How Fructophilic Lactic Acid Bacteria May
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A Taxonomic Note on the Genus Lactobacillus
Taxonomic Description template 1 A taxonomic note on the genus Lactobacillus: 2 Description of 23 novel genera, emended description 3 of the genus Lactobacillus Beijerinck 1901, and union 4 of Lactobacillaceae and Leuconostocaceae 5 Jinshui Zheng1, $, Stijn Wittouck2, $, Elisa Salvetti3, $, Charles M.A.P. Franz4, Hugh M.B. Harris5, Paola 6 Mattarelli6, Paul W. O’Toole5, Bruno Pot7, Peter Vandamme8, Jens Walter9, 10, Koichi Watanabe11, 12, 7 Sander Wuyts2, Giovanna E. Felis3, #*, Michael G. Gänzle9, 13#*, Sarah Lebeer2 # 8 '© [Jinshui Zheng, Stijn Wittouck, Elisa Salvetti, Charles M.A.P. Franz, Hugh M.B. Harris, Paola 9 Mattarelli, Paul W. O’Toole, Bruno Pot, Peter Vandamme, Jens Walter, Koichi Watanabe, Sander 10 Wuyts, Giovanna E. Felis, Michael G. Gänzle, Sarah Lebeer]. 11 The definitive peer reviewed, edited version of this article is published in International Journal of 12 Systematic and Evolutionary Microbiology, https://doi.org/10.1099/ijsem.0.004107 13 1Huazhong Agricultural University, State Key Laboratory of Agricultural Microbiology, Hubei Key 14 Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, P.R. China. 15 2Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience 16 Engineering, University of Antwerp, Antwerp, Belgium 17 3 Dept. of Biotechnology, University of Verona, Verona, Italy 18 4 Max Rubner‐Institut, Department of Microbiology and Biotechnology, Kiel, Germany 19 5 School of Microbiology & APC Microbiome Ireland, University College Cork, Co. Cork, Ireland 20 6 University of Bologna, Dept. of Agricultural and Food Sciences, Bologna, Italy 21 7 Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit 22 Brussel, Brussels, Belgium 23 8 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, 24 Belgium 25 9 Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, Canada 26 10 Department of Biological Sciences, University of Alberta, Edmonton, Canada 27 11 National Taiwan University, Dept. -
Genome Evolution of a Bee- Associated Bacterium
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1953 Genome evolution of a bee- associated bacterium ANDREA GARCÍA-MONTANER ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-0986-6 UPPSALA urn:nbn:se:uu:diva-416847 2020 Dissertation presented at Uppsala University to be publicly examined in A1:111a, Biomedicinskt centrum (BMC), Husargatan 3, Uppsala, Thursday, 24 September 2020 at 09:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Professor Matthias Horn (Department of Microbial Ecology and Ecosystem Science, Division of Microbial Ecology). Abstract García-Montaner, A. 2020. Genome evolution of a bee-associated bacterium. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1953. 80 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-0986-6. The use of large-scale comparative genomics allows us to explore the genetic diversity and mechanisms of evolution of related organisms. This thesis has focused on the application of such approaches to study Lactobacillus kunkeei, a bacterial inhabitant of the honeybee gut. We produced 102 novel complete genomes from L. kunkeei, which were used in four large comparative studies. In the first study, 41 bacterial strains were isolated from the crop of honeybees whose populations were geographically isolated. Their genome sequences revealed differences in gene contents, including the mobilome, which were mostly phylogroup- specific. However, differences in strain diversity and co-occurrence between both locations were observed. In the second study, we obtained 61 bacterial isolates from neighboring hives at different timepoints during the summer. -
A Taxonomic Note on the Genus Lactobacillus
TAXONOMIC DESCRIPTION Zheng et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.004107 A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae Jinshui Zheng1†, Stijn Wittouck2†, Elisa Salvetti3†, Charles M.A.P. Franz4, Hugh M.B. Harris5, Paola Mattarelli6, Paul W. O’Toole5, Bruno Pot7, Peter Vandamme8, Jens Walter9,10, Koichi Watanabe11,12, Sander Wuyts2, Giovanna E. Felis3,*,†, Michael G. Gänzle9,13,*,† and Sarah Lebeer2† Abstract The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and gen- otypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade- specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host- adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacil- lus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, -
A Holistic Review on Euro-Asian Lactic Acid Bacteria Fermented Cereals and Vegetables
microorganisms Review A Holistic Review on Euro-Asian Lactic Acid Bacteria Fermented Cereals and Vegetables Tolulope Joshua Ashaolu 1,2 and Anna Reale 3,* 1 Smart Agriculture Research and Application Team, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam; [email protected] 2 Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 758307, Vietnam 3 Institute of Food Science, National Research Council, ISA-CNR, 83100 Avellino, Italy * Correspondence: [email protected]; Tel.: +39-0825-299541 Received: 1 July 2020; Accepted: 31 July 2020; Published: 3 August 2020 Abstract: Lactic acid fermentation is one of the oldest methods used worldwide to preserve cereals and vegetables. Europe and Asia have long and huge traditions in the manufacturing of lactic acid bacteria (LAB)-fermented foods. They have different cultures, religions and ethnicities with the available resources that strongly influence their food habits. Many differences and similarities exist with respect to raw substrates, products and microbes involved in the manufacture of fermented products. Many of them are produced on industrial scale with starter cultures, while others rely on spontaneous fermentation, produced homemade or in traditional events. In Europe, common LAB-fermented products made from cereals include traditional breads, leavened sweet doughs, and low and non-alcoholic cereal-based beverages, whereas among vegetable ones prevail sauerkraut, cucumber pickles and olives. In Asia, the prevailing LAB-fermented cereals include acid-leavened steamed breads or pancakes from rice and wheat, whereas LAB-fermented vegetables are more multifarious, such as kimchi, sinki, khalpi, dakguadong, jiang-gua, soidon and sauerkraut. Here, an overview of the main Euro-Asiatic LAB-fermented cereals and vegetables was proposed, underlining the relevance of fermentation as a tool for improving cereals and vegetables, and highlighting some differences and similarities among the Euro-Asiatic products. -
Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-Trna
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.09.290726; this version posted September 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 of 51 1 Phylotype-Level Characterization of Complex Lactobacilli Communities Using 2 a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) 3 Gene Amplicon Sequencing Approach 4 5 Shaktheeshwari Silvaraju,a Nandita Menon,a Huan Fan,a Kevin Lim,a Sandra 6 Kittelmanna# 7 8 aWilmar International Limited, WIL@NUS Corporate Laboratory, Centre for 9 Translational Medicine, National University of Singapore, Singapore. 10 11 Running Head: pheS-based species-level profiling of lactobacilli 12 13 #Address correspondence to [email protected]. 14 Shaktheeshwari Silvaraju and Nandita Menon contributed equally to this work. 15 Author order was determined on the basis of starting date on this project. 16 17 18 Keywords: amplicon sequencing, fermented food, host-associated lactobacilli, 19 Lactobacillus, Pediococcus, taxonomic framework. bioRxiv preprint doi: https://doi.org/10.1101/2020.09.09.290726; this version posted September 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 2 of 51 20 ABSTRACT 21 The ‘lactobacilli’ to date encompass more than 270 closely related species that were 22 recently re-classified into 26 genera. Because of their relevance to industry, there is 23 a need to distinguish between closely related, yet metabolically and regulatory 24 distinct species, e.g., during monitoring of biotechnological processes or screening of 25 samples of unknown composition. -
Phylotype-Level Characterization of Complex Lactobacilli Communities Using a High-Throughput, High-Resolution Phenylalanyl-Trna
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.09.290726; this version posted September 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 of 51 1 Phylotype-Level Characterization of Complex Lactobacilli Communities Using 2 a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) 3 Gene Amplicon Sequencing Approach 4 5 Shaktheeshwari Silvaraju,a Nandita Menon,a Huan Fan,a Kevin Lim,a Sandra 6 Kittelmanna# 7 8 aWilmar International Limited, WIL@NUS Corporate Laboratory, Centre for 9 Translational Medicine, National University of Singapore, Singapore. 10 11 Running Head: pheS-based species-level profiling of lactobacilli 12 13 #Address correspondence to [email protected]. 14 Shaktheeshwari Silvaraju and Nandita Menon contributed equally to this work. 15 Author order was determined on the basis of starting date on this project. 16 17 18 Keywords: amplicon sequencing, fermented food, host-associated lactobacilli, 19 Lactobacillus, Pediococcus, taxonomic framework. bioRxiv preprint doi: https://doi.org/10.1101/2020.09.09.290726; this version posted September 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 2 of 51 20 ABSTRACT 21 The ‘lactobacilli’ to date encompass more than 270 closely related species that were 22 recently re-classified into 26 genera. Because of their relevance to industry, there is 23 a need to distinguish between closely related, yet metabolically and regulatory 24 distinct species, e.g., during monitoring of biotechnological processes or screening of 25 samples of unknown composition. -
Biodiversity of Oenological Lactic Acid Bacteria: Species- and Strain-Dependent Plus/Minus Effects on Wine Quality and Safety
fermentation Review Biodiversity of Oenological Lactic Acid Bacteria: Species- and Strain-Dependent Plus/Minus Effects on Wine Quality and Safety Vittorio Capozzi 1,† , Maria Tufariello 2,† , Nicola De Simone 3, Mariagiovanna Fragasso 3 and Francesco Grieco 2,* 1 National Research Council—Institute of Sciences of Food Production (ISPA) c/o CS-DAT, Via Michele Protano, 71121 Foggia, Italy; [email protected] 2 National Research Council—Institute of Sciences of Food Production (ISPA), Via Prov.le, Lecce-Monteroni, 73100 Lecce, Italy; [email protected] 3 Department of Agriculture, Food, Natural Resources, and Engineering, University of Foggia, 71121 Foggia, Italy; [email protected] (N.D.S.); [email protected] (M.F.) * Correspondence: [email protected]; Tel.: +39-0832422612 † These authors contributed equally to this work. Abstract: Winemaking depends on several elaborate biochemical processes that see as protagonist ei- ther yeasts or lactic acid bacteria (LAB) of oenological interest. In particular, LAB have a fundamental role in determining the quality chemical and aromatic properties of wine. They are essential not only for malic acid conversion, but also for producing several desired by-products due to their important enzymatic activities that can release volatile aromatic compounds during malolactic fermentation (e.g., esters, carbonyl compounds, thiols, monoterpenes). In addition, LAB in oenology can act as bioprotectors and reduce the content of undesired compounds. On the other hand, LAB can affect wine consumers’ health, as they can produce harmful compounds such as biogenic amines and ethyl carbamate under certain conditions during fermentation. Several of these positive and negative Citation: Capozzi, V.; Tufariello, M.; properties are species- and strain-dependent characteristics. -
Unique Niche-Specific Adaptation of Fructophilic Lactic Acid Bacteria and Proposal of Three Apilactobacillus Species As Novel Me
Maeno et al. BMC Microbiology (2021) 21:41 https://doi.org/10.1186/s12866-021-02101-9 RESEARCH ARTICLE Open Access Unique niche-specific adaptation of fructophilic lactic acid bacteria and proposal of three Apilactobacillus species as novel members of the group Shintaro Maeno1, Hiroya Nishimura1, Yasuhiro Tanizawa2, Leon Dicks3, Masanori Arita2,4 and Akihito Endo1* Abstract Background: Fructophilic lactic acid bacteria (FLAB) found in D-fructose rich niches prefer D-fructose over D- glucose as a growth substrate. They need electron acceptors for growth on D-glucose. The organisms share carbohydrate metabolic properties. Fructobacillus spp., Apilactobacillus kunkeei, and Apilactobacillus apinorum are members of this unique group. Here we studied the fructophilic characteristics of recently described species Apilactobacillus micheneri, Apilactobacillus quenuiae, and Apilactobacillus timberlakei. Results: The three species prefer D-fructose over D-glucose and only metabolize D-glucose in the presence of electron acceptors. The genomic characteristics of the three species, i.e. small genomes and thus a low number of coding DNA sequences, few genes involved in carbohydrate transport and metabolism, and partial deletion of adhE gene, are characteristic of FLAB. The three species thus are novel members of FLAB. Reduction of genes involved in carbohydrate transport and metabolism in accordance with reduction of genome size were the common characteristics of the family Lactobacillaceae, but FLAB markedly reduced the gene numbers more than other species in the family. Pan-genome analysis of genes involved in metabolism displayed a lack of specific carbohydrate metabolic pathways in FLAB, leading to a unique cluster separation. Conclusions: The present study expanded FLAB group. -
I Degradation of Wheat Germ Agglutinin and Amylase-Trypsin Inhibitors During Sourdough Fermentation by Luis Eutimio Rojas Tovar
Degradation of Wheat Germ Agglutinin and Amylase-Trypsin Inhibitors During Sourdough Fermentation by Luis Eutimio Rojas Tovar A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Food Science and Technology Department of Agricultural, Food and Nutritional Science University of Alberta © Luis Eutimio Rojas Tovar, 2020 i Abstract Non Celiac Wheat Sensitivity (NCWS), an intolerance to the ingestion of wheat products, has increased considerably during the past few years. In sensitive individuals, NCWS manifests by intestinal and extra intestinal symptoms in different ways. Two wheat protein fractions have been linked to NCWS, amylase-trypsin inhibitors (ATI) and wheat germ agglutinin (WGA). Physicians recommend that individuals with NCWS adhere to a gluten free diet. However, gluten free diets are often associated with a reduced diversity of products, a higher price and lower sensory and nutritional quality. Thus, it was the objective of this study to explore the possibility of using sourdough fermentation to reduce the bioactivity of these two proteins linked to NCWS in wheat bread. White pastry flour was used to analyze ATI and whole wheat flour for WGA experiments. The analytical techniques used to determine the fate of ATIs and WGA through the fermentation were size exclusion high performance liquid chromatography (SEC-HPLC), and enzyme-linked immunosorbent assay (ELISA). During fermentation, the pH of the dough decreased to 3.9 ± 0.2, which promoted the degradation of ATI from oligomers into monomers; ATI monomers are less harmful when consumed. WGA is also modified during sourdough fermentation depending on the reducing capabilities of the strains used. -
Microorganisms
microorganisms Review Lactic Acid Bacteria as Antibacterial Agents to Extend the Shelf Life of Fresh and Minimally Processed Fruits and Vegetables: Quality and Safety Aspects Sofia Agriopoulou 1 , Eygenia Stamatelopoulou 1, Monika Sachadyn-Król 2 and Theodoros Varzakas 1,* 1 Department of Food Science and Technology, University of the Peloponnese, Antikalamos, 24100 Kalamata, Greece; [email protected] (S.A.); [email protected] (E.S.) 2 Department of Chemistry, Faculty of Food Sciences and Biotechnology, University of Life Sciences in Lublin, 20950 Lublin, Poland; [email protected] * Correspondence: [email protected]; Tel.: +30-27210-45279 Received: 3 June 2020; Accepted: 22 June 2020; Published: 24 June 2020 Abstract: Eating fresh fruits and vegetables is, undoubtedly, a healthy habit that should be adopted by everyone (particularly due to the nutrients and functional properties of fruits and vegetables). However, at the same time, due to their production in the external environment, there is an increased risk of their being infected with various pathogenic microorganisms, some of which cause serious foodborne illnesses. In order to preserve and distribute safe, raw, and minimally processed fruits and vegetables, many strategies have been proposed, including bioprotection. The use of lactic acid bacteria in raw and minimally processed fruits and vegetables helps to better maintain their quality by extending their shelf life, causing a significant reduction and inhibition of the action of important foodborne pathogens. The antibacterial effect of lactic acid bacteria is attributed to its ability to produce antimicrobial compounds, including bacteriocins, with strong competitive action against many microorganisms. The use of bacteriocins, both separately and in combination with edible coatings, is considered a very promising approach for microbiological quality, and safety for postharvest storage of raw and minimally processed fruits and vegetables. -
Lactic Acid Bacteria
Lactic Acid Bacteria Subjects: Microbiology Contributors: Sofia Agriopoulou , Eygenia Stamatelopoulou , Monika Sachadyn-Król , THEODOROS VARZAKAS Submitted by: Sofia Agriopoulou Definition The antibacterial effect of lactic acid bacteria is attributed to its ability to produce antimicrobial compounds, including bacteriocins, with strong competitive action against many microorganisms. The use of bacteriocins, both separately and in combination with edible coatings, is considered a very promising approach for microbiological quality, and safety for postharvest storage of raw and minimally processed fruits and vegetables. 1. Abstract Lactic acid bacteria (LAB) are generally accepted as safe microorganisms playing important roles in food fermentation and preservation, either by the presence of natural microbiota or through the addition of starter cultures under controlled conditions. The preservation effect exerted by LAB is mainly due to the production of lactic and acetic acids but also due to several other antimicrobial compounds with important anti-bacterial effect. Fruit and vegetables are an important part of human diets and provide multiple health benefits. However, due to the short shelf-life of fresh and minimally-processed fruit and vegetables, significant losses occur throughout the food distribution chain. Shelf-life extension requires preserving both the quality and safety of food products. Increasing the shelf-life of fresh and fresh-cut fruit and vegetables is challenging, but can be achieved by physical, chemical or biological methods. Foodborne diseases are a growing public health problem worldwide, particularly for infants, children and the elderly. Consumption of fresh fruits and vegetables is associated with a growing number of foodborne outbreaks due to bacterial contamination of these products. Postharvest management of fresh fruits and vegetables storage can be achieved through the use of lactic acid bacteria.