Recent advances in tools to map the microbiome

Shi, Hao; Grodner, Benjamin; Vlaminck, Iwijn De

doi:10.1016/j.cobme.2021.100289

Cited by 13 publications

(9 citation statements)

References 61 publications

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“…Advances in DNA sequencing and bioinformatics have enabled an increased understanding of gut microbiota architecture and function [ 3 ]. Bacteria are by far the dominant microbe within the microbiota architecture, but other microbes include viruses, fungi and archaea [ 4 ].…”

Section: Microbiota Structurementioning

confidence: 99%

Gut Microbes and Neuropathology: Is There a Causal Nexus?

Dinan

2022

Pathogens

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The gut microbiota is a virtual organ which produces a myriad of molecules that the brain and other organs require. Humans and microbes are in a symbiotic relationship, we feed the microbes, and in turn, they provide us with essential molecules. Bacteroidetes and Firmicutes phyla account for around 80% of the total human gut microbiota, and approximately 1000 species of bacteria have been identified in the human gut. In adults, the main factors influencing microbiota structure are diet, exercise, stress, disease and medications. In this narrative review, we explore the involvement of the gut microbiota in Parkinson’s disease, Alzheimer’s disease, multiple sclerosis and autism, as these are such high-prevalence disorders. We focus on preclinical studies that increase the understanding of disease pathophysiology. We examine the potential for targeting the gut microbiota in the development of novel therapies and the limitations of the currently published clinical studies. We conclude that while the field shows enormous promise, further large-scale studies are required if a causal link between these disorders and gut microbes is to be definitively established.

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Section: Microbiota Structurementioning

confidence: 99%

Gut Microbes and Neuropathology: Is There a Causal Nexus?

Dinan

2022

Pathogens

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“…In such circumstances, the use of system-specific sequencing may be necessary to characterize the microbial community at sufficient taxonomic resolution to determine how many relevant species are present and in what proportions. While just a few years ago this may have been costly and challenging, recent advances in sequencing technology and simultaneous reductions in cost have now made this an accessible and routine task. , …”

Section: Emerging Opportunities For Phage-based Biocontrolmentioning

confidence: 99%

“…While just a few years ago this may have been costly and challenging, recent advances in sequencing technology and simultaneous reductions in cost have now made this an accessible and routine task. 26,27 Beyond knowledge of the microbial community composition, phage-based approaches benefit from detailed knowledge of the target bacterium, recognizing that major functional differences can exist between strains of the same bacterial species. For example, E. coli Nissle 1917 is a probiotic strain used to treat inflammatory intestinal diseases, 28 while E. coli O157:H7 is a serotype that causes severe, acute hemorrhagic diarrhea.…”

Section: ■ Introductionmentioning

confidence: 99%

Renaissance for Phage-Based Bacterial Control

Schwarz

Mathieu

Gomez

et al. 2021

Environ. Sci. Technol.

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Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.

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“…Understanding the human microbiota ecology is a challenging task but with enormous envisioned value for medical purposes. , Host colonization models have been built by (i) imaging transparent animals, such as Caenorhabditis elegans and zebrafish, ,, (ii) DNA sequencing of laser capture microdissections of ex vivo discrete gut regions of mice, or (iii) mapping of microbes in ex vivo organs using confocal microscopy . However, even animal models expressing human phenotypes are still limited to fully understand the complexity of host–microbe interactions due to the evident distinct anatomical, physiological, or immune features. − …”

Section: Discussionmentioning

confidence: 99%

“…The human body is a reservoir of complex microbial communities that establish host–microbe interactions with profound implications in health and disease . As our understanding of host–microbe ecology improves, it is expected that the microbiota will become a valuable resource for novel diagnostic and therapeutic approaches. , As a consequence, the human microbiome has been extensively characterized in the last decades, providing detailed information regarding the diversity and abundance of microbial communities. − Biopsy samples collected from patients have also provided snapshots of the spatial distribution of microorganisms before downstream characterization. ,, However, studying gut microbiota in biopsy samples has several limitations such as the laxative preparation of the bowel that significantly changes microbiota, insufficient biomass, contaminations while handling the samples, and risk of bleeding and infection. This strategy is also unsuitable for the examination of microbiota in healthy volunteers due to the invasive character of the technique …”

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confidence: 99%

Liposome Delivery of Nucleic Acids in Bacteria: Toward In Vivo Labeling of Human Microbiota

et al. 2022

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Development of specific probes to study the in vivo spatial distribution of microorganisms is essential to understand the ecology of human microbiota. Herein, we assess the possibility of using liposomes loaded with fluorescently labeled nucleic acid mimics (LipoNAMs) to image Gram-negative and Gram-positive bacteria. We proved that liposome fusion efficiencies were similar in both Gram-negative and Gram-positive bacteria but that the efficiency was highly dependent on the lipid concentration. Notably, LipoNAMs were significantly more effective for the internalization of oligonucleotides in bacteria than the fixation/permeabilization methods commonly used in vitro. Furthermore, a structural and morphological assessment of the changes on bacteria allowed us to observe that liposomes increased the permeability of the cell envelope especially in Gram-negative bacteria. Considering the delivery efficiency and permeabilization effect, lipid concentrations of approximately 5 mM should be selected to maximize the detection of bacteria without compromising the bacterial cellular structure.

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Recent advances in tools to map the microbiome

Cited by 13 publications

References 61 publications

Gut Microbes and Neuropathology: Is There a Causal Nexus?

Gut Microbes and Neuropathology: Is There a Causal Nexus?

Renaissance for Phage-Based Bacterial Control

Liposome Delivery of Nucleic Acids in Bacteria: Toward In Vivo Labeling of Human Microbiota

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