Perspective and Guidelines for Metaproteomics in Microbiome Studies

Zhang, Xu; Figeys, Daniel

doi:10.1021/acs.jproteome.9b00054

Cited by 84 publications

(98 citation statements)

References 87 publications

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“…Hence, the metaproteomic readouts can also be used to assess the microbiome biomass and analyze community structure [23]. Metaproteomics has been previously validated to estimate the microbiome and individual microbe biomasses [24], and it readily quantifies the bacterial species responsible for > 90% of the total microbiome biomass [25], making it sufficient for a fast-pass drug screening application.…”

Section: Introductionmentioning

confidence: 99%

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

et al. 2020

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Background: Human-targeted drugs may exert off-target effects or can be repurposed to modulate the gut microbiota. However, our understanding of such effects is limited due to a lack of rapid and scalable assay to comprehensively assess microbiome responses to drugs. Drugs and other compounds can drastically change the overall abundance, taxonomic composition, and functions of a gut microbiome.Results: Here, we developed an approach to screen compounds against individual microbiomes in vitro, using metaproteomics to both measure absolute bacterial abundances and to functionally profile the microbiome. Our approach was evaluated by testing 43 compounds (including 4 antibiotics) against 5 individual microbiomes. The method generated technically highly reproducible readouts, including changes of overall microbiome abundance, microbiome composition, and functional pathways. Results show that besides the antibiotics, the compounds berberine and ibuprofen inhibited the accumulation of biomass during in vitro growth of the microbiota. By comparing genus and species level-biomass contributions, selective antibacterial-like activities were found with 35 of the 39 non-antibiotic compounds. Seven of the compounds led to a global alteration of the metaproteome, with apparent compound-specific patterns of functional responses. The taxonomic distributions of altered proteins varied among drugs, i.e., different drugs affect functions of different members of the microbiome. We also showed that bacterial function can shift in response to drugs without a change in the abundance of the bacteria.Conclusions: Current drug-microbiome interaction studies largely focus on relative microbiome composition and microbial drug metabolism. In contrast, our workflow enables multiple insights into microbiome absolute abundance and functional responses to drugs. The workflow is robust, reproducible, and quantitative and is scalable for personalized high-throughput drug screening applications.

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Section: Introductionmentioning

confidence: 99%

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

et al. 2020

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“…It has been validated that metaproteomics is a good estimator of biomass contributions of microbiome members [22]. Despite its coverage could not compare to that of the genomic sequencing-based technologies, metaproteomics could confidently quantify proteins of the bacterial species that constitute>90% of the total biomass [23], making it sufficient for a fast-pass drug screening application.…”

Section: Introductionmentioning

confidence: 99%

RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

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et al. 2019

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13Background: Human-targeted drugs may exert off-target effects on the gut microbiota. 14 However, our understanding of such effects is limited due to a lack of rapid and scalable assay to 15 comprehensively assess microbiome responses to drugs. Drugs can drastically change the overall 16 microbiome abundance, microbial composition and functions of a gut microbiome. Although we 17 could comprehensively observe these microbiome responses using a series of tests, for the 18 purpose of a drug screening, it is important to decrease the number of analytical tools used. 19 Results: Here, we developed an approach to screen compounds against individual microbiomes 20 in vitro using metaproteomics adapted for both absolute bacterial abundances and functional 21 profiling of the microbiome. Our approach was evaluated by testing 43 compounds (including 22 four antibiotics) against five individual microbiomes. The method generated technically highly 23 reproducible readouts, including changes of overall microbiome abundance, microbiome 24 composition and functional pathways. Results show that besides the antibiotics, compounds 25 berberine and ibuprofen inhibited the accumulation of biomass during in vitro growth of the 26 microbiome. By comparing genus and species level-biomass contributions, selective 27 antibacterial-like activities were found with 36 of the 39 non-antibiotic compounds. Seven of our 28 compounds led to a global alteration of the metaproteome, with apparent compound-specific 29 patterns of functional responses. The taxonomic distributions of responded proteins varied 30 among drugs, i.e. different drugs affect functions of different members of the microbiome. We 31 also showed that bacterial function can shift in response to drugs without a change in the 32 abundance of the bacteria.33Conclusions: Current drug-microbiome interaction studies largely focus on relative microbiome 34 composition and microbial drug metabolism. In contrast, our workflow enables multiple insights 35 into microbiome absolute abundance and functional responses to drugs using metaproteomics as 36 the one-stop screening tool. The workflow is robust, reproducible and quantitative, and is 37 scalable for personalized high-throughput drug screening applications. 38

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“…Bioinformatics is an integral part of proteomics research (Goh, 2018). For protein identification, bottom‐up metaproteomics requires taxonomy‐specific peptides for microbial community identification, quantification, functional annotation, and biological classification or metabolic analysis (Zhang & Figeys, 2019b). Several bioinformatics analysis software and platforms are available, such as Unipept (Gurdeep Singh et al., 2019), MetaLab (Cheng et al., 2017), ProteoStorm (Beyter, Lin, Yu, Pieper, & Bafna, 2018), and Galaxy (Jagtap et al., 2015).…”

Section: Metaproteomics Analysis Methodsmentioning

confidence: 99%

Metaproteomics insights into traditional fermented foods and beverages

Yang

Fan

2020

Comp Rev Food Sci Food Safe

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Traditional fermented foods and beverages (TFFB) are important dietary components. Multi‐omics techniques have been applied to all aspects of TFFB research to clarify the composition and nutritional value of TFFB, and to reveal the microbial community, microbial interactions, fermentative kinetics, and metabolic profiles during the fermentation process of TFFB. Because of the advantages of metaproteomics in providing functional information, this technology has increasingly been used in research to assess the functional diversity of microbial communities. Metaproteomics is gradually gaining attention in the field of TFFB research because it can reveal the nature of microorganism function at the protein level. This paper reviews the common methods of metaproteomics applied in TFFB research; systematically summarizes the results of metaproteomics research on TFFB, such as sauces, wines, fermented tea, cheese, and fermented fish; and compares the differences in conclusions reached through metaproteomics versus other omics methods. Metaproteomics has great advantages in revealing the microbial functions in TFFB and the interaction between the materials and microbial community. In the future, metaproteomics should be further applied to the study of functional protein markers and protein interaction in TFFB; multi‐omics technology requires further integration to reveal the molecular nature of TFFB fermentation.

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Perspective and Guidelines for Metaproteomics in Microbiome Studies

Cited by 84 publications

References 87 publications

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

RapidAIM: A culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

Metaproteomics insights into traditional fermented foods and beverages

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