1
|
Chu DT, Vu TQ, Bui NL, Thi HV, Vu TD, Hoang DA, Van TT, Truong DT. Variation in body weight, glucose/insulin tolerances, blood lipids and liver enzymes in mice in response to a high-fat-diet from lard. Biochem Biophys Res Commun 2024; 733:150430. [PMID: 39043000 DOI: 10.1016/j.bbrc.2024.150430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024]
Abstract
It raises questions about the impact of lard on the health and the differences in individual responses. Therefore, we developed a model of mice fed with high fat (HF) from lard in 130 days. The weight of the mice was measured every two days. Glucose tolerance test and insulin tolerance tests were performed at 70 days and 130 days of experiment. At the end of the study, the fat tissue was collected to check the weight, and a blood sample was collected to check the blood lipids and liver enzymes. Surprisingly, mice responded variously to the HF by being classified into two groups, one group had significantly high gained weight (HG_HF) versus the mice fed a standard diet (STD) (p < 0.001), and another group (LG_HF) has not difference in body weight compared to the STD groups. This phenomenon in body weight is directly reflected by the white fat accumulation, but not by brown fat. Eating HF from lard for a long time can disrupt glucose tolerance and cause dyslipidemia in mice, even in the LG_HF group, but can not disrupt insulin tolerance and cause liver enzyme disorders. In summary, our findings are a wake-up call for many cases where eating HF from lard does not gain weight and not increase the white fat storage, but still has the potential to cause adverse health effects. Further studies are encouraged to understand the molecular mechanisms that causes the body to regulate its weight and responses when eating HF from lard, especially in the LG_HF group.
Collapse
Affiliation(s)
- Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Viet Nam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Viet Nam.
| | - Tri-Quang Vu
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Viet Nam
| | - Nhat-Le Bui
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Viet Nam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Viet Nam
| | - Hue-Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Viet Nam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Viet Nam
| | - Thuy-Duong Vu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Viet Nam
| | - Duc-Anh Hoang
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Viet Nam
| | - Thai Than Van
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Viet Nam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Viet Nam
| | - Dang Tien Truong
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Viet Nam
| |
Collapse
|
2
|
Tan J, Fu B, Zhao X, Ye L. Novel Techniques and Models for Studying the Role of the Gut Microbiota in Drug Metabolism. Eur J Drug Metab Pharmacokinet 2024; 49:131-147. [PMID: 38123834 DOI: 10.1007/s13318-023-00874-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
The gut microbiota, known as the second human genome, plays a vital role in modulating drug metabolism, significantly impacting therapeutic outcomes and adverse effects. Emerging research has elucidated that the microbiota mediates a range of modifications of drugs, leading to their activation, inactivation, or even toxication. In diverse individuals, variations in the gut microbiota can result in differences in microbe-drug interactions, underscoring the importance of personalized approaches in pharmacotherapy. However, previous studies on drug metabolism in the gut microbiota have been hampered by technical limitations. Nowadays, advances in biotechnological tools, such as microbially derived metabolism screening and microbial gene editing, have provided a deeper insight into the mechanism of drug metabolism by gut microbiota, moving us toward personalized therapeutic interventions. Given this situation, our review summarizes recent advances in the study of gut-microbiota-mediated drug metabolism and showcases techniques and models developed to navigate the challenges posed by the microbial involvement in drug action. Therefore, we not only aim at understanding the complex interaction between the gut microbiota and drugs and outline the development of research techniques and models, but we also summarize the specific applications of new techniques and models in researching gut-microbiota-mediated drug metabolism, with the expectation of providing new insights on how to study drug metabolism by gut microbiota.
Collapse
Affiliation(s)
- Jianling Tan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Bingxuan Fu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xiaojie Zhao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Ling Ye
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| |
Collapse
|
3
|
Kumar B, Lorusso E, Fosso B, Pesole G. A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions. Front Microbiol 2024; 15:1343572. [PMID: 38419630 PMCID: PMC10900530 DOI: 10.3389/fmicb.2024.1343572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition and functional potential. However, a critical challenge in this field is the lack of standard and comprehensive metadata associated with raw data, hindering the ability to perform robust data stratifications and consider confounding factors. In this comprehensive review, we categorize publicly available microbiome data into five types: shotgun sequencing, amplicon sequencing, metatranscriptomic, metabolomic, and metaproteomic data. We explore the importance of metadata for data reuse and address the challenges in collecting standardized metadata. We also, assess the limitations in metadata collection of existing public repositories collecting metagenomic data. This review emphasizes the vital role of metadata in interpreting and comparing datasets and highlights the need for standardized metadata protocols to fully leverage metagenomic data's potential. Furthermore, we explore future directions of implementation of Machine Learning (ML) in metadata retrieval, offering promising avenues for a deeper understanding of microbial communities and their ecological roles. Leveraging these tools will enhance our insights into microbial functional capabilities and ecological dynamics in diverse ecosystems. Finally, we emphasize the crucial metadata role in ML models development.
Collapse
Affiliation(s)
- Bablu Kumar
- Università degli Studi di Milano, Milan, Italy
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
| | - Erika Lorusso
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Bruno Fosso
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari A. Moro, Bari, Italy
- National Research Council, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| |
Collapse
|
4
|
Pietilä S, Suomi T, Elo LL. Introducing untargeted data-independent acquisition for metaproteomics of complex microbial samples. ISME COMMUNICATIONS 2022; 2:51. [PMID: 37938742 PMCID: PMC9723653 DOI: 10.1038/s43705-022-00137-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/27/2022] [Accepted: 06/14/2022] [Indexed: 05/17/2023]
Abstract
Mass spectrometry-based metaproteomics is a relatively new field of research that enables the characterization of the functionality of microbiota. Recently, we demonstrated the applicability of data-independent acquisition (DIA) mass spectrometry to the analysis of complex metaproteomic samples. This allowed us to circumvent many of the drawbacks of the previously used data-dependent acquisition (DDA) mass spectrometry, mainly the limited reproducibility when analyzing samples with complex microbial composition. However, the DDA-assisted DIA approach still required additional DDA data on the samples to assist the analysis. Here, we introduce, for the first time, an untargeted DIA metaproteomics tool that does not require any DDA data, but instead generates a pseudospectral library directly from the DIA data. This reduces the amount of required mass spectrometry data to a single DIA run per sample. The new DIA-only metaproteomics approach is implemented as a new open-source software package named glaDIAtor, including a modern web-based graphical user interface to facilitate wide use of the tool by the community.
Collapse
Affiliation(s)
- Sami Pietilä
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Tomi Suomi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.
- Institute of Biomedicine, University of Turku, FI-20520, Turku, Finland.
| |
Collapse
|
5
|
Mordant A, Kleiner M. Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes. Microbiol Spectr 2021; 9:e0187721. [PMID: 34908431 PMCID: PMC8672883 DOI: 10.1128/spectrum.01877-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/31/2021] [Indexed: 12/20/2022] Open
Abstract
A critical step in studies of the intestinal microbiome using meta-omics approaches is the preservation of samples before analysis. Preservation is essential for approaches that measure gene expression, such as metaproteomics, which is used to identify and quantify proteins in microbiomes. Intestinal microbiome samples are typically stored by flash-freezing and storage at -80°C, but some experimental setups do not allow for immediate freezing of samples. In this study, we evaluated methods to preserve fecal microbiome samples for metaproteomics analyses when flash-freezing is not possible. We collected fecal samples from C57BL/6 mice and stored them for 1 and 4 weeks using the following methods: flash-freezing in liquid nitrogen, immersion in RNAlater, immersion in 95% ethanol, immersion in a RNAlater-like buffer, and combinations of these methods. After storage, we extracted protein and prepared peptides for liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis to identify and quantify peptides and proteins. All samples produced highly similar metaproteomes, except for ethanol-preserved samples that were distinct from all other samples in terms of protein identifications and protein abundance profiles. Flash-freezing and RNAlater (or RNAlater-like treatments) produced metaproteomes that differed only slightly, with less than 0.7% of identified proteins differing in abundance. In contrast, ethanol preservation resulted in an average of 9.5% of the identified proteins differing in abundance between ethanol and the other treatments. Our results suggest that preservation at room temperature in RNAlater or an RNAlater-like solution performs as well as freezing for the preservation of intestinal microbiome samples before metaproteomics analyses. IMPORTANCE Metaproteomics is a powerful tool to study the intestinal microbiome. By identifying and quantifying a large number of microbial, dietary, and host proteins in microbiome samples, metaproteomics provides direct evidence of the activities and functions of microbial community members. A critical step for metaproteomics workflows is preserving samples before analysis because protein profiles are susceptible to fast changes in response to changes in environmental conditions (air exposure, temperature changes, etc.). This study evaluated the effects of different preservation treatments on the metaproteomes of intestinal microbiome samples. In contrast to prior work on preservation of fecal samples for metaproteomics analyses, we ensured that all steps of sample preservation were identical so that all differences could be attributed to the preservation method.
Collapse
Affiliation(s)
- Angie Mordant
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| |
Collapse
|
6
|
Hardouin P, Chiron R, Marchandin H, Armengaud J, Grenga L. Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives. Genes (Basel) 2021; 12:892. [PMID: 34207804 PMCID: PMC8227082 DOI: 10.3390/genes12060892] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Cystic fibrosis (CF) is a hereditary disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, triggering dysfunction of the anion channel in several organs including the lung and gut. The main cause of morbidity and mortality is chronic infection. The microbiota is now included among the additional factors that could contribute to the exacerbation of patient symptoms, to treatment outcome, and more generally to the phenotypic variability observed in CF patients. In recent years, various omics tools have started to shed new light on microbial communities associated with CF and host-microbiota interactions. In this context, proteomics targets the key effectors of the responses from organisms, and thus their phenotypes. Recent advances are promising in terms of gaining insights into the CF microbiota and its relation with the host. This review provides an overview of the contributions made by proteomics and metaproteomics to our knowledge of the complex host-microbiota partnership in CF. Considering the strengths and weaknesses of proteomics-based approaches in profiling the microbiota in the context of other diseases, we illustrate their potential and discuss possible strategies to overcome their limitations in monitoring both the respiratory and intestinal microbiota in sample from patients with CF.
Collapse
Affiliation(s)
- Pauline Hardouin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, 30207 Bagnols-sur-Cèze, France;
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
| | - Raphael Chiron
- HydroSciences Montpellier, CNRS, IRD, Université de Montpellier, Centre de Ressources et de Compétences de la Mucoviscidose, CHU de Montpellier, 34093 Montpellier, France;
| | - Hélène Marchandin
- HydroSciences Montpellier, CNRS, IRD, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 34093 Nîmes, France;
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200 Bagnols-sur-Cèze, France;
| |
Collapse
|
7
|
Ramírez-Acosta S, Arias-Borrego A, Navarro-Roldán F, Selma-Royo M, Calatayud M, Collado MC, Huertas-Abril PV, Abril N, Barrera TG. Omic methodologies for assessing metal(-loid)s-host-microbiota interplay: A review. Anal Chim Acta 2021; 1176:338620. [PMID: 34399890 DOI: 10.1016/j.aca.2021.338620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 03/12/2021] [Accepted: 04/01/2021] [Indexed: 02/08/2023]
Abstract
Omic methodologies have become key analytical tools in a wide number of research topics such as systems biology, environmental analysis, biomedicine or food analysis. They are especially useful when they are combined providing a new perspective and a holistic view of the analytical problem. Methodologies for microbiota analysis have been mostly focused on genome sequencing. However, information provided by these metagenomic studies is limited to the identification of the presence of genes, taxa and their inferred functionality. To achieve a deeper knowledge of microbial functionality in health and disease, especially in dysbiosis conditions related to metal and metalloid exposure, the introduction of additional meta-omic approaches including metabolomics, metallomics, metatranscriptomics and metaproteomics results essential. The possible impact of metals and metalloids on the gut microbiota and their effects on gut-brain axis (GBA) only begin to be figured out. To this end new analytical workflows combining powerful tools are claimed such as high resolution mass spectrometry and heteroatom-tagged proteomics for the absolute quantification of metal-containing biomolecules using the metal as a "tag" in a sensitive and selective detector (e.g. ICP-MS). This review focus on current analytical methodologies related with the analytical techniques and procedures available for metallomics and microbiota analysis with a special attention on their advantages and drawbacks.
Collapse
Affiliation(s)
- Sara Ramírez-Acosta
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain
| | - Ana Arias-Borrego
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain
| | - Francisco Navarro-Roldán
- Department of Integrated Sciences, Cell Biology, Faculty of Experimental Sciences, University of Huelva, Spain
| | - Marta Selma-Royo
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Marta Calatayud
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Agustin Escardino 7, 46980, Paterna, Valencia, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Agustin Escardino 7, 46980, Paterna, Valencia, Spain.
| | - Paula V Huertas-Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain.
| | - Tamara García Barrera
- Research Center of Natural Resources, Health and the Environment (RENSMA), Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., Huelva, Spain.
| |
Collapse
|
8
|
Tsutaya T, Mackie M, Sawafuji R, Miyabe-Nishiwaki T, Olsen JV, Cappellini E. Faecal proteomics as a novel method to study mammalian behaviour and physiology. Mol Ecol Resour 2021; 21:1808-1819. [PMID: 33720532 PMCID: PMC8360081 DOI: 10.1111/1755-0998.13380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/28/2021] [Accepted: 03/10/2021] [Indexed: 11/30/2022]
Abstract
Mammalian faeces can be collected noninvasively during field research and provide valuable information on the ecology and evolution of the source individuals. Undigested food remains, genome/metagenome, steroid hormones, and stable isotopes obtained from faecal samples provide evidence on diet, host/symbiont genetics, and physiological status of the individuals. However, proteins in mammalian faeces have hardly been studied, which hinders the molecular investigations into the behaviour and physiology of the source individuals. Here, we apply mass spectrometry-based proteomics to faecal samples (n = 10), collected from infant, juvenile, and adult captive Japanese macaques (Macaca fuscata), to describe the proteomes of the source individual, of the food it consumed, and its intestinal microbes. The results show that faecal proteomics is a useful method to: (i) investigate dietary changes along with breastfeeding and weaning, (ii) reveal the taxonomic and histological origin of the food items consumed, and (iii) estimate physiological status inside intestinal tracts. These types of insights are difficult or impossible to obtain through other molecular approaches. Most mammalian species are facing extinction risk and there is an urgent need to obtain knowledge on their ecology and evolution for better conservation strategy. The faecal proteomics framework we present here is easily applicable to wild settings and other mammalian species, and provides direct evidence of their behaviour and physiology.
Collapse
Affiliation(s)
- Takumi Tsutaya
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan.,Biogeochemistry Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Meaghan Mackie
- Evolutionary Genomics Section, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Rikai Sawafuji
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan
| | | | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Evolutionary Genomics Section, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
9
|
Johns MS, Petrelli NJ. Microbiome and colorectal cancer: A review of the past, present, and future. Surg Oncol 2021; 37:101560. [PMID: 33848761 DOI: 10.1016/j.suronc.2021.101560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 11/22/2020] [Accepted: 03/28/2021] [Indexed: 12/27/2022]
Abstract
The gastrointestinal tract is home to diverse and abundant microorganisms, collectively referred to as the microbiome. This ecosystem typically contains trillions of microbial cells that play an important role in regulation of human health. The microbiome has been implicated in host immunity, nutrient absorption, digestion, and metabolism. In recent years, researchers have shown that alteration of the microbiome is associated with disease development, such as obesity, inflammatory bowel disease, and cancer. This review discusses the five decades of research into the human microbiome and the development of colorectal cancer - the historical context including experiments that sparked interest, the explosion of research that has occurred in the last decade, and finally the future of testing and treatment.
Collapse
Affiliation(s)
- Michael S Johns
- Department of Surgical Oncology, Helen F. Graham Cancer Center, ChristianaCare, Newark, DE, USA.
| | - Nicholas J Petrelli
- Department of Surgical Oncology, Helen F. Graham Cancer Center, ChristianaCare, Newark, DE, USA
| |
Collapse
|
10
|
Couvillion SP, Agrawal N, Colby SM, Brandvold KR, Metz TO. Who Is Metabolizing What? Discovering Novel Biomolecules in the Microbiome and the Organisms Who Make Them. Front Cell Infect Microbiol 2020; 10:388. [PMID: 32850487 PMCID: PMC7410922 DOI: 10.3389/fcimb.2020.00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/25/2020] [Indexed: 12/14/2022] Open
Abstract
Even as the field of microbiome research has made huge strides in mapping microbial community composition in a variety of environments and organisms, explaining the phenotypic influences on the host by microbial taxa-both known and unknown-and their specific functions still remain major challenges. A pressing need is the ability to assign specific functions in terms of enzymes and small molecules to specific taxa or groups of taxa in the community. This knowledge will be crucial for advancing personalized therapies based on the targeted modulation of microbes or metabolites that have predictable outcomes to benefit the human host. This perspective article advocates for the combined use of standards-free metabolomics and activity-based protein profiling strategies to address this gap in functional knowledge in microbiome research via the identification of novel biomolecules and the attribution of their production to specific microbial taxa.
Collapse
Affiliation(s)
- Sneha P. Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Neha Agrawal
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Sean M. Colby
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristoffer R. Brandvold
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, United States
| | - Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| |
Collapse
|
11
|
A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota. Sci Rep 2020; 10:12411. [PMID: 32709972 PMCID: PMC7381632 DOI: 10.1038/s41598-020-69241-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 07/08/2020] [Indexed: 01/09/2023] Open
Abstract
Gut microbiota participates in diverse metabolic and homeostatic functions related to health and well-being. Its composition varies between individuals, and depends on factors related to host and microbial communities, which need to adapt to utilize various nutrients present in gut environment. We profiled fecal microbiota in 63 healthy adult individuals using metaproteomics, and focused on microbial CAZy (carbohydrate-active) enzymes involved in glycan foraging. We identified two distinct CAZy profiles, one with many Bacteroides-derived CAZy in more than one-third of subjects (n = 25), and it associated with high abundance of Bacteroides in most subjects. In a smaller subset of donors (n = 8) with dietary parameters similar to others, microbiota showed intense expression of Prevotella-derived CAZy including exo-beta-(1,4)-xylanase, xylan-1,4-beta-xylosidase, alpha-l-arabinofuranosidase and several other CAZy belonging to glycosyl hydrolase families involved in digestion of complex plant-derived polysaccharides. This associated invariably with high abundance of Prevotella in gut microbiota, while in subjects with lower abundance of Prevotella, microbiota showed no Prevotella-derived CAZy. Identification of Bacteroides- and Prevotella-derived CAZy in microbiota proteome and their association with differences in microbiota composition are in evidence of individual variation in metabolic specialization of gut microbes affecting their colonizing competence.
Collapse
|
12
|
Metaproteomic analysis of human gut microbiome in digestive and metabolic diseases. Adv Clin Chem 2020; 97:1-12. [PMID: 32448430 DOI: 10.1016/bs.acc.2019.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metaproteomics, as a subfield of proteomics, has quickly emerged as a pivotal tool for global characterization of a microbiome system at a functional level. It has been increasingly applied in studying human digestive and metabolic diseases, and provides information-rich data to identify the dysbiosis of human gut microbiome related to healthy or disease states to elucidate the molecular events underlying host-microbiota interplays. While significant technical challenges still exist, this emerging technology has been demonstrated to provide essential information in interrogating functional changes in the human gut microbiome, complementary to metagenomics and metatranscriptomics. This chapter overviews the overall metaproteomic work flow and its recent applications in studying human gut microbiome relevant to digestive and metabolic diseases.
Collapse
|
13
|
Kumar P, Johnson JE, Easterly C, Mehta S, Sajulga R, Nunn B, Jagtap PD, Griffin TJ. A Sectioning and Database Enrichment Approach for Improved Peptide Spectrum Matching in Large, Genome-Guided Protein Sequence Databases. J Proteome Res 2020; 19:2772-2785. [DOI: 10.1021/acs.jproteome.0c00260] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Praveen Kumar
- Bioinformatics and Computational Biology, University of Minnesota−Rochester, Rochester, Minnesota 55904, United States
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - James E. Johnson
- Minnesota Supercomputing Institute, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Caleb Easterly
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Subina Mehta
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Ray Sajulga
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Brook Nunn
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Pratik D. Jagtap
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Timothy J. Griffin
- Biochemistry Molecular Biology and Biophysics, University of Minnesota−Twin Cities, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
14
|
Interactions of dietary fat with the gut microbiota: Evaluation of mechanisms and metabolic consequences. Clin Nutr 2020; 39:994-1018. [DOI: 10.1016/j.clnu.2019.05.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/25/2019] [Accepted: 05/01/2019] [Indexed: 12/12/2022]
|
15
|
Haange SB, Jehmlich N, Krügel U, Hintschich C, Wehrmann D, Hankir M, Seyfried F, Froment J, Hübschmann T, Müller S, Wissenbach DK, Kang K, Buettner C, Panagiotou G, Noll M, Rolle-Kampczyk U, Fenske W, von Bergen M. Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss. MICROBIOME 2020; 8:13. [PMID: 32033593 PMCID: PMC7007695 DOI: 10.1186/s40168-020-0788-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/13/2020] [Indexed: 05/02/2023]
Abstract
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. Video abstract.
Collapse
Affiliation(s)
- Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Ute Krügel
- Rudolf Boehm Institute of Pharmacology and Toxicology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Constantin Hintschich
- Neuroendocrine Regulation of Energy Homeostasis Group, IFB Adiposity Diseases, Leipzig, Germany
| | - Dorothee Wehrmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Mohammed Hankir
- Neuroendocrine Regulation of Energy Homeostasis Group, IFB Adiposity Diseases, Leipzig, Germany
- Current address: Department of Experimental Surgery, Wuerzburg University Hospital, Wuerzburg, Germany
| | - Florian Seyfried
- Department of General, Visceral, Vascular and Pediatric Surgery, Wuerzburg University Hospital, Wuerzburg, Germany
| | - Jean Froment
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Thomas Hübschmann
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Dirk K. Wissenbach
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Current address: Institute of Forensic Medicine, Jena University Hospital, Jena, Germany
| | - Kang Kang
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoll Institute, Jena, Germany
| | - Christian Buettner
- Institute for Bioanalysis, Faculty of Applied Sciences, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Group, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Matthias Noll
- Institute for Bioanalysis, Faculty of Applied Sciences, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Wiebke Fenske
- Neuroendocrine Regulation of Energy Homeostasis Group, IFB Adiposity Diseases, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| |
Collapse
|
16
|
Ezzeldin S, El-Wazir A, Enany S, Muhammad A, Johar D, Osama A, Ahmed E, Shikshaky H, Magdeldin S. Current Understanding of Human Metaproteome Association and Modulation. J Proteome Res 2019; 18:3539-3554. [PMID: 31262181 DOI: 10.1021/acs.jproteome.9b00301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During the last decade, metaproteomics has provided a better understanding and functional characterization of the microbiome. A large body of evidence now reveals interspecies, species of bacteria-host interactions, via the secreted modulatory microbial protein "metaproteome". Although high-throughput state-of-art mass spectrometry has recently empowered metaproteomics, its profile remains unclear, and, most importantly, the exact consequences and underlying mechanism of these protein molecules on the host are insufficiently understood. Here we address the current progress in the study of the human metaproteome, suggesting possible modulation, a metaproteome dysbiotic signature, challenges, and future perspectives.
Collapse
Affiliation(s)
- Shahd Ezzeldin
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt
| | - Aya El-Wazir
- Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine , Suez Canal University , 41522 Ismailia , Egypt.,Center of Excellence of Molecular and Cellular Medicine , Suez Canal University , 41522 Ismailia , Egypt
| | - Shymaa Enany
- Department of Microbiology and Immunology, Faculty of Pharmacy , Suez Canal University , 41522 Ismailia , Egypt
| | - Abdelrahman Muhammad
- Department of Biomedical Engineering , Higher Technological Institute , 44634 Sharqia , Egypt
| | - Dina Johar
- Biomedical Sciences Program, University of Science and Technology , Zewail City of Science and Technology , 12588 Giza , Egypt
| | - Aya Osama
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt
| | - Eman Ahmed
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt.,Department of Pharmacology, Faculty of Veterinary Medicine , Suez Canal University , 41522 Ismailia , Egypt
| | - Hassan Shikshaky
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt
| | - Sameh Magdeldin
- Proteomics and Metabolomics Unit, Department of Basic Research , Children's Cancer Hospital Egypt 57357 , 11441 Cairo , Egypt.,Department of Physiology, Faculty of Veterinary Medicine , Suez Canal University , 41522 Ismailia , Egypt
| |
Collapse
|
17
|
Issa Isaac N, Philippe D, Nicholas A, Raoult D, Eric C. Metaproteomics of the human gut microbiota: Challenges and contributions to other OMICS. CLINICAL MASS SPECTROMETRY 2019; 14 Pt A:18-30. [DOI: 10.1016/j.clinms.2019.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 12/22/2022]
|
18
|
Govender Y, Gabriel I, Minassian V, Fichorova R. The Current Evidence on the Association Between the Urinary Microbiome and Urinary Incontinence in Women. Front Cell Infect Microbiol 2019; 9:133. [PMID: 31119104 PMCID: PMC6504689 DOI: 10.3389/fcimb.2019.00133] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/12/2019] [Indexed: 01/26/2023] Open
Abstract
Urinary incontinence (UI) is a burdensome condition with high prevalence in middle-aged to older women and an unclear etiology. Advances in our understanding of host-microbe interactions in the urogenital tract have stimulated interest in the urinary microbiome. DNA sequencing and enhanced urine culture suggest that similarly to other mucosal sites, the urinary bladder of healthy individuals harbors resident microbial communities that may play distinct roles in bladder function. This review focused on the urobiome (expanded quantitative urine culture-based or genomic sequencing-based urinary microbiome) associated with different subtypes of UI, including stress, urgency and mixed urinary incontinence, and related syndromes, such as interstitial cystitis and overactive bladder in women, contrasted to urinary tract infections. Furthermore, we examined clinical evidence for the association of the urinary microbiome with responses to pharmacotherapy for amelioration of UI symptoms. Although published studies are still relatively limited in number, study design and sample size, cumulative evidence suggests that certain Lactobacillus species may play a role in maintaining a healthy bladder milieu. Higher bacterial diversity in the absence of Lactobacillus dominance was associated with urgency UI and resistance to anticholinergic treatment for this condition. UI may also facilitate the persistence of uropathogens following antibiotic treatment, which in turn can alter the commensal/potentially beneficial microbial communities. Risk factors of UI, including age, menopausal status, sex steroid hormones, and body mass index may also impact the urinary microbiome. However, it is yet unclear whether the effects of these risks factors on UI are mediated by urinary host-microbe interactions and a mechanistic link with the female urogenital microbiome is still to be established. Strategies for future research are suggested.
Collapse
Affiliation(s)
- Yashini Govender
- Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States
| | - Iwona Gabriel
- Division of Urogynecology, Brigham and Women's Hospital, Boston, MA, United States
| | - Vatche Minassian
- Division of Urogynecology, Brigham and Women's Hospital, Boston, MA, United States
| | - Raina Fichorova
- Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States
| |
Collapse
|
19
|
Couvillion SP, Zhu Y, Nagy G, Adkins JN, Ansong C, Renslow RS, Piehowski PD, Ibrahim YM, Kelly RT, Metz TO. New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. Analyst 2019; 144:794-807. [PMID: 30507980 PMCID: PMC6349538 DOI: 10.1039/c8an01574k] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass-spectrometry based omics technologies - namely proteomics, metabolomics and lipidomics - have enabled the molecular level systems biology investigation of organisms in unprecedented detail. There has been increasing interest for gaining a thorough, functional understanding of the biological consequences associated with cellular heterogeneity in a wide variety of research areas such as developmental biology, precision medicine, cancer research and microbiome science. Recent advances in mass spectrometry (MS) instrumentation and sample handling strategies are quickly making comprehensive omics analyses of single cells feasible, but key breakthroughs are still required to push through remaining bottlenecks. In this review, we discuss the challenges faced by single cell MS-based omics analyses and highlight recent technological advances that collectively can contribute to comprehensive and high throughput omics analyses in single cells. We provide a vision of the potential of integrating pioneering technologies such as Structures for Lossless Ion Manipulations (SLIM) for improved sensitivity and resolution, novel peptide identification tactics and standards free metabolomics approaches for future applications in single cell analysis.
Collapse
Affiliation(s)
- Sneha P Couvillion
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae. Proteomes 2019; 7:proteomes7010002. [PMID: 30626002 PMCID: PMC6473847 DOI: 10.3390/proteomes7010002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 12/25/2022] Open
Abstract
The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.
Collapse
|
21
|
Kunath BJ, Minniti G, Skaugen M, Hagen LH, Vaaje-Kolstad G, Eijsink VGH, Pope PB, Arntzen MØ. Metaproteomics: Sample Preparation and Methodological Considerations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:187-215. [DOI: 10.1007/978-3-030-12298-0_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
22
|
Lin H, He QY, Shi L, Sleeman M, Baker MS, Nice EC. Proteomics and the microbiome: pitfalls and potential. Expert Rev Proteomics 2018; 16:501-511. [PMID: 30223687 DOI: 10.1080/14789450.2018.1523724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Human symbiotic microbiota are now known to play important roles in human health and disease. Significant progress in our understanding of the human microbiome has been driven by recent technological advances in the fields of genomics, transcriptomics, and proteomics. As a complementary method to metagenomics, proteomics is enabling detailed protein profiling of the microbiome to decipher its structure and function and to analyze its relationship with the human body. Fecal proteomics is being increasingly applied to discover and validate potential health and disease biomarkers, and Therapeutic Goods Administration (TGA)-approved instrumentation and a range of clinical assays are being developed that will collectively play key roles in advancing personalized medicine. Areas covered: This review will introduce the complexity of the microbiome and its role in health and disease (in particular the gastrointestinal tract or gut microbiome), discuss current genomic and proteomic methods for studying this system, including the discovery of potential biomarkers, and outline the development of clinically accepted protocols leading to personalized medicine. Expert commentary: Recognition of the important role the microbiome plays in both health and disease is driving current research in this key area. A proteogenomics approach will be essential to unravel the biologies underlying this complex network.
Collapse
Affiliation(s)
- Huafeng Lin
- a Department of Biotechnology , College of Life Science and Technology, Jinan University , Guangzhou , Guangdong , China.,b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Qing-Yu He
- c Institute of Life and Health Engineering, College of Life Science and Technology , Jinan University , Guangzhou , China
| | - Lei Shi
- b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Mark Sleeman
- d Biomedicine Discovery Institute , Monash University , Melbourne , Australia
| | - Mark S Baker
- e Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , Australia
| | - Edouard C Nice
- f Department of Biochemistry and Molecular Biology , Monash University , Melbourne , Victoria , Australia
| |
Collapse
|
23
|
Ma Y, Yates JR. Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications? Expert Rev Proteomics 2018; 15:545-554. [PMID: 30005169 PMCID: PMC6329588 DOI: 10.1080/14789450.2018.1500902] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Measuring the immediate changes in cells that arise from changing environmental conditions is crucial to understanding the underlying mechanisms involved. These changes can be measured with metabolic stable isotope fully labeled proteomes, but requires looking for changes in the midst of a large background. In addition, labeling efficiency can be an issue in primary and fully differentiated cells. Area covered: Azidohomoalanine (AHA), an analog of methionine, can be accepted by cellular translational machinery and incorporated into newly synthesized proteins (NSPs). AHA-NSPs can be coupled to biotin via CuAAC-mediated click-chemistry and enriched using avidin-based affinity purification. Thus, AHA-containing proteins or peptides can be enriched and efficiently separated from the whole proteome. In this review, we describe the development of mass spectrometry (MS) based AHA strategies and discuss their potential to measure proteins involved in immune response, secretome, gut microbiome, and proteostasis as well as their potential for clinical uses. Expert commentary: AHA strategies have been used to identify synthesis activity and to compare two biological conditions in various biological model organisms. In combination with instrument development, improved sample preparation and fractionation strategies, MS-based AHA strategies have the potential for broad application, and the methods should translate into clinical use.
Collapse
Affiliation(s)
- Yuanhui Ma
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
| | - John R Yates
- a Departments of Molecular Medicine and Neurobiology , The Scripps Research Institute , La Jolla , CA , USA
| |
Collapse
|
24
|
Activity-Based Protein Profiling-Enabling Multimodal Functional Studies of Microbial Communities. Curr Top Microbiol Immunol 2018; 420:1-21. [PMID: 30406866 DOI: 10.1007/82_2018_128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
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.
Collapse
|
25
|
Requena T, Martínez-Cuesta MC, Peláez C. Diet and microbiota linked in health and disease. Food Funct 2018; 9:688-704. [DOI: 10.1039/c7fo01820g] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Diet has shaped microbiota profiles through human evolution.
Collapse
Affiliation(s)
- T. Requena
- Department of Food Biotechnology and Microbiology
- Institute of Food Science Research
- 28049 Madrid
- Spain
| | - M. C. Martínez-Cuesta
- Department of Food Biotechnology and Microbiology
- Institute of Food Science Research
- 28049 Madrid
- Spain
| | - C. Peláez
- Department of Food Biotechnology and Microbiology
- Institute of Food Science Research
- 28049 Madrid
- Spain
| |
Collapse
|
26
|
Proteomics and the human microbiome: where we are today and where we would like to be. Emerg Top Life Sci 2017; 1:401-409. [DOI: 10.1042/etls20170051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022]
Abstract
What are all these hundreds of different bacterial species doing in and on us? What interactions occur between the host and the microbes, and between the microbes themselves? By studying proteins, metaproteomics tries to find preliminary answers to these questions. There is daunting complexity around this; in fact, many of these proteins have never been studied before. This article is an introduction to the field of metaproteomics in the context of the human microbiome. It summarizes where we are and what we have learnt so far. The focus will be on faecal proteomics as most metaproteomics research has been conducted on that sample type. Metaproteomics has made major advances in the past decade, but new sample preparation strategies, improved mass spectrometric analysis and, most importantly, data analysis and interpretation have the potential to pave the way for large-cohort metaproteomics.
Collapse
|