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Zhou P, Hao X, Liu Y, Yang Z, Xu M, Liu S, Zhang S, Yang T, Wang X, Wang Y. Determination of the protective effects of Hua-Zhuo-Jie-Du in chronic atrophic gastritis by regulating intestinal microbiota and metabolites: combination of liquid chromatograph mass spectrometer metabolic profiling and 16S rRNA gene sequencing. Chin Med 2021; 16:37. [PMID: 33933119 PMCID: PMC8088729 DOI: 10.1186/s13020-021-00445-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022] Open
Abstract
Background
Hua-Zhuo-Jie-Du (HZJD), a Chinese herbal prescription consisting of 11 herbs, is commonly used in China to treat chronic atrophic gastritis (CAG). We aimed to determine the effect of HZJD on the microbiome-associated metabolic changes in CAG rats. Methods
The CAG rat models were induced by 1-methyl-3-nitro-1-nitrosoguanidine (MNNG) combined with irregular fasting and 2% sodium salicylate, which was intragastrically administrated in fasted animals for 24 weeks. The CAG rats in the Chinese medicine (CM) group were administered a daily dose of 14.81 g/kg/day HZJD, and the vitacoenzyme (V) group were administered a daily dose of 0.08 g/kg/day vitacoenzyme. All animals were treated for 10 consecutive weeks, consecutively. Hematoxylin and eosin (H&E) staining was used to assess the histopathological changes in the gastric tissues. An integrated approach based on liquid chromatograph mass spectrometer (LC-MS) metabolic profiling combined with 16S rRNA gene sequencing was carried out to assess the effects of HZJD on CAG rats. Spearman analysis was used to calculate the correlation coefficient between the different intestinal microbiota and the metabolites. Results The H&E results indicated that HZJD could improve the pathological condition of CAG rats. The LC–MS results indicated that HZJD could significantly improve 21 gastric mucosal tissue perturbed metabolites in CAG rats; the affected metabolites were found to be involved in multiple metabolic pathways, such as the central carbon metabolism in cancer. The results of 16S rRNA gene sequencing indicated that HZJD could regulate the diversity, microbial composition, and abundance of the intestinal microbiota of CAG rats. Following HZJD treatment, the relative abundance of Turicibacter was increased, and the relative abundance of Desulfococcus and Escherichia were decreased in the CM group when compared with the M group. Spearman analysis revealed that perturbed intestinal microbes had a strong correlation with differential metabolites, Escherichia exhibited a negative correlation with l-Leucine, Turicibacter was negatively correlated with urea, and Desulfococcus exhibited a positive correlation with trimethylamine, and a negative correlation with choline. Conclusions HZJD could protect CAG by regulating intestinal microbiota and its metabolites.
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Affiliation(s)
- Pingping Zhou
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China
| | - Xinyu Hao
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China
| | - Yu Liu
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China
| | - Zeqi Yang
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China
| | - Miaochan Xu
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China
| | - Shaowei Liu
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China
| | - Shixiong Zhang
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China
| | - Tianxiao Yang
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China
| | - Xiaomei Wang
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China
| | - Yangang Wang
- Hebei University of Chinese Medicine, Xinshi South Road No 326, Qiaoxi District, Hebei, 050091, Shijiazhuang, China. .,Beijing University of Chinese Medicine Third Affiliated Hospital, Anwai Xiaoguan Street No. 51, Chaoyang District, 100029, Beijing, China.
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Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole. Proc Natl Acad Sci U S A 2020; 117:6114-6120. [PMID: 32123098 DOI: 10.1073/pnas.1916974117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacterial chemotaxis to prominent microbiota metabolites such as indole is important in the formation of microbial communities in the gastrointestinal (GI) tract. However, the basis of chemotaxis to indole is poorly understood. Here, we exposed Escherichia coli to a range of indole concentrations and measured the dynamic responses of individual flagellar motors to determine the chemotaxis response. Below 1 mM indole, a repellent-only response was observed. At 1 mM indole and higher, a time-dependent inversion from a repellent to an attractant response was observed. The repellent and attractant responses were mediated by the Tsr and Tar chemoreceptors, respectively. Also, the flagellar motor itself mediated a repellent response independent of the receptors. Chemotaxis assays revealed that receptor-mediated adaptation to indole caused a bipartite response-wild-type cells were attracted to regions of high indole concentration if they had previously adapted to indole but were otherwise repelled. We propose that indole spatially segregates cells based on their state of adaptation to repel invaders while recruiting beneficial resident bacteria to growing microbial communities within the GI tract.
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Karmakar R, Uday Bhaskar RVS, Jesudasan RE, Tirumkudulu MS, Venkatesh KV. Enhancement of Swimming Speed Leads to a More-Efficient Chemotactic Response to Repellent. Appl Environ Microbiol 2016; 82:1205-1214. [PMID: 26655753 PMCID: PMC4751852 DOI: 10.1128/aem.03397-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/02/2015] [Indexed: 11/20/2022] Open
Abstract
Negative chemotaxis refers to the motion of microorganisms away from regions with high concentrations of chemorepellents. In this study, we set controlled gradients of NiCl2, a chemorepellent, in microchannels to quantify the motion of Escherichia coli over a broad range of concentrations. The experimental technique measured the motion of the bacteria in space and time and further related the motion to the local concentration profile of the repellent. Results show that the swimming speed of bacteria increases with an increasing concentration of repellent, which in turn enhances the drift velocity. The contribution of the increased swimming speed to the total drift velocity was in the range of 20 to 40%, with the remaining contribution coming from the modulation of the tumble frequency. A simple model that incorporates receptor dynamics, including adaptation, intracellular signaling, and swimming speed variation, was able to qualitatively capture the observed trend in drift velocity.
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Affiliation(s)
- Richa Karmakar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - R V S Uday Bhaskar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Rajesh E Jesudasan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Mahesh S Tirumkudulu
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - K V Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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Resource availability shapes microbial motility and mediates early-stage formation of microbial clusters in biological wastewater treatment processes. Appl Microbiol Biotechnol 2013; 98:1459-67. [DOI: 10.1007/s00253-013-5109-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/07/2013] [Accepted: 07/08/2013] [Indexed: 12/01/2022]
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Streif S, Staudinger WF, Oesterhelt D, Marwan W. Quantitative analysis of signal transduction in motile and phototactic cells by computerized light stimulation and model based tracking. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2009; 80:023709. [PMID: 19256655 DOI: 10.1063/1.3076408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To investigate the responses of Halobacterium salinarum to stimulation with light (phototaxis and photokinesis), we designed an experimental setup consisting of optical devices for automatic video image acquisition and computer-controlled light stimulation, and developed algorithms to analyze physiological responses of the cells. Cells are categorized as motile and nonmotile by a classification scheme based on the square displacement of cell positions. Computerized tracking based on a dynamic model of the stochastic cell movement and a Kalman filter-based algorithm allows smoothed estimates of the cell tracks and the detection of physiological responses to complex stimulus patterns. The setup and algorithms were calibrated which allows quantitative measurements and systematic analysis of cellular sensing and response. Overall, the setup is flexible, extensible, and consists mainly of commercially available products. This facilitates modifications of the setup and algorithms for physiological studies of the motility of cells or microorganisms.
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Affiliation(s)
- Stefan Streif
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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Borrok MJ, Kolonko EM, Kiessling LL. Chemical probes of bacterial signal transduction reveal that repellents stabilize and attractants destabilize the chemoreceptor array. ACS Chem Biol 2008; 3:101-9. [PMID: 18278851 DOI: 10.1021/cb700211s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The signal transduction cascade responsible for bacterial chemotaxis serves as a model for understanding how cells perceive and respond to their environments. Bacteria react to chemotactic signals by migrating toward attractants and away from repellents. Recent data suggest that the amplification of attractant stimuli depends on receptor collaboration: occupied and unoccupied chemoreceptors act together to relay attractant signals. Attractant signal transmission, therefore, depends on the organization of the chemoreceptors into a lattice of signaling proteins. The importance of this lattice for transducing repellent signals was unexplored. Here, we investigate the role of inter-receptor communication on repellent responses in Escherichia coli. Previously, we found that multivalent displays of attractants are more potent than their monovalent counterparts. To examine the importance of the chemoreceptor lattice in repellent signaling, we synthesized ligands displaying multiple copies of the repellent leucine. Monomeric leucine and low-valency leucine-displaying polymers were sensed as repellents. In contrast, multivalent displays of leucine capable of binding multiple chemoreceptors function not as potent repellents but as attractants. Intriguingly, chemical cross-linking studies indicate that these multivalent ligands, like monovalent attractants, disrupt the cellular chemoreceptor lattice. Thus, repellents stabilize the intrinsic chemoreceptor lattice, and attractants destabilize it. These results indicate that signals can be transmitted with high sensitivity via the disruption of protein-protein interactions. Moreover, our data demonstrate that repellents can be transformed into attractants merely by their multivalent display. These results have implications for designing agonists and antagonists for other signaling systems.
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Affiliation(s)
- M. Jack Borrok
- Department of Biochemistry
- Department of Chemistry
- University of Wisconsin, Madison, Wisconsin 53706
| | - Erin M. Kolonko
- Department of Biochemistry
- Department of Chemistry
- University of Wisconsin, Madison, Wisconsin 53706
| | - Laura L. Kiessling
- Department of Biochemistry
- Department of Chemistry
- University of Wisconsin, Madison, Wisconsin 53706
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Wright S, Walia B, Parkinson JS, Khan S. Differential activation of Escherichia coli chemoreceptors by blue-light stimuli. J Bacteriol 2006; 188:3962-71. [PMID: 16707688 PMCID: PMC1482890 DOI: 10.1128/jb.00149-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enteric bacteria tumble, swim slowly, and are then paralyzed upon exposure to 390- to 530-nm light. Here, we analyze this complex response in Escherichia coli using standard fluorescence microscope optics for excitation at 440 +/- 5 nm. The slow swimming and paralysis occurred only in dye-containing growth media or buffers. Excitation elicited complete paralysis within a second in 1 muM proflavine dye, implying specific motor damage, but prolonged tumbling in buffer alone. The tumbling half-response times were subsecond for onset but more than a minute for recovery. The response required the chemotaxis signal protein CheY and receptor-dependent activation of its kinase CheA. The study of deletion mutants revealed a specific requirement for either the aerotaxis receptor Aer or the chemoreceptor Tar but not the Tar homolog Tsr. The action spectrum of the wild-type response was consistent with a flavin, but the chromophores remain to be identified. The motile response processed via Aer was sustained, with recovery to either step-up or -down taking more than a minute. The response processed via Tar was transient, recovering on second time scales comparable to chemotactic responses. The response duration and amplitude were dependent on relative expression of Aer, Tar, and Tsr. The main response features were reproduced when each receptor was expressed singly from a plasmid in a receptorless host strain. However, time-resolved motion analysis revealed subtle kinetic differences that reflect the role of receptor cluster interactions in kinase activation-deactivation dynamics.
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Affiliation(s)
- Stuart Wright
- Molecular Biology Consortium, 2201 W. Campbell Park Drive, Chicago, IL 60612, USA.
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Mitchell JG, Kogure K. Bacterial motility: links to the environment and a driving force for microbial physics. FEMS Microbiol Ecol 2006; 55:3-16. [PMID: 16420610 DOI: 10.1111/j.1574-6941.2005.00003.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial motility was recognized 300 years ago. Throughout this history, research into motility has led to advances in microbiology and physics. Thirty years ago, this union helped to make run and tumble chemotaxis the paradigm for bacterial movement. This review highlights how this paradigm has expanded and changed, and emphasizes the following points. The absolute magnitude of swimming speed is ecologically important because it helps determine vulnerability to Brownian motion, sensitivity to gradients, the type of receptors used and the cost of moving, with some bacteria moving at 1 mm s(-1). High costs for high speeds are offset by the benefit of resource translocation across submillimetre redox and other environmental gradients. Much of environmental chemotaxis appears adapted to respond to gradients of micrometres, rather than migrations of centimetres. In such gradients, control of ion pumps is particularly important. Motility, at least in the ocean, is highly intermittent and the speed is variable within a run. Subtleties in flagellar physics provide a variety of reorientation mechanisms. Finally, while careful physical analysis has contributed to our current understanding of bacterial movement, tactic bacteria are increasingly widely used as experimental and theoretical model systems in physics.
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Affiliation(s)
- James G Mitchell
- Marine Microbiology, Ocean Research Institute, University of Tokyo, Tokyo, Japan.
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Michalodimitrakis KM, Sourjik V, Serrano L. Plasticity in amino acid sensing of the chimeric receptor Taz. Mol Microbiol 2006; 58:257-66. [PMID: 16164563 DOI: 10.1111/j.1365-2958.2005.04821.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Taz is a chimeric receptor consisting of the periplasmic, transmembrane and most of the HAMP linker domains of the Escherichia coli aspartate receptor (Tar(Ec)) and the cytoplasmic signalling domain of the E. coli osmosensor EnvZ. Aspartate is one of several attractant ligands normally sensed by Tar and it interacts with Taz to induce OmpR-dependent transcription from the ompC promoter--albeit with reduced sensitivity relative to the chemotactic response it evokes via Tar. By combining Taz with a reporter system that expresses green fluorescent protein (GFP) from the ompC promoter, we were able to examine the interaction of Taz with all 20 natural amino acids. Some amino acids (Leu, Met, Val and Ser) reduced GFP expression, which in the case of leucine is likely attributed to a direct effect on the receptor, rather than an indirect effect through the leucine responsive protein (Lrp). Surprisingly, amino acids like Met and Ser--which are also attractants for Tar--'inhibited' Taz. Moreover, Taz exhibits a higher sensitivity to Leu compared with Asp, which is the inverse of Tar. Our results show the exquisite sensitivity of chemotactic receptors. Small conformational changes induced by making the chimera may have changed the way it responds to different amino acids.
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Abstract
We have analyzed repellent signal processing in Escherichia coli by flash photorelease of leucine from photolabile precursors. We found that 1). response amplitudes of free-swimming cell populations increased with leucine jump concentration, with an apparent Hill coefficient of 1.3 and a half-maximal dose of 14.4 microM; 2). at a 0-0.5 mM leucine concentration jump sufficient to obtain a saturation motile response, the swimming cell response time of approximately 0.05 s was several-fold more rapid than the motor response time of 0.39 +/- 0.18 s measured by following the rotation of cells tethered by a single flagellum to quartz coverslips; and 3). the motor response time of individual cells was correlated with rotation bias but not cell size. These results provide information on amplification, rate-limiting step, and flagellar bundle mechanics during repellent signal processing. The difference between the half-maximal dose for the excitation response and the corresponding value reported for adaptation provides an estimate of the increase in the rate of formation of CheYP, the phosphorylated form of the signal protein CheY. The estimated increase gives a lower limit receptor kinase coupling ratio of 6.0. The magnitude and form of the motor response time distribution argue for it being determined by the poststimulus switching probability rather than CheYP turnover, diffusion, or binding. The temporal difference between the tethered and swimming cell response times to repellents can be quantitatively accounted for and suggests that one flagellum is sufficient to cause a measurable change of direction in which a bacterium swims.
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Affiliation(s)
- Shahid Khan
- Molecular Biology Consortium, Chicago, Illinois, USA.
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