Metaproteomic strategies and applications for gut microbial research

Xiao, Mingming; Yang, Jing; Feng, Yi; Zhu, Yan; Chai, Xin; Wang, Yuefei

doi:10.1007/s00253-017-8215-7

Cited by 31 publications

(24 citation statements)

References 97 publications

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“…Metabolomics is currently considered as the most appropriate omics technology to investigate complex, polygenic, and multifactorial diseases with a strong multisystemic metabolic nature which have been successfully used to investigate functional changes after RYGB [20][21][22]. Recently, several studies have shown that metaproteomics which involves the high-throughput characterisation of the entire constituent profile of microbial proteins provides promising insights of functional aspects in microbiome research [23][24][25].…”

Section: Introductionmentioning

confidence: 99%

Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss

et al. 2020

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Background: Roux-en-Y gastric bypass (RYGB) surgery is a last-resort treatment to induce substantial and sustained weight loss in cases of severe obesity. This anatomical rearrangement affects the intestinal microbiota, but so far, little information is available on how it interferes with microbial functionality and microbial-host interactions independently of weight loss. Methods: A rat model was employed where the RYGB-surgery cohort is compared to sham-operated controls which were kept at a matched body weight by food restriction. We investigated the microbial taxonomy and functional activity using 16S rRNA amplicon gene sequencing, metaproteomics, and metabolomics on samples collected from theileum, the cecum, and the colon, and separately analysed the lumen and mucus-associated microbiota. Results: Altered gut architecture in RYGB increased the relative occurrence of Actinobacteria, especially Bifidobacteriaceae and Proteobacteria, while in general, Firmicutes were decreased although Streptococcaceae and Clostridium perfringens were observed at relative higher abundances independent of weight loss. A decrease of conjugated and secondary bile acids was observed in the RYGB-gut lumen. The arginine biosynthesis pathway in the microbiota was altered, as indicated by the changes in the abundance of upstream metabolites and enzymes, resulting in lower levels of arginine and higher levels of aspartate in the colon after RYGB. Conclusion: The anatomical rearrangement in RYGB affects microbiota composition and functionality as well as changes in amino acid and bile acid metabolism independently of weight loss. The shift in the taxonomic structure of the microbiota after RYGB may be mediated by the resulting change in the composition of the bile acid pool in the gut and by changes in the composition of nutrients in the gut.

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Section: Introductionmentioning

confidence: 99%

Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss

et al. 2020

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“…Recently, metagenomic analyses based on DNA sequencing have provided unprecedented profiling of microbial communities in various environments. However, this approach provides little information about the functions of the communities (18). Metaproteomics, measuring the complete protein composition expressed by a microbial community, can link proteins to specific microbes and thus provide insight into the functions and diversity of microbial communities (18).…”

mentioning

confidence: 99%

“…However, this approach provides little information about the functions of the communities (18). Metaproteomics, measuring the complete protein composition expressed by a microbial community, can link proteins to specific microbes and thus provide insight into the functions and diversity of microbial communities (18). Similarly, metabolomics, characterizing the downstream products of gene expression, depicts the active metabolic pathways and provides information on their importance in biological processes (19).…”

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confidence: 99%

Structural and Functional Changes in Prokaryotic Communities in Artificial Pit Mud during Chinese Baijiu Production

et al. 2020

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The Chinese alcoholic beverage strong-flavor baijiu (SFB) gets its characteristic flavor during fermentation in cellars lined with pit mud. Microbes in the pit mud produce key precursors of flavor esters. The maturation time of natural pit mud of over 20 years has promoted attempts to produce artificial pit mud (APM) with a shorter maturation time. However, knowledge about the molecular basis of APM microbial dynamics and associated functional variation during SFB brewing is limited, and the role of this variability in high-quality SFB production remains poorly understood. We studied APM maturation in new cellars until the fourth brewing batch using 16S rRNA gene amplicon sequencing, quantitative PCR, metaproteomics, and metabolomics techniques. A total of 36 prokaryotic classes and 195 genera were detected. Bacilli and Clostridia dominated consistently, and the relative abundance of Bacilli decreased along with the APM maturation. Even though both amplicon sequencing and quantitative PCR showed increased abundance of Clostridia, the levels of most of the Clostridium proteins were similar in both the first- and fourth-batch APM samples. Six genera correlated with eight or more major flavor compounds in SFB samples. Functional prediction suggested that the prokaryotic communities in the fourth-batch APM samples were actively engaged in organic acid metabolism, and the detected higher concentrations of proteins and metabolites in the corresponding metabolic pathways supported the prediction. This multi-omics approach captured changes in the abundances of specific microbial species, proteins, and metabolites during APM maturation, which are of great significance for the optimization of APM culture technique. IMPORTANCE Strong-flavor baijiu (SFB) accounts for more than 70% of all Chinese liquor production. In the Chinese baijiu brewing industry, artificial pit mud (APM) has been widely used since the 1960s to construct fermentation cellars for production of high-quality SFB. To gain insights at the systems level into the mechanisms driving APM prokaryotic taxonomic and functional dynamics and into how this variation is connected with high-quality SFB production, we performed the first combined metagenomic, metaproteomic, and metabolomic analyses of this brewing microecosystem. Together, the multi-omics approach enabled us to develop a more complete picture of the changing metabolic processes occurring in APM microbial communities during high-quality SFB production, which will be helpful for further optimization of APM culture technique and improvement of SFB quality.

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“…The wide dynamic range of peptide abundances, co-elution limiting detection of low abundance peptides, and difficulties developing sequence databases are even more pronounced in these highly complex systems where hundreds to thousands of different taxa may be present. To address this problem enrichment strategies, sample fractionation, and two-dimensional chromatography have all been employed (Biteen et al 2016; Moon et al 2018; Mayers et al 2017; Gilbert et al 2016, 2018; Xiao et al 2017; Jansson and Hofmockel 2018; Jansson and Baker 2016). However, these steps can dramatically limit the number of samples that can be analyzed.…”

Section: Challenges Of Microbiome Proteomics and How Abpp Can Facilitatementioning

confidence: 99%

Activity-Based Protein Profiling—Enabling Multimodal Functional Studies of Microbial Communities

Whidbey

Wright

2018

Current Topics in Microbiology and Immunology

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Microorganisms living in community are critical to life on Earth, playing numerous and profound roles in the environment and human and animal health. Though their essentiality to life is clear, the mechanistic underpinnings of community structure, interactions, and functions are largely unexplored and in need of function-dependent technologies to unravel the mysteries. Activity-based protein profiling offers unprecedented molecular-level characterization of functions within microbial communities and provides an avenue to determine how external exposures result in functional alterations to microbiomes. Herein, we illuminate the current state and prospective contributions of ABPP as it relates to microbial communities. We provide details on the design, development, and validation of probes, challenges associated with probing in complex microbial communities, provide some specific examples of the biological applications of ABPP in microbes and microbial communities, and highlight potential areas for development. The future of ABPP holds real promise for understanding and considerable impact in microbiome studies associated with personalized medicine, precision agriculture, veterinary health, environmental studies, and beyond.

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Metaproteomic strategies and applications for gut microbial research

Cited by 31 publications

References 97 publications

Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss

Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss

Structural and Functional Changes in Prokaryotic Communities in Artificial Pit Mud during Chinese Baijiu Production

Activity-Based Protein Profiling—Enabling Multimodal Functional Studies of Microbial Communities

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