environment, Princeton UniversityPrincetonUnited States
| | - Daniel B Amchin
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Ricard Alert
- Lewis-Sigler Institute for Integrative Genomics, Princeton UniversityPrincetonUnited States
- Princeton Center for Theoretical Science, Princeton UniversityPrincetonUnited States
| | - Jenna Anne Ott
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
| | - Sujit Sankar Datta
- Department of Chemical and Biological Engineering, Princeton UniversityPrincetonUnited States
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Updegraff T, Schiff-Clark G, Gossett H, Parsi S, Peterson R, Whittaker R, Dennison C, Davis M, Bray J, Boden R, Scott K. Thiomicrorhabdus heinhorstiae sp. nov. and Thiomicrorhabdus cannonii sp. nov.: novel sulphur-oxidizing chemolithoautotrophs isolated from the chemocline of Hospital Hole, an anchialine sinkhole in Spring Hill, Florida, USA. Int J Syst Evol Microbiol 2022; 72. [PMID: 35275805 DOI: 10.1099/ijsem.0.005233] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1T and HH3T represent novel species belonging to the genus Thiomicrorhabdus. The genome G+C fraction of HH1T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C16 : 1, C18 : 1 and C16 : 0, with the addition of C10:0 3-OH in HH1T and C12 : 0 in HH3T. Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic growth or use of nitrate as a terminal electron acceptor. Strain HH1T grew from pH 6.5 to 8.5, with an optimum of pH 7.4, whereas strain HH3T grew from pH 6 to 8 with an optimum of pH 7.5. Growth was observed between 15-35 °C with optima of 32.8 °C for HH1T and 32 °C for HH3T. HH1T grew in media with [NaCl] 80-689 mM, with an optimum of 400 mM, while HH3T grew at 80-517 mM, with an optimum of 80 mM. The name Thiomicrorhabdus heinhorstiae sp. nov. is proposed, and the type strain is HH1T (=DSM 111584T=ATCC TSD-240T). The name Thiomicrorhabdus cannonii sp. nov is proposed, and the type strain is HH3T (=DSM 111593T=ATCC TSD-241T).
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Affiliation(s)
- Tatum Updegraff
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Grayson Schiff-Clark
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Hunter Gossett
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Sheila Parsi
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Rebecca Peterson
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Robert Whittaker
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Clare Dennison
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - Madison Davis
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
| | - James Bray
- Department of Zoology, University of Oxford, Oxford, UK
| | - Rich Boden
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK.,Marine Institute, University of Plymouth, Drake Circus, Plymouth, UK
| | - Kathleen Scott
- Department of Integrative Biology, University of South Florida, East Fowler Avenue, Tampa, FL, USA
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39
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Pérez‐Rodríguez S, García‐Aznar JM, Gonzalo‐Asensio J. Microfluidic devices for studying bacterial taxis, drug testing and biofilm formation. Microb Biotechnol 2022; 15:395-414. [PMID: 33645897 PMCID: PMC8867988 DOI: 10.1111/1751-7915.13775] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
Some bacteria have coevolved to establish symbiotic or pathogenic relationships with plants, animals or humans. With human association, the bacteria can cause a variety of diseases. Thus, understanding bacterial phenotypes at the single-cell level is essential to develop beneficial applications. Traditional microbiological techniques have provided great knowledge about these organisms; however, they have also shown limitations, such as difficulties in culturing some bacteria, the heterogeneity of bacterial populations or difficulties in recreating some physical or biological conditions. Microfluidics is an emerging technique that complements current biological assays. Since microfluidics works with micrometric volumes, it allows fine-tuning control of the test conditions. Moreover, it allows the recruitment of three-dimensional (3D) conditions, in which several processes can be integrated and gradients can be generated, thus imitating physiological 3D environments. Here, we review some key microfluidic-based studies describing the effects of different microenvironmental conditions on bacterial response, biofilm formation and antimicrobial resistance. For this aim, we present different studies classified into six groups according to the design of the microfluidic device: (i) linear channels, (ii) mixing channels, (iii) multiple floors, (iv) porous devices, (v) topographic devices and (vi) droplet microfluidics. Hence, we highlight the potential and possibilities of using microfluidic-based technology to study bacterial phenotypes in comparison with traditional methodologies.
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Affiliation(s)
- Sandra Pérez‐Rodríguez
- Aragón Institute of Engineering Research (I3A)Department of Mechanical EngineeringUniversity of ZaragozaZaragoza50018Spain
- Multiscale in Mechanical and Biological Engineering (M2BE)IIS‐AragónZaragozaSpain
- Grupo de Genética de MicobacteriasDepartment of Microbiology, Faculty of MedicineUniversity of ZaragozaIIS AragónZaragoza50009Spain
| | - José Manuel García‐Aznar
- Aragón Institute of Engineering Research (I3A)Department of Mechanical EngineeringUniversity of ZaragozaZaragoza50018Spain
- Multiscale in Mechanical and Biological Engineering (M2BE)IIS‐AragónZaragozaSpain
| | - Jesús Gonzalo‐Asensio
- Grupo de Genética de MicobacteriasDepartment of Microbiology, Faculty of MedicineUniversity of ZaragozaIIS AragónZaragoza50009Spain
- CIBER Enfermedades RespiratoriasInstituto de Salud Carlos IIIMadrid28029Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI)Zaragoza50018Spain
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40
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Liberti A, Leigh BA, Graham Z, Natarajan O, Dishaw LJ. A Role for Secreted Immune Effectors in Microbial Biofilm Formation Revealed by Simple In Vitro Assays. Methods Mol Biol 2022; 2421:127-140. [PMID: 34870816 DOI: 10.1007/978-1-0716-1944-5_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of biofilms is critical for the successful and stable colonization of mucosal surfaces by microbes, which often build three-dimensional environments by exuding exopolysaccharides and other macromolecules such as proteins, lipids, and even DNA. It is not just bacteria, but fungi such as yeast, that form these adherent interacting communities. Historically, biofilms have been studied in the context of pathogenesis, but only recently it has been recognized that important relationships among members of host-associated microbiomes are maintained within the context of biofilms. Host immune responses impact biofilm formation in various ways; for example, it is likely that formation of stable biofilms by non-pathogens improves barrier defenses by not just filling available niche spaces but also by helping to ward off pathogens directly. Recently, it was found that soluble immune effector molecules such as immunoglobulin A (IgA) in mammals serve essential roles in modulating complex biofilm communities in ways that benefit the host. Additional lines of evidence from other secreted immune effectors, such as the variable region-containing chitin-binding proteins (VCBPs) in protochordates, now suggest that this phenomenon is much more widespread than previously recognized. The activity of these immune molecules also likely serves roles beyond those of simple defense strategies; rather, they may be improving the outcome of symbiotic interactions benefiting the host. Thus, traditional immune assays that are aimed at studying the function of secreted immune effectors, such as agglutination assays, should take into account the possibility that the first observation may not be the last if the microbes under study are not directly killed. Here, we describe a series of simple approaches to characterize biofilm formation when bacteria (or yeast) are cultured in the presence of a secreted immune effector. To model this approach, we use microbes isolated from the gut of Ciona robusta, each grown in the presence or absence of VCBPs. The approaches defined here are amenable to diverse model systems and their microbes.
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Affiliation(s)
- Assunta Liberti
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Brittany A Leigh
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Zachary Graham
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA
| | - Ojas Natarajan
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA
| | - Larry J Dishaw
- Department of Pediatrics, Morsani College of Medicine, Children's Research Institute, University of South Florida, Saint Petersburg, FL, USA.
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41
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Kurzthaler C, Mandal S, Bhattacharjee T, Löwen H, Datta SS, Stone HA. A geometric criterion for the optimal spreading of active polymers in porous media. Nat Commun 2021; 12:7088. [PMID: 34873164 PMCID: PMC8648790 DOI: 10.1038/s41467-021-26942-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 10/21/2021] [Indexed: 11/26/2022] Open
Abstract
Efficient navigation through disordered, porous environments poses a major challenge for swimming microorganisms and future synthetic cargo-carriers. We perform Brownian dynamics simulations of active stiff polymers undergoing run-reverse dynamics, and so mimic bacterial swimming, in porous media. In accord with experiments of Escherichia coli, the polymer dynamics are characterized by trapping phases interrupted by directed hopping motion through the pores. Our findings show that the spreading of active agents in porous media can be optimized by tuning their run lengths, which we rationalize using a coarse-grained model. More significantly, we discover a geometric criterion for the optimal spreading, which emerges when their run lengths are comparable to the longest straight path available in the porous medium. Our criterion unifies results for porous media with disparate pore sizes and shapes and for run-and-tumble polymers. It thus provides a fundamental principle for optimal transport of active agents in densely-packed biological and environmental settings.
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Affiliation(s)
- Christina Kurzthaler
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA.
| | - Suvendu Mandal
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany.
- Institut für Physik der kondensierten Materie, Technische Universität Darmstadt, 64289, Darmstadt, Germany.
| | - Tapomoy Bhattacharjee
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, USA
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, India
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Sujit S Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, 08544, USA.
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42
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Mattingly HH, Kamino K, Machta BB, Emonet T. Escherichia coli chemotaxis is information limited. NATURE PHYSICS 2021; 17:1426-1431. [PMID: 35035514 PMCID: PMC8758097 DOI: 10.1038/s41567-021-01380-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/10/2021] [Indexed: 05/08/2023]
Abstract
Organisms acquire and use information from their environment to guide their behaviour. However, it is unclear whether this information quantitatively limits their behavioural performance. Here, we relate information to the ability of Escherichia coli to navigate up chemical gradients, the behaviour known as chemotaxis. First, we derive a theoretical limit on the speed with which cells climb gradients, given the rate at which they acquire information. Next, we measure cells' gradient-climbing speeds and the rate of information acquisition by their chemotaxis signaling pathway. We find that E. coli make behavioural decisions with much less than the one bit required to determine whether they are swimming up-gradient. Some of this information is irrelevant to gradient climbing, and some is lost in communication to behaviour. Despite these limitations, E. coli climb gradients at speeds within a factor of two of the theoretical bound. Thus, information can limit the performance of an organism, and sensory-motor pathways may have evolved to efficiently use information acquired from the environment.
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Affiliation(s)
- H H Mattingly
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - K Kamino
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
| | - B B Machta
- Department of Physics, Yale University
- Systems Biology Institute, West Campus, Yale University
| | - T Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- Quantitative Biology Institute, Yale University
- Department of Physics, Yale University
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43
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Narla AV, Cremer J, Hwa T. A traveling-wave solution for bacterial chemotaxis with growth. Proc Natl Acad Sci U S A 2021; 118:e2105138118. [PMID: 34819366 PMCID: PMC8640786 DOI: 10.1073/pnas.2105138118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial cells navigate their environment by directing their movement along chemical gradients. This process, known as chemotaxis, can promote the rapid expansion of bacterial populations into previously unoccupied territories. However, despite numerous experimental and theoretical studies on this classical topic, chemotaxis-driven population expansion is not understood in quantitative terms. Building on recent experimental progress, we here present a detailed analytical study that provides a quantitative understanding of how chemotaxis and cell growth lead to rapid and stable expansion of bacterial populations. We provide analytical relations that accurately describe the dependence of the expansion speed and density profile of the expanding population on important molecular, cellular, and environmental parameters. In particular, expansion speeds can be boosted by orders of magnitude when the environmental availability of chemicals relative to the cellular limits of chemical sensing is high. Analytical understanding of such complex spatiotemporal dynamic processes is rare. Our analytical results and the methods employed to attain them provide a mathematical framework for investigations of the roles of taxis in diverse ecological contexts across broad parameter regimes.
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Affiliation(s)
- Avaneesh V Narla
- Department of Physics, University of California San Diego, La Jolla, CA 92093
| | - Jonas Cremer
- Biology Department, Stanford University, Stanford, CA 94305
| | - Terence Hwa
- Department of Physics, University of California San Diego, La Jolla, CA 92093;
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44
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Colin R, Ni B, Laganenka L, Sourjik V. Multiple functions of flagellar motility and chemotaxis in bacterial physiology. FEMS Microbiol Rev 2021; 45:fuab038. [PMID: 34227665 PMCID: PMC8632791 DOI: 10.1093/femsre/fuab038] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model bacteria. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
| | - Bin Ni
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
- College of Resources and Environmental Science, National Academy of Agriculture Green Development, China Agricultural University, Yuanmingyuan Xilu No. 2, Beijing 100193, China
| | - Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
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45
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Bai Y, He C, Chu P, Long J, Li X, Fu X. Spatial modulation of individual behaviors enables an ordered structure of diverse phenotypes during bacterial group migration. eLife 2021; 10:67316. [PMID: 34726151 PMCID: PMC8563000 DOI: 10.7554/elife.67316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022] Open
Abstract
Coordination of diverse individuals often requires sophisticated communications and high-order computational abilities. Microbial populations can exhibit diverse individualistic behaviors, and yet can engage in collective migratory patterns with a spatially sorted arrangement of phenotypes. However, it is unclear how such spatially sorted patterns emerge from diverse individuals without complex computational abilities. Here, by investigating the single-cell trajectories during group migration, we discovered that, despite the constant migrating speed of a group, the drift velocities of individual bacteria decrease from the back to the front. With a Langevin-type modeling framework, we showed that this decreasing profile of drift velocities implies the spatial modulation of individual run-and-tumble random motions, and enables the bacterial population to migrate as a pushed wave front. Theoretical analysis and stochastic simulations further predicted that the pushed wave front can help a diverse population to stay in a tight group, while diverse individuals perform the same type of mean reverting processes around centers orderly aligned by their chemotactic abilities. This mechanism about the emergence of orderly collective migration from diverse individuals is experimentally demonstrated by titration of bacterial chemoreceptor abundance. These results reveal a simple computational principle for emergent ordered behaviors from heterogeneous individuals. Organisms living in large groups often have to move together in order to navigate, forage for food, and increase their roaming range. Such groups are often made up of distinct individuals that must integrate their different behaviors in order to migrate in the same direction at a similar pace. For instance, for the bacteria Escherichia coli to travel as a condensed group, they must coordinate their response to a set of chemical signals called chemoattractants that tell them where to go. The chemoattractants surrounding the bacteria are unequally distributed so that there is more of them at the front than the back of the group. During migration, each bacterium moves towards this concentration gradient in a distinct way, spontaneously rotating its direction in a ‘run-and-tumble’ motion that guides it towards areas where there are high levels of these chemical signals. In addition to this variability, how well individual bacteria are able to swim up the gradient also differs within the population. Bacteria that are better at sensing the chemoattractant gradient are placed at the front of the group, while those that are worst are shifted towards the back. This spatial arrangement is thought to help the bacteria migrate together. But how E. coli organize themselves in to this pattern is unclear, especially as they cannot communicate directly with one another and display such diverse, randomized behaviors. To help answer this question, Bai, He et al. discovered a general principle that describes how single bacterial cells move within a group. The results showed that E. coli alter their run-and-tumble motion depending on where they reside within the population: individuals at the rear drift faster so they can catch up with the group, while those leading the group drift slower to draw themselves back. This ‘reversion behavior’ allows the migrating bacteria to travel at a constant speed around a mean position relative to the group. A cell’s drifting speed is determined by how well it moves towards the chemoattractant and its response to the concentration gradient. As a result, the mean position around which the bacterium accelerates or deaccelerates will vary depending on how sensitive it is to the chemoattractant gradient. The E. coli therefore spatially arrange themselves so that the more sensitive bacteria are located at the front of the group where the gradient is shallower; and cells that are less sensitive are located towards the back where the gradient is steeper. These findings suggest a general principle for how bacteria form ordered patterns whilst migrating as a collective group. This behavior could also apply to other populations of distinct individuals, such as ants following a trail or flocks of birds migrating in between seasons.
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Affiliation(s)
- Yang Bai
- CAS Key Laboratory for Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Caiyun He
- CAS Key Laboratory for Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Pan Chu
- CAS Key Laboratory for Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Junjiajia Long
- Yale University, Department of Physics, New Haven, United States
| | - Xuefei Li
- CAS Key Laboratory for Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiongfei Fu
- CAS Key Laboratory for Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,University of Chinese Academy of Sciences, Beijing, China
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Kim JH, Weerawongwiwat V, Yoon JH, Lee JS, Sukhoom A, Kim W. Snuella sedimenti sp. nov., isolated from marine sediment. Arch Microbiol 2021; 203:5437-5443. [PMID: 34405260 DOI: 10.1007/s00203-021-02528-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 12/29/2022]
Abstract
A Gram stain-negative, aerobic, motile by gliding, rod-shaped bacterial strain CAU 1569T was isolated from marine sediment on Shido Island in Incheon. It grew at 20-37 °C (optimum, 30 °C), pH 6.0-9.0 (optimum, 7.0), 2-6% NaCl (w/v) (optimum, 2%). Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CAU 1569T formed a distinct lineage with only the type strain of Snuella. Strain CAU 1569T showed high similarity to S. lapsa KACC 14152T (95.8%), Mariniflexile gromovii KMM KCTC 12570T, Aestuariibaculum marinum KCTC 52521T (95.4%), A. suncheonense KACC 16186T (94.6%) and Yeosuana aromativorans KCCM 42019T (94.4%). The genome contained 57 contigs, 3,437 protein-coding gene, 3 rRNAs (5, 16, and 23S), 43 tRNAs, and with a 35.7 mol% G + C content. The DDH value between strain CAU 1569T and S. lapsa KACC 14152T was 39.4 ± 0.6%. The only isoprenoid quinone was menaquinone 6 (MK-6). The major fatty acids were iso-C15:0, C15:1-iso G, and C17:0 iso 3-OH. Strain CAU 1569T contained diphosphatidylglycerol, aminoglycolipid, unidentified aminolipid, and three unidentified lipids. Based on phylogenetic, genomic, physiologic, and chemotaxonomic characterizations, strain CAU 1569T represents a novel Snuella species, which the name Snuella sedimenti sp. nov. is proposed. The type of strain is CAU 1569T (= KCTC 82409T = MCCC 1K05670T).
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Affiliation(s)
- Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Ampaitip Sukhoom
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea.
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Ren WT, Meng FX, Guo LL, Sun L, Xu XW, Zhou P, Wu YH. Luteirhabdus pelagi gen. nov., sp. nov., a novel member of the family Flavobacteriaceae, isolated from the West Pacific Ocean. Arch Microbiol 2021; 203:6021-6031. [PMID: 34698880 PMCID: PMC8590676 DOI: 10.1007/s00203-021-02557-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/02/2022]
Abstract
A Gram-stain-negative, aerobic, and yellow-pigmented bacterium, designated A3-108T, was isolated from seawater of the West Pacific Ocean. Cells were non-motile and rod-shaped, with carotenoid-type pigments. Strain A3-108T grew at pH 6.0–8.5 (optimum 6.5) and 15–40 °C (optimum 28 °C), in the presence of 0.5–10% (w/v) NaCl (optimum 1.0%). It possessed the ability to produce H2S. Based on the 16S rRNA gene analysis, strain A3-108T exhibited highest similarity with Aureisphaera salina A6D-50T (90.6%). Phylogenetic analysis shown that strain A3-108T affiliated with members of the family Flavobacteriaceae and represented an independent lineage. The principal fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:1 G, and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The sole isoprenoid quinone was MK-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified aminolipid and one unidentified lipid. The ANIb, in silico DDH and AAI values among the genomes of strain A3-108T and three reference strains were 67.3–71.1%, 18.7–22.1%, and 58.8–71.4%, respectively. The G + C content was 41.0%. Distinctness of the phylogenetic position as well as differentiating chemotaxonomic and other phenotypic traits revealed that strain A3-108T represented a novel genus and species of the family Flavobacteriaceae, for which the name Luteirhabdus pelagi gen. nov., sp. nov. is proposed (type strain, A3-108T = CGMCC 1.18821T = KCTC 82563T).
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Affiliation(s)
- Wen-Ting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Fan-Xu Meng
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Li-Li Guo
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China.,College of Life and Environmental Science, Hunan University of Arts and Science, Changde, 415000, People's Republic of China
| | - Li Sun
- State Research Center of Island Exploitation and Management, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China.
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China. .,School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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Strakova N, Korena K, Gelbicova T, Kulich P, Karpiskova R. A Rapid Culture Method for the Detection of Campylobacter from Water Environments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18116098. [PMID: 34198825 PMCID: PMC8200967 DOI: 10.3390/ijerph18116098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
The natural environment and water are among the sources of Campylobacter jejuni and Campylobacter coli. A limited number of protocols exist for the isolation of campylobacters in poorly filterable water. Therefore, the goal of our work was to find a more efficient method of Campylobacter isolation and detection from wastewater and surface water than the ISO standard. In the novel rapid culture method presented here, samples are centrifuged at high speed, and the resuspended pellet is inoculated on a filter, which is placed on Campylobacter selective mCCDA agar. The motile bacteria pass through the filter pores, and mCCDA agar suppresses the growth of background microbiota on behalf of campylobacters. This culture-based method is more efficient for the detection and isolation of Campylobacter jejuni and Campylobacter coli from poorly filterable water than the ISO 17995 standard. It also is less time-consuming, taking only 72 h and comprising three steps, while the ISO standard method requires five or six steps and 144-192 h. This novel culture method, based on high-speed centrifugation, bacterial motility, and selective cultivation conditions, can be used for the detection and isolation of various bacteria from water samples.
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Bhattacharjee T, Amchin DB, Ott JA, Kratz F, Datta SS. Chemotactic migration of bacteria in porous media. Biophys J 2021; 120:3483-3497. [PMID: 34022238 DOI: 10.1016/j.bpj.2021.05.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/11/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022] Open
Abstract
Chemotactic migration of bacteria-their ability to direct multicellular motion along chemical gradients-is central to processes in agriculture, the environment, and medicine. However, current understanding of migration is based on studies performed in bulk liquid, despite the fact that many bacteria inhabit tight porous media such as soils, sediments, and biological gels. Here, we directly visualize the chemotactic migration of Escherichia coli populations in well-defined 3D porous media in the absence of any other imposed external forcing (e.g., flow). We find that pore-scale confinement is a strong regulator of migration. Strikingly, cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Furthermore, confinement markedly alters the dynamics and morphology of the migrating population-features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values to reflect the influence of pore-scale confinement. Our work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in complex environments.
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Affiliation(s)
- Tapomoy Bhattacharjee
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey
| | - Daniel B Amchin
- Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Jenna A Ott
- Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Felix Kratz
- Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Sujit S Datta
- Chemical and Biological Engineering, Princeton University, Princeton, New Jersey.
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Alkaline pH Increases Swimming Speed and Facilitates Mucus Penetration for Vibrio cholerae. J Bacteriol 2021; 203:JB.00607-20. [PMID: 33468594 PMCID: PMC8088521 DOI: 10.1128/jb.00607-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/05/2021] [Indexed: 01/05/2023] Open
Abstract
The diarrheal disease cholera is still a burden for populations in developing countries with poor sanitation. To develop effective vaccines and prevention strategies against Vibrio cholerae, we must understand the initial steps of infection leading to the colonization of the small intestine. Intestinal mucus is the first line of defense against intestinal pathogens. It acts as a physical barrier between epithelial tissues and the lumen that enteropathogens must overcome to establish a successful infection. We investigated the motile behavior of two Vibrio cholerae strains (El Tor C6706 and Classical O395) in mucus using single-cell tracking in unprocessed porcine intestinal mucus. We determined that V. cholerae can penetrate mucus using flagellar motility and that alkaline pH increases swimming speed and, consequently, improves mucus penetration. Microrheological measurements indicate that changes in pH between 6 and 8 (the physiological range for the human small intestine) had little effect on the viscoelastic properties of mucus. Finally, we determined that acidic pH promotes surface attachment by activating the mannose-sensitive hemagglutinin (MshA) pilus in V. cholerae El Tor C6706 without a measurable change in the total cellular concentration of the secondary messenger cyclic dimeric GMP (c-di-GMP). Overall, our results support the hypothesis that pH is an important factor affecting the motile behavior of V. cholerae and its ability to penetrate mucus. Therefore, changes in pH along the human small intestine may play a role in determining the preferred site for V. cholerae during infection. IMPORTANCE The diarrheal disease cholera is still a burden for populations in developing countries with poor sanitation. To develop effective vaccines and prevention strategies against Vibrio cholerae, we must understand the initial steps of infection leading to the colonization of the small intestine. To infect the host and deliver the cholera toxin, V. cholerae has to penetrate the mucus layer protecting the intestinal tissues. However, the interaction of V. cholerae with intestinal mucus has not been extensively investigated. In this report, we demonstrated using single-cell tracking that V. cholerae can penetrate intestinal mucus using flagellar motility. In addition, we observed that alkaline pH improves the ability of V. cholerae to penetrate mucus. This finding has important implications for understanding the dynamics of infection, because pH varies significantly along the small intestine, between individuals, and between species. Blocking mucus penetration by interfering with flagellar motility in V. cholerae, reinforcing the mucosa, controlling intestinal pH, or manipulating the intestinal microbiome will offer new strategies to fight cholera.
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