Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease

Figures & data

Table 1. Tools for characterizing the IBD Microbiome.

Technology	Tool description	Relevance to IBD	Drawbacks
Experimental Methods
IgA-Seq	Flow cytometry method that allows bacteria coated with IgA to be separated from bulk and identified by sequencing methods.^Citation6–10	Identified increased levels of IgA-coating in IBD and differential binding of pathobionts^Citation7,Citation11,Citation12 i.e. invasive E.coli in CD patients.^Citation13 Disrupted IgA recognition of pathogenic morphologies of C.albicans.^Citation14	This technique captures immune-recognized microbes, but discrimination of pathobionts from commensals can be challenging.
GC/MS and LC/MS	Mass spectrometry methods facilitating the characterization of the metabolic environment in the gut.	Identification of metabolomic biomarkers for IBD.^Citation5,Citation15 Identified lower levels of short-chain fatty acids,^Citation16–19 tryptophan,^Citation20–22 and bile acid^Citation23,Citation24 metabolism in IBD.	Sample preparation influences which metabolites are extracted, ionized and detected.^Citation25 Instrument differences can impact molecular resolution, and method of choice (targeted vs untargeted) affects specificity, sensitivity and quantification.^Citation26
SCFA Derivatization	SCFAs are small and volatile, which makes identification difficult with traditional GC/MS approaches. New derivatization techniques have recently been developed to improve SCFA quantification.^Citation27–32	SCFAs play a role in numerous cellular and immunological processes, such as stimulating the production of mucins, reducing intestinal permeability and promoting anti-inflammatory pathways.^Citation33 Restoration of SCFA via direct administration or restoration of their microbial producers are being explored as therapeutics for IBD.^Citation34–36	Time-consuming, and can affect simultaneous measurement of SCFAs and other molecules in the samples.^Citation28
Ultrahigh-Performance metabolomics to detect low abundant Trp metabolites	Liquid chromatography tandem mass spectrometry with electrospray ionization (UHPLC-ESI-MS/MS) was recently designed to study Trp metabolites. Offers better resolution and allows measurement of low-abundance metabolites downstream of Trp metabolism.^Citation37	Some common metabolomic methods focus on major metabolites, but other less-abundant downstream-metabolic products are also altered in IBD.^Citation20,Citation38	High cost. Some metabolites may be unstable in solution. May need optimization to increase confidence in the concentration of certain metabolites.^Citation37
Computational Methods
Strain-level identification of bacteria	MetaPhlAn2/3,^Citation39,Citation40 Kraken2,^Citation41 Strainer,^Citation42 StrainFinder,^Citation43 mOTUs,^Citation44 inStrain.^Citation45	MetaPhlAn2 has been applied to IBD cohort data to identify and define IBD-like consortia^Citation15,Citation46–48 and predict treatment response.^Citation49	Data processing by different metagenomic pipelines can lead to radically different results.
Fungi identification	FindFungi,^Citation50 HumanMycobiomeScan,^Citation51 CCMetagen.^Citation52	Early work indicates that Fungi may play a role in IBD’s onset and progression.^Citation53–56	These methods are largely untested on IBD datasets. Most data on the IBD mycobiome has been analyzed using custom pipelines.
Viral identification	PhiSpy,^Citation57 VirSorter,^Citation58 PHASTER.^Citation59	Recent work shows that the IBD virome may show increased viral diversity and abundance.^Citation60–67	These methods are largely untested on IBD datasets. Most data on the IBD virome has been analyzed using custom pipelines.
Microbial network analysis	SparCC,^Citation68 SPIEC-EASI^Citation69 and MENAP,^Citation70 MDSINE.^Citation71	Network analysis implicated E.coli and O. formigenes as IBD-associated taxa.^Citation72	The use of cross-sectional data can mean that microbial networks in different states may be compared and combined into a single network. Time series data allows the application of the Lotka-Volterra framework, though this approach is vulnerable to changes in absolute abundance.

Figure 1. Opportunities for microbiome therapeutics in IBD. a. Fecal Microbiota Transplant (FMT) transplants whole microbial communities from healthy donors into IBD patients and has shown promising results particularly in the treatment of UC. b. Bacterial engineering can be used to enhance the beneficial properties of bacterial strains, including targeted delivery of therapeutic molecules, which offers important efficacy and safety advantages compared to the use of FMTs or molecules delivered systemically. c. Phage therapy or “decolonization”, currently being explored for CD and UC, selectively targets and removes specific bacteria associated with disease, without disrupting other members of the gut microbiota. d. Biologic therapies, which can induce clinical and histological healing, are the current standard of care in IBD. Lack of response, development of resistance and side effects remain challenges for some patients. e. The aberrant microbiome of IBD patients has a reduced capacity to produce metabolites that modulate intestinal homeostasis. Direct administration or modulation of the microbiome to enhance the production of such metabolites is being explored as potential therapeutics for IBD. f. Microbial consortia designed to induce specific immune responses are also being investigated as therapeutics in animal models and pioneered in human studies. Image created with BioRender.com.

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