scholarly journals Quantitative Imaging of Gut Microbiota Spatial Organization

2015 ◽  
Vol 18 (4) ◽  
pp. 478-488 ◽  
Author(s):  
Kristen A. Earle ◽  
Gabriel Billings ◽  
Michael Sigal ◽  
Joshua S. Lichtman ◽  
Gunnar C. Hansson ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Spatial Organization ◽  
Quantitative Imaging

scholarly journals A quantitative imaging-based screen reveals the exocyst as a network hub connecting endocytosis and exocytosis

2015 ◽  
Vol 26 (13) ◽  
pp. 2519-2534 ◽  
Author(s):  
Mini Jose ◽  
Sylvain Tollis ◽  
Deepak Nair ◽  
Romain Mitteau ◽  
Christophe Velours ◽  
...  
Keyword(s):  
Systems Analysis ◽  
Spatial Organization ◽  
Quantitative Imaging ◽  
Golgi Vesicle ◽  
Biological Processes ◽  
Cellular Polarity ◽  
Vesicle Dynamics ◽  
Maintenance Systems ◽  
Resolution Single ◽  
Single Vesicle

The coupling of endocytosis and exocytosis underlies fundamental biological processes ranging from fertilization to neuronal activity and cellular polarity. However, the mechanisms governing the spatial organization of endocytosis and exocytosis require clarification. Using a quantitative imaging-based screen in budding yeast, we identified 89 mutants displaying defects in the localization of either one or both pathways. High-resolution single-vesicle tracking revealed that the endocytic and exocytic mutants she4∆ and bud6∆ alter post-Golgi vesicle dynamics in opposite ways. The endocytic and exocytic pathways display strong interdependence during polarity establishment while being more independent during polarity maintenance. Systems analysis identified the exocyst complex as a key network hub, rich in genetic interactions with endocytic and exocytic components. Exocyst mutants displayed altered endocytic and post-Golgi vesicle dynamics and interspersed endocytic and exocytic domains compared with control cells. These data are consistent with an important role for the exocyst in coordinating endocytosis and exocytosis.

scholarly journals A fiber-deprived diet disturbs the fine-scale spatial architecture of the murine colon microbiome

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Alessandra Riva ◽  
Orest Kuzyk ◽  
Erica Forsberg ◽  
Gary Siuzdak ◽  
Carina Pfann ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Spatial Organization ◽  
Distal Colon ◽  
Fine Scale ◽  
Mucus Layer ◽  
Local Effects ◽  
Spatial Structuring ◽  
Laser Capture ◽  
Spatial Architecture ◽  
Murine Colon

Abstract Compartmentalization of the gut microbiota is thought to be important to system function, but the extent of spatial organization in the gut ecosystem remains poorly understood. Here, we profile the murine colonic microbiota along longitudinal and lateral axes using laser capture microdissection. We found fine-scale spatial structuring of the microbiota marked by gradients in composition and diversity along the length of the colon. Privation of fiber reduces the diversity of the microbiota and disrupts longitudinal and lateral gradients in microbiota composition. Both mucus-adjacent and luminal communities are influenced by the absence of dietary fiber, with the loss of a characteristic distal colon microbiota and a reduction in the mucosa-adjacent community, concomitant with depletion of the mucus layer. These results indicate that diet has not only global but also local effects on the composition of the gut microbiota, which may affect function and resilience differently depending on location.

scholarly journals Predicting the Longitudinally and Radially Varying Gut Microbiota Composition Using Multi-Scale Microbial Metabolic Modeling

Processes ◽  
2019 ◽  
Vol 7 (7) ◽  
pp. 394 ◽  
Author(s):  
Chan ◽  
Friedman ◽  
Wu ◽  
Maranas
Keyword(s):  
Gut Microbiota ◽  
Spatial Organization ◽  
Driving Forces ◽  
Optimization Problems ◽  
Oxygen Availability ◽  
Anatomical Site ◽  
Microbiota Composition ◽  
Dynamic Framework ◽  
Genome Scale ◽  
Gut Microbiota Composition

Background: The gut microbiota is a heterogeneous group of microbes that is spatially distributed along various sections of the intestines and across the mucosa and lumen in each section. Understanding the dynamics between the spatially differential microbial populations and the driving forces for the observed spatial organization will provide valuable insights into important questions such as the nature of colonization of the infant gut and different types of inflammatory bowel disease localized in different regions of the intestines. However, in most studies, the microbiota is sampled only at a single site (often feces) or from a particular anatomical site of the intestines. Differential oxygen availability is putatively a key factor shaping the spatial organization. Results: To test this hypothesis, we constructed a community genome-scale metabolic model consisting of representative organisms for the major phyla present in the human gut microbiome. By solving step-wise optimization problems embedded in a dynamic framework to predict community metabolism and integrate the mucosally-adherent with the luminal microbiome between consecutive sections along the intestines, we were able to capture (i) the essential features of the spatially differential composition of obligate anaerobes vs. facultative anaerobes and aerobes determined experimentally, and (ii) the accumulation of microbial biomass in the lumen. Sensitivity analysis suggests that the spatial organization depends primarily on the oxygen-per-microbe availability in each region. Oxygen availability is reduced relative to the ~100-fold increase in mucosal microbial density along the intestines, causing the switch between aerobes and anaerobes. Conclusion: The proposed integrated dynamic framework is able to predict spatially differential gut microbiota composition using microbial genome-scale metabolic models and test hypotheses regarding the dynamics of the gut microbiota. It can potentially become a valuable tool for exploring therapeutic strategies for site-specific perturbation of the gut microbiota and the associated metabolic activities.

scholarly journals 3D imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa

2021 ◽  
Author(s):  
Octavio Mondragón-Palomino ◽  
Roberta Poceviciute ◽  
Antti Lignell ◽  
Jessica A. Griffiths ◽  
Heli Takko ◽  
...  
Keyword(s):  
Spatial Pattern ◽  
3D Imaging ◽  
Spatial Organization ◽  
High Spatial Resolution ◽  
Bacterial Colonization ◽  
Quantitative Imaging ◽  
Taxonomic Composition ◽  
Host Tissue ◽  
Imaging Approach ◽  
Biogeographical Analysis

Improving our understanding of host-microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the 3D spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 days after recovery when overall bacterial loads returned to pre-antibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern was resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that bacterial taxa are distributed differently within crypts, with Lactobacilli laying closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.

scholarly journals Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D)

2017 ◽  
Vol 114 (35) ◽  
pp. E7321-E7330 ◽  
Author(s):  
Weizhe Li ◽  
Ronald N. Germain ◽  
Michael Y. Gerner
Keyword(s):  
Quantitative Analysis ◽  
High Resolution ◽  
Spatial Organization ◽  
Quantitative Imaging ◽  
Cell Types ◽  
Cell Populations ◽  
Lymphoid Tissues ◽  
Protein Fluorescence ◽  
Cellular Analysis ◽  
Multiple Cell

Organ homeostasis, cellular differentiation, signal relay, and in situ function all depend on the spatial organization of cells in complex tissues. For this reason, comprehensive, high-resolution mapping of cell positioning, phenotypic identity, and functional state in the context of macroscale tissue structure is critical to a deeper understanding of diverse biological processes. Here we report an easy to use method, clearing-enhanced 3D (Ce3D), which generates excellent tissue transparency for most organs, preserves cellular morphology and protein fluorescence, and is robustly compatible with antibody-based immunolabeling. This enhanced signal quality and capacity for extensive probe multiplexing permits quantitative analysis of distinct, highly intermixed cell populations in intact Ce3D-treated tissues via 3D histo-cytometry. We use this technology to demonstrate large-volume, high-resolution microscopy of diverse cell types in lymphoid and nonlymphoid organs, as well as to perform quantitative analysis of the composition and tissue distribution of multiple cell populations in lymphoid tissues. Combined with histo-cytometry, Ce3D provides a comprehensive strategy for volumetric quantitative imaging and analysis that bridges the gap between conventional section imaging and disassociation-based techniques.

scholarly journals Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice

2017 ◽  
Vol 114 (43) ◽  
pp. E9105-E9114 ◽  
Author(s):  
Jessica L. Mark Welch ◽  
Yuko Hasegawa ◽  
Nathan P. McNulty ◽  
Jeffrey I. Gordon ◽  
Gary G. Borisy
Keyword(s):  
Gut Microbiota ◽  
Spatial Organization ◽  
Spatial Scales ◽  
Simultaneous Detection ◽  
Proximal Colon ◽  
Bacterial Strains ◽  
Microbial Succession ◽  
Human Gut ◽  
The Face ◽  
Gnotobiotic Mice

Knowledge of the spatial organization of the gut microbiota is important for understanding the physical and molecular interactions among its members. These interactions are thought to influence microbial succession, community stability, syntrophic relationships, and resiliency in the face of perturbations. The complexity and dynamism of the gut microbiota pose considerable challenges for quantitative analysis of its spatial organization. Here, we illustrate an approach for addressing this challenge, using (i) a model, defined 15-member consortium of phylogenetically diverse, sequenced human gut bacterial strains introduced into adult gnotobiotic mice fed a polysaccharide-rich diet, and (ii) in situ hybridization and spectral imaging analysis methods that allow simultaneous detection of multiple bacterial strains at multiple spatial scales. Differences in the binding affinities of strains for substrates such as mucus or food particles, combined with more rapid replication in a preferred microhabitat, could, in principle, lead to localized clonally expanded aggregates composed of one or a few taxa. However, our results reveal a colonic community that is mixed at micrometer scales, with distinct spatial distributions of some taxa relative to one another, notably at the border between the mucosa and the lumen. Our data suggest that lumen and mucosa in the proximal colon should be conceptualized not as stratified compartments but as components of an incompletely mixed bioreactor. Employing the experimental approaches described should allow direct tests of whether and how specified host and microbial factors influence the nature and functional contributions of “microscale” mixing to the dynamic operations of the microbiota in health and disease.

scholarly journals Direct imaging of the circular chromosome in a live bacterium

2018 ◽  
Author(s):  
Fabai Wu ◽  
Aleksandre Japaridze ◽  
Xuan Zheng ◽  
Jacob W. J. Kerssemakers ◽  
Cees Dekker
Keyword(s):  
Spatial Organization ◽  
Quantitative Imaging ◽  
Origin Of Replication ◽  
Circular Chromosome ◽  
E Coli ◽  
Domain Boundaries ◽  
Transcription Regulators ◽  
And Function ◽  
Organizational Principles ◽  
Dna Density

New assays for quantitative imaging1–6 and sequencing7–11 have yielded great progress towards understanding the organizational principles of chromosomes. Yet, even for the well-studied model bacterium Escherichia coli, many basic questions remain unresolved regarding chromosomal (sub-)structure2,11, its mechanics1,2,12 and dynamics13,14, and the link between structure and function1,15,16. Here we resolve the spatial organization of the circular chromosome of bacteria by directly imaging the chromosome in live E. coli cells with a broadened cell shape. The chromosome was observed to exhibit a torus topology with a 4.2 μm toroidal length and 0.4 μm bundle thickness. On average, the DNA density along the chromosome shows dense right and left arms that branch from a lower-density origin of replication, and are connected at the terminus of replication by an ultrathin flexible string of DNA. At the single-cell level, the DNA density along the torus is found to be strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. We show that prominent domain boundaries at the terminus and origin of replication are induced by MatP proteins, while weaker transient domain boundaries are facilitated by the global transcription regulators HU and Fis. These findings provide an architectural basis for the understanding of the spatial organization of bacterial genomes.

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