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Article ; Online: Gut Microbiome Proteomics in Food Allergies.

Abril, Ana G / Carrera, Mónica / Sánchez-Pérez, Ángeles / Villa, Tomás G

International journal of molecular sciences

2023 Volume 24, Issue 3

Abstract: Food allergies (FA) have dramatically increased in recent years, particularly in developed countries. It is currently well-established that food tolerance requires the strict maintenance of a specific microbial consortium in the gastrointestinal (GI) ... ...

Abstract	Food allergies (FA) have dramatically increased in recent years, particularly in developed countries. It is currently well-established that food tolerance requires the strict maintenance of a specific microbial consortium in the gastrointestinal (GI) tract microbiome as alterations in the gut microbiota can lead to dysbiosis, causing inflammation and pathogenic intestinal conditions that result in the development of FA. Although there is currently not enough knowledge to fully understand how the interactions between gut microbiota, host responses and the environment cause food allergies, recent advances in '-omics' technologies (i.e., proteomics, genomics, metabolomics) and in approaches involving systems biology suggest future headways that would finally allow the scientific understanding of the relationship between gut microbiome and FA. This review summarizes the current knowledge in the field of FA and insights into the future advances that will be achieved by applying proteomic techniques to study the GI tract microbiome in the field of FA and their medical treatment. Metaproteomics, a proteomics experimental approach of great interest in the study of GI tract microbiota, aims to analyze and identify all the proteins in complex environmental microbial communities; with shotgun proteomics, which uses liquid chromatography (LC) for separation and tandem mass spectrometry (MS/MS) for analysis, as it is the most promising technique in this field.
MeSH term(s)	Humans ; Gastrointestinal Microbiome ; Proteomics/methods ; Tandem Mass Spectrometry ; Microbiota/physiology ; Food Hypersensitivity
Language	English
Publishing date	2023-01-23
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24032234
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Article ; Online: Comprehensive shotgun proteomic characterization and virulence factors of seafood spoilage bacteria.

Abril, Ana G / Calo-Mata, Pilar / Villa, Tomás G / Böhme, Karola / Barros-Velázquez, Jorge / Sánchez-Pérez, Ángeles / Pazos, Manuel / Carrera, Mónica

Food chemistry

2024 Volume 448, Page(s) 139045

Abstract: This article summarizes the characterization, by shotgun proteomics, of 11 bacterial strains identified as responsible for seafood spoilage. A total of 4455 peptide spectrum matches, corresponding to 4299 peptides and 3817 proteins were identified. ... ...

Abstract	This article summarizes the characterization, by shotgun proteomics, of 11 bacterial strains identified as responsible for seafood spoilage. A total of 4455 peptide spectrum matches, corresponding to 4299 peptides and 3817 proteins were identified. Analyses of data determined the functional pathways they are involved in. The proteins identified were integrated into a protein-protein network that involves 371 nodes and 3016 edges. Those proteins are implicated in energy pathways, peptidoglycan biosynthesis, spermidine/putrescine metabolism. An additional 773 peptides were characterized as virulence factors, that participates in bacterial pathogenesis; while 14 peptides were defined as biomarkers, as they can be used to differentiate the bacterial species present. This report represents the most extensive proteomic repository available in the field of seafood spoilage bacteria; the data substantially advances the understanding of seafood decay, as well as provides fundamental bases for the recognition of the bacteria existent in seafood that cause spoilage during food processing/storage.
MeSH term(s)	Seafood/microbiology ; Seafood/analysis ; Proteomics ; Virulence Factors/metabolism ; Virulence Factors/genetics ; Bacterial Proteins/metabolism ; Bacterial Proteins/genetics ; Bacteria/metabolism ; Bacteria/isolation & purification ; Bacteria/classification ; Bacteria/genetics ; Animals ; Food Microbiology
Chemical Substances	Virulence Factors ; Bacterial Proteins
Language	English
Publishing date	2024-03-20
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2024.139045
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Article ; Online: Shotgun proteomic analyses of Pseudomonas species isolated from fish products.

Abril, Ana G / Calo-Mata, Pilar / Böhme, Karola / Villa, Tomás G / Barros-Velázquez, Jorge / Sánchez-Pérez, Ángeles / Pazos, Manuel / Carrera, Mónica

Food chemistry

2024 Volume 450, Page(s) 139342

Abstract: Numerous Pseudomonas species can infect aquatic animals, such as farmed rainbow trout, sea trout, sea bass, and sea bream, by causing disease or stress reactions. In aquaculture facilities, a number of Pseudomonas species have been isolated and ... ...

Abstract	Numerous Pseudomonas species can infect aquatic animals, such as farmed rainbow trout, sea trout, sea bass, and sea bream, by causing disease or stress reactions. In aquaculture facilities, a number of Pseudomonas species have been isolated and identified as the main pathogens. The present study describes the characterization of 18 Pseudomonas strains, isolated from fish products using shotgun proteomics. The bacterial proteomes obtained were further analyzed to identify the main functional pathway proteins involved. In addition, this study revealed the presence of 1015 non-redundant peptides related to virulence factors. An additional 25 species-specific peptides were identified as putative Pseudomonas spp. biomarkers. The results constitute the largest dataset, described thus far for the rapid identification and characterization of Pseudomonas species present in edible fish; furthermore, these data can provide the basis for further research into the development of new therapies against these harmful pathogens.
Language	English
Publishing date	2024-04-12
Publishing country	England
Document type	Journal Article
ZDB-ID	243123-3
ISSN	1873-7072 ; 0308-8146
ISSN (online)	1873-7072
ISSN	0308-8146
DOI	10.1016/j.foodchem.2024.139342
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Article ; Online: High-Resolution Comparative and Quantitative Proteomics of Biogenic-Amine-Producing Bacteria and Virulence Factors Present in Seafood.

Abril, Ana G / Calo-Mata, Pilar / Villa, Tomás G / Böhme, Karola / Barros-Velázquez, Jorge / Sánchez-Pérez, Ángeles / Pazos, Manuel / Carrera, Mónica

Journal of agricultural and food chemistry

2024 Volume 72, Issue 8, Page(s) 4448–4463

Abstract: The presence of biogenic amines (histamine, tyramine, putrescine, and cadaverine) in seafood is a significant concern for food safety. This review describes for the first time a shotgun quantitative proteomics strategy to evaluate and compare foodborne ... ...

Abstract	The presence of biogenic amines (histamine, tyramine, putrescine, and cadaverine) in seafood is a significant concern for food safety. This review describes for the first time a shotgun quantitative proteomics strategy to evaluate and compare foodborne strains of bacteria that produce biogenic amines in seafoods. This approach recognized 35,621 peptide spectrum matches, belonging to 20,792 peptides, and 4621 proteins. It allowed the determination of functional pathways and the classification of the strains into hierarchical clusters. The study identified a protein-protein interaction network involving 1160 nodes/10,318 edges. Proteins were related to energy pathways, spermidine biosynthesis, and putrescine metabolism. Label-free quantitative proteomics allowed the identification of differentially regulated proteins in specific strains such as putrescine aminotransferase, arginine decarboxylase, and l-histidine-binding protein. Additionally, 123 peptides were characterized as virulence factors and 299 peptide biomarkers were selected to identify bacterial species in fish products. This study presents the most extensive proteomic repository and progress in the science of food biogenic bacteria and could be applied in the food industry for the detection of bacterial contamination that produces histamine and other biogenic amines during food processing/storage.
MeSH term(s)	Animals ; Histamine ; Putrescine ; Proteomics ; Virulence Factors ; Biogenic Amines/metabolism ; Bacteria/metabolism ; Fish Products ; Peptides ; Seafood/microbiology
Chemical Substances	Histamine (820484N8I3) ; Putrescine (V10TVZ52E4) ; Virulence Factors ; Biogenic Amines ; Peptides
Language	English
Publishing date	2024-02-16
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	241619-0
ISSN	1520-5118 ; 0021-8561
ISSN (online)	1520-5118
ISSN	0021-8561
DOI	10.1021/acs.jafc.3c06607
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Article ; Online: Oral lichen planus: a microbiologist point of view.

Villa, Tomás G / Sánchez-Pérez, Ángeles / Sieiro, Carmen

International microbiology : the official journal of the Spanish Society for Microbiology

2021 Volume 24, Issue 3, Page(s) 275–289

Abstract: Oral lichen planus (OLP) is a chronic disease of uncertain etiology, although it is generally considered as an immune-mediated disease that affects the mucous membranes and even the skin and nails. Over the years, this disease was attributed to a variety ...

Abstract	Oral lichen planus (OLP) is a chronic disease of uncertain etiology, although it is generally considered as an immune-mediated disease that affects the mucous membranes and even the skin and nails. Over the years, this disease was attributed to a variety of causes, including different types of microorganisms. This review analyzes the present state of the art of the disease, from a microbiological point of view, while considering whether or not the possibility of a microbial origin for the disease can be supported. From the evidence presented here, OLP should be considered an immunological disease, as it was initially proposed, as opposed to an illness of microbiological origin. The different microorganisms so far described as putative disease-causing agents do not fulfill Koch's postulates; they are, actually, not the cause, but a result of the disease that provides the right circumstances for microbial colonization. This means that, at this stage, and unless new data becomes available, no microorganism can be envisaged as the causative agent of lichen planus.
MeSH term(s)	Bacteria ; Fungi ; Host Microbial Interactions ; Humans ; Immunity ; Lichen Planus, Oral/immunology ; Lichen Planus, Oral/microbiology ; Lichen Planus, Oral/pathology ; Microbiota ; Mouth Mucosa/pathology ; Skin/pathology ; Viruses
Language	English
Publishing date	2021-03-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1454951-7
ISSN	1618-1905 ; 1139-6709
ISSN (online)	1618-1905
ISSN	1139-6709
DOI	10.1007/s10123-021-00168-y
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Article ; Online: Mastering the control of the Rho transcription factor for biotechnological applications.

Villa, Tomás G / Abril, Ana G / Sánchez-Pérez, Angeles

Applied microbiology and biotechnology

2021 Volume 105, Issue 10, Page(s) 4053–4071

Abstract: The present review represents an update on the fundamental role played by the Rho factor, which facilitates the process of Rho-dependent transcription termination in the prokaryotic world; it also provides a summary of relevant mutations in the Rho ... ...

Abstract	The present review represents an update on the fundamental role played by the Rho factor, which facilitates the process of Rho-dependent transcription termination in the prokaryotic world; it also provides a summary of relevant mutations in the Rho factor and the insights they provide into the functions carried out by this protein. Furthermore, a section is dedicated to the putative future use of Rho (the 'taming' of Rho) to facilitate biotechnological processes and adapt them to different technological contexts. Novel bacterial strains can be designed, containing mutations in the rho gene, that are better suited for different biotechnological applications. This process can obtain novel microbial strains that are adapted to lower temperatures of fermentation, shorter production times, exhibit better nutrient utilization, or display other traits that are beneficial in productive Biotechnology. Additional important issues reviewed here include epistasis, the design of TATA boxes, the role of small RNAs, and the manipulation of clathrin-mediated endocytosis, by some pathogenic bacteria, to invade eukaryotic cells. KEY POINTS: • It is postulated that controlling the action of the prokaryotic Rho factor could generate major biotechnological improvements, such as an increase in bacterial productivity or a reduction of the microbial-specific growth rate. • The review also evaluates the putative impact of epistatic mechanisms on Biotechnology, both as possible responsible for unexpected failures in gene cloning and more important for the genesis of new strains for biotechnological applications • The use of clathrin-coated vesicles by intracellular bacterial microorganisms is included too and proposed as a putative delivery mechanism, for drugs and vaccines.
MeSH term(s)	Bacteria/genetics ; Biotechnology ; Rho Factor/genetics ; Transcription Factors/genetics ; Transcription, Genetic
Chemical Substances	Rho Factor ; Transcription Factors
Language	English
Publishing date	2021-05-08
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-021-11326-7
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Article ; Online: The Role of the Gallbladder, the Intestinal Barrier and the Gut Microbiota in the Development of Food Allergies and Other Disorders.

Abril, Ana G / Villa, Tomás G / Sánchez-Pérez, Ángeles / Notario, Vicente / Carrera, Mónica

International journal of molecular sciences

2022 Volume 23, Issue 22

Abstract: The microbiota present in the gastrointestinal tract is involved in the development or prevention of food allergies and autoimmune disorders; these bacteria can enter the gallbladder and, depending on the species involved, can either be benign or cause ... ...

Abstract	The microbiota present in the gastrointestinal tract is involved in the development or prevention of food allergies and autoimmune disorders; these bacteria can enter the gallbladder and, depending on the species involved, can either be benign or cause significant diseases. Occlusion of the gallbladder, usually due to the presence of calculi blocking the bile duct, facilitates microbial infection and inflammation, which can be serious enough to require life-saving surgery. In addition, the biliary salts are secreted into the intestine and can affect the gut microbiota. The interaction between the gut microbiota, pathogenic organisms, and the human immune system can create intestinal dysbiosis, generating a variety of syndromes including the development of food allergies and autoimmune disorders. The intestinal microbiota can aggravate certain food allergies, which become severe when the integrity of the intestinal barrier is affected, allowing bacteria, or their metabolites, to cross the intestinal barrier and invade the bloodstream, affecting distal body organs. This article deals with health conditions and severe diseases that are either influenced by the gut flora or caused by gallbladder obstruction and inflammation, as well as putative treatments for those illnesses.
MeSH term(s)	Humans ; Gastrointestinal Microbiome ; Gallbladder ; Intestines/microbiology ; Food Hypersensitivity ; Inflammation ; Autoimmune Diseases
Language	English
Publishing date	2022-11-18
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms232214333
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Article: The Use of Bacteriophages in Biotechnology and Recent Insights into Proteomics.

Abril, Ana G / Carrera, Mónica / Notario, Vicente / Sánchez-Pérez, Ángeles / Villa, Tomás G

Antibiotics (Basel, Switzerland)

2022 Volume 11, Issue 5

Abstract: Phages have certain features, such as their ability to form protein-protein interactions, that make them good candidates for use in a variety of beneficial applications, such as in human or animal health, industry, food science, food safety, and ... ...

Abstract	Phages have certain features, such as their ability to form protein-protein interactions, that make them good candidates for use in a variety of beneficial applications, such as in human or animal health, industry, food science, food safety, and agriculture. It is essential to identify and characterize the proteins produced by particular phages in order to use these viruses in a variety of functional processes, such as bacterial detection, as vehicles for drug delivery, in vaccine development, and to combat multidrug resistant bacterial infections. Furthermore, phages can also play a major role in the design of a variety of cheap and stable sensors as well as in diagnostic assays that can either specifically identify specific compounds or detect bacteria. This article reviews recently developed phage-based techniques, such as the use of recombinant tempered phages, phage display and phage amplification-based detection. It also encompasses the application of phages as capture elements, biosensors and bioreceptors, with a special emphasis on novel bacteriophage-based mass spectrometry (MS) applications.
Language	English
Publishing date	2022-05-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2681345-2
ISSN	2079-6382
ISSN	2079-6382
DOI	10.3390/antibiotics11050653
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Article: Mastering the control of the Rho transcription factor for biotechnological applications

Villa, Tomás G / Abril, Ana G / Sánchez-Pérez, Angeles

Applied microbiology and biotechnology. 2021 May, v. 105, no. 10

2021

Abstract	The present review represents an update on the fundamental role played by the Rho factor, which facilitates the process of Rho-dependent transcription termination in the prokaryotic world; it also provides a summary of relevant mutations in the Rho factor and the insights they provide into the functions carried out by this protein. Furthermore, a section is dedicated to the putative future use of Rho (the ‘taming’ of Rho) to facilitate biotechnological processes and adapt them to different technological contexts. Novel bacterial strains can be designed, containing mutations in the rho gene, that are better suited for different biotechnological applications. This process can obtain novel microbial strains that are adapted to lower temperatures of fermentation, shorter production times, exhibit better nutrient utilization, or display other traits that are beneficial in productive Biotechnology. Additional important issues reviewed here include epistasis, the design of TATA boxes, the role of small RNAs, and the manipulation of clathrin-mediated endocytosis, by some pathogenic bacteria, to invade eukaryotic cells. KEY POINTS: • It is postulated that controlling the action of the prokaryotic Rho factor could generate major biotechnological improvements, such as an increase in bacterial productivity or a reduction of the microbial-specific growth rate. • The review also evaluates the putative impact of epistatic mechanisms on Biotechnology, both as possible responsible for unexpected failures in gene cloning and more important for the genesis of new strains for biotechnological applications • The use of clathrin-coated vesicles by intracellular bacterial microorganisms is included too and proposed as a putative delivery mechanism, for drugs and vaccines.
Keywords	biotechnology ; endocytosis ; epistasis ; fermentation ; genes ; nutrient utilization ; transcription factors ; transcription termination
Language	English
Dates of publication	2021-05
Size	p. 4053-4071.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	NAL-AP-2-clean ; Review
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-021-11326-7
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Article ; Online: Proteomic Characterization of Antibiotic Resistance in

Abril, Ana G / Carrera, Mónica / Böhme, Karola / Barros-Velázquez, Jorge / Calo-Mata, Pilar / Sánchez-Pérez, Angeles / Villa, Tomás G

International journal of molecular sciences

2021 Volume 22, Issue 15

Abstract: ... ...

Abstract	Some
MeSH term(s)	ATP-Binding Cassette Transporters/chemistry ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/chemistry ; Chromatography, Liquid/methods ; Drug Resistance, Multiple, Bacterial ; Genes, Bacterial ; Listeria/classification ; Listeria/drug effects ; Listeria/genetics ; Listeria/pathogenicity ; Peptides/chemistry ; Proteome/chemistry ; Proteomics/methods ; Spectrometry, Mass, Electrospray Ionization/methods ; Tandem Mass Spectrometry/methods ; Virulence Factors/chemistry
Chemical Substances	ATP-Binding Cassette Transporters ; Anti-Bacterial Agents ; Bacterial Proteins ; Peptides ; Proteome ; Virulence Factors
Language	English
Publishing date	2021-07-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22158141
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