Imaging Commensal Microbiota and Pathogenic Bacteria in the Gut

Lin, Liang; Du, Yahui; Song, Jia; Wang, Wei; Yang, Chaoyong

doi:10.1021/acs.accounts.1c00068

Cited by 52 publications

(36 citation statements)

References 62 publications

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“…Here, we fill this fundamental gap in our knowledge by harnessing the power of microfluidics-microscopy ( Łapińska et al, 2019 ; Cama et al, 2020 ) combined with fluorescent antibiotic-derived probes ( Stone et al, 2018 ; Lin et al, 2021 ; Blaskovich et al, 2019 ) as well as unlabelled antibiotics. This approach allows us to examine the interactions between the major classes of antibiotics and hundreds of live individual bacteria in real-time whilst they are being dosed with the drugs.…”

Section: Introductionmentioning

confidence: 99%

Fast bacterial growth reduces antibiotic accumulation and efficacy

Łapińska

Voliotis

Lee

et al. 2022

eLife

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Phenotypic variations between individual microbial cells play a key role in the resistance of microbial pathogens to pharmacotherapies. Nevertheless, little is known about cell individuality in antibiotic accumulation. Here, we hypothesise that phenotypic diversification can be driven by fundamental cell-to-cell differences in drug transport rates. To test this hypothesis, we employed microfluidics-based single-cell microscopy, libraries of fluorescent antibiotic probes and mathematical modelling. This approach allowed us to rapidly identify phenotypic variants that avoid antibiotic accumulation within populations of Escherichia coli, Pseudomonas aeruginosa, Burkholderia cenocepacia, and Staphylococcus aureus. Crucially, we found that fast growing phenotypic variants avoid macrolide accumulation and survive treatment without genetic mutations. These findings are in contrast with the current consensus that cellular dormancy and slow metabolism underlie bacterial survival to antibiotics. Our results also show that fast growing variants display significantly higher expression of ribosomal promoters before drug treatment compared to slow growing variants. Drug-free active ribosomes facilitate essential cellular processes in these fast-growing variants, including efflux that can reduce macrolide accumulation. We used this new knowledge to eradicate variants that displayed low antibiotic accumulation through the chemical manipulation of their outer membrane inspiring new avenues to overcome current antibiotic treatment failures.

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Section: Introductionmentioning

confidence: 99%

Fast bacterial growth reduces antibiotic accumulation and efficacy

Łapińska

Voliotis

Lee

et al. 2022

eLife

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“…Some antibiotics function by directly binding to a specific bacterial surface structure, thus providing the opportunity to use these drugs as probes for bacteria [ 115 ]. Fluorophore-derivatized antibiotics probes retaining bacterial-binding ability have been a handy tool in isolating bacteria and have been utilized in tracking different bacterial species both in vitro and in vivo [ 116 ].…”

Section: Introductionmentioning

confidence: 99%

Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation

et al. 2022

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Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes.

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“…Comparative analyses of the silkworm gut microbiome revealed that the gut microbiota compositions and abundance were changed dramatically after N. bombycis infection, and these differences might be associated with the gut health of the host 50,51 . The occurrence and codiversity pattern of the silkworm gut microbiota was significantly altered by N. bombycis .…”

Section: Discussionmentioning

confidence: 99%

“…48,49 Comparative analyses of the silkworm gut microbiome revealed that the gut microbiota compositions and abundance were changed dramatically after N. bombycis infection, and these differences might be associated with the gut health of the host. 50,51 The occurrence and codiversity pattern of the silkworm gut microbiota was significantly altered by N. bombycis. High microbial diversity can improve community stability, which may explain why a more intertwined and complex network was present in samples with healthy silkworms.…”

Section: Discussionmentioning

confidence: 99%

The gut commensal bacterium Enterococcus faecalis LX10 contributes to defending against Nosema bombycis infection in Bombyx mori

Zhang

Feng

et al. 2022

Pest Management Science

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BACKGROUND: Microsporidia, a group of obligate intracellular fungal-related parasites, have been used as efficient biocontrol agents for agriculture and forestry pests due to their host specificity and transovarial transmission. They mainly infect insect pests through the intestinal tract, but the interactions between microsporidia and the gut microbiota of the host have not been well demonstrated.RESULTS: Based on the microsporidia-Bombyx mori model, we report that the susceptibility of silkworms to exposure to the microsporidium Nosema bombycis was both dose and time dependent. Comparative analyses of the silkworm gut microbiome revealed substantially increased abundance of Enterococcus belonging to Firmicutes after N. bombycis infection. Furthermore, a bacterial strain (LX10) was obtained from the gut of B. mori and identified as Enterococcus faecalis based on 16S rRNA sequence analysis. E. faecalis LX10 reduced the N. bombycis spore germination rate and the infection efficiency in vitro and in vivo, as confirmed by bioassay tests and histopathological analyses. In addition, after simultaneous oral feeding with E. faecalis LX10 and N. bombycis, gene (Akirin, Cecropin A, Mesh, Ssk, DUOX and NOS) expression, hydrogen peroxide and nitric oxide levels, and glutathione S-transferase (GST) activity showed different degrees of recovery and correction compared with those under N. bombycis infection alone. Finally, the enterococcin LX protein was identified from sterile LX10 fermentation liquid based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis.CONCLUSION: Altogether, the results revealed that E. faecalis LX10 with anti-N. bombycis activity might play an important role in protecting silkworms from microsporidia. Removal of these specific commensal bacteria with antibiotics and utilization of transgenic symbiotic systems may effectively improve the biocontrol value of microsporidia.

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Imaging Commensal Microbiota and Pathogenic Bacteria in the Gut

Abstract: Integrative use of sequential D-amino acid metabolic labeling and FISH staining revealed the in vivo growth and division patterns of mouse gut bacteria, including those that have never been cultured or studied in vitro.

Cited by 52 publications

References 62 publications

Fast bacterial growth reduces antibiotic accumulation and efficacy

Fast bacterial growth reduces antibiotic accumulation and efficacy

Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation

The gut commensal bacterium Enterococcus faecalis LX10 contributes to defending against Nosema bombycis infection in Bombyx mori

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