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The biogeography of infection revisited

Abstract

Many microbial communities, including those involved in chronic human infections, are patterned at the micron scale. In this Review, we summarize recent work that has defined the spatial arrangement of microorganisms in infection and begun to demonstrate how changes in spatial patterning correlate with disease. Advances in microscopy have refined our understanding of microbial micron-scale biogeography in samples from humans. These findings then serve as a benchmark for studying the role of spatial patterning in preclinical models, which provide experimental versatility to investigate the interplay between biogeography and pathogenesis. Experimentation using preclinical models has begun to show how spatial patterning influences the interactions between cells, their ability to coexist, their virulence and their recalcitrance to treatment. Future work to study the role of biogeography in infection and the functional biogeography of microorganisms will further refine our understanding of the interplay of spatial patterning, pathogen virulence and disease outcomes.

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Fig. 1: Polymicrobial biogeography can determine the severity of disease and treatment outcomes.
Fig. 2: Microbiogeography of human-associated microbial communities is the benchmark for in vitro preclinical models.
Fig. 3: Preclinical in vitro model SCFM2 provides a platform to study biological implications of microbiogeography.

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Acknowledgements

The authors thank the Cystic Fibrosis foundation for a postdoctoral fellowship to S.A. (AZIMI18F0); the National Institutes of Health (NIH) for funding to G.R.L. (F32DE027281 and K99DE031018); and NIH Grants R01DE023193, R01DE020100 and 1R01GM116547 and a grant from the Shurl and Kay Curci Foundation to M.W.

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Correspondence to Marvin Whiteley.

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Nature Reviews Microbiology thanks Gary Borisy, Kevin Foster, Nicholas Jakubovics and Jessica Mark Welch for their contribution to the peer review of this work.

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Glossary

Biogeography

The spatial assembly and distribution of various organisms in an environment through time.

Microbiogeography

The spatial patterning of microorganisms at the micron scale within a single environment.

Quorum sensing

The detection of an increased concentration of small signal molecules at high cell density, which can control gene expression in bacterial populations.

Cystic fibrosis

A disorder that is caused by mutation(s) in the cystic fibrosis transmembrane conductance regulator gene, which affects cells that produce mucus, sweat and digestive enzymes. In people with cystic fibrosis, the build-up of mucus in the airways results in chronic polymicrobial lung infections.

Function

A physiological property of a bacterium, such as glucose catabolism or motility.

Catalysed reporter deposition FISH

(CARD-FISH). In CARD-FISH, the nucleotide probe is conjugated to horseradish peroxidase that amplifies the fluorescence in situ hybridization (FISH) signal. This method is used for bacterial taxa or bacterial functions with inherently low signal, for example bacteria with low ribosome content.

Double labelling of oligonucleotide probes FISH

(DOPE-FISH). DOPE-FISH uses 5′ and 3′ double-labelled oligonucleotide probes to increase the fluorescence in situ hybridization (FISH) signal.

Combinatorial labelling and spectral imaging FISH

(CLASI-FISH). Simultaneous fluorescence in situ hybridization (FISH) labelling of individual taxa using multiple fluorophores. By mixing the fluorophore combinations used for each taxon, this method enables the detection of tens to hundreds of taxa concurrently. Spectral imaging is usually followed by linear unmixing analysis to differentiate between taxa.

Alginate

An exopolysaccharide produced by Pseudomonas aeruginosa that helps cells to attach to surfaces and form biofilms.

Extracellular DNA

(eDNA). eDNA can be produced by host cells or bacteria. It is one of the main components of the biofilm matrix that can provide structural scaffold for bacterial cells and may play a role in protecting bacterial cells in response to host cells and antibiotics.

NETosis

Neutrophil extracellular traps (NETs) are nucleic acid and intracellular components that are forced out of polymorphonuclear leukocytes in response to microorganisms and proinflammatory cytokines. NETosis is a type of programmed cell death in polymorphonuclear leukocytes such as neutrophils that functions as cellular defence. During NETosis, cells force out their chromatin, forming sticky traps that can trap bacterial cells.

Mucin

A type of high molecular weight glycosylated protein produced by epithelial cells in animals that forms gels and is found in high levels in lung infections. Bovine and porcine mucins can be purchased commercially, which has led to their use in numerous preclinical models.

Hybridization chain reaction

The detection and quantification of RNA transcripts using exogenously added fluorophore-conjugated DNA hairpins. These hairpins self-assemble, amplifying their signal.

Coagulase

An enzyme produced by several types of bacteria that converts the soluble protein fibrinogen in blood to insoluble fibrin, leading to clot formation.

Preclinical infection models

In vitro and in vivo models used to study microbial infection.

Raman microscopy

A combination of laser-based imaging and Raman spectroscopy to detect the differential excitation levels of photons. This method is used to identify certain molecules without disturbing the spatial arrangement of the samples.

Atomic force microscopy

A powerful imaging technique that uses a fine and specific tip attached to a cantilever that scans along the surface of a sample. The changes in contact forces between the tip and the surface of the sample are recorded by a laser beam that generates an accurate topographic image of the surface at nanometre resolution.

Surface plasmon resonance imaging

A label-free imaging method that is used to detect and measure the attachment level and surface properties of bacterial biofilms. This method analyses changes in the angle of reflected light of a surface covered with the sample of interest, compared with a control surface.

Scanning electrochemical microscopy

A label-free microscopy method using probes that detect redox reactions and can provide an electrochemical map of an environment.

Imaging mass spectrometry

Mass spectrometry performed across a spatial plane to build a map of detected chemicals.

Hydroxyapatite

A mineral form of calcium apatite that is the main component of tooth enamel and bones.

Fibrin

A glycosylated protein in blood formed by the enzymatic action of a serine protease on soluble fibrinogen. Polymerized fibrin leads to clotting of the blood.

Transferrin

A glycoprotein that binds to iron and transports iron through the bloodstream.

Keratinocyte

A cell that forms the outer layer of skin and produces keratin to form a protective barrier.

Organoid

A small, differentiated collection of cells containing similar cell types and functions as an organ. Organoids are produced in vitro using stem cells derived from the organ of interest that are cultured in a medium containing growth factors and extracellular matrix.

Organ-on-a-chip

A cell culture device that contains a multichannel 3D microfluidics chip, designed to mimic the physical and chemical properties of an organ. Organ-on-a-chip models can provide a structured microenvironment for high-throughput assessment of bacterial–host interactions, for instance in response to various stimuli.

Glycol methacrylate resin

An ester form of epoxy resin that can be used instead of paraffin for embedding biological samples for better quality imaging.

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Azimi, S., Lewin, G.R. & Whiteley, M. The biogeography of infection revisited. Nat Rev Microbiol 20, 579–592 (2022). https://doi.org/10.1038/s41579-022-00683-3

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