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Sonets IV, Solovyev MA, Ivanova VA, Vasiluev PA, Kachalkin AV, Ochkalova SD, Korobeynikov AI, Razin SV, Ulianov SV, Tyakht AV. Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider. Food Microbiol 2024; 121:104520. [PMID: 38637082 DOI: 10.1016/j.fm.2024.104520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 04/20/2024]
Abstract
Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.
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Affiliation(s)
- Ignat V Sonets
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.
| | - Mikhail A Solovyev
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | | | - Petr A Vasiluev
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Research Center for Medical Genetics, Moscow, Russia
| | - Aleksey V Kachalkin
- Department of Soil Biology, Faculty of Soil Science, Lomonosov Moscow State University, Moscow, Russia; G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, Russia
| | - Sofia D Ochkalova
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, Saint Petersburg, 197101, Russia; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199004, Russia
| | - Anton I Korobeynikov
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199004, Russia; Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, 199004, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - Alexander V Tyakht
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
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Werum V, Ehrmann M. Dellaglioa spp. an underestimated genus isolated from high-oxygen modified-atmosphere packaged meat. Food Microbiol 2024; 117:104398. [PMID: 37919006 DOI: 10.1016/j.fm.2023.104398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
The genus Dellaglioa (D.) actually comprises two species, i.e., D. algida and the recently described species D. carnosa. Both species are adapted to cold and have been typically recovered from meat products. However, their importance has thus far been underestimated, since routine culture-based analysis failed to support their growth. Furthermore, their occurrence on meat packed under high-oxygen MA conditions (HiOx-MAP) is controversial because they have been described as being oxygen-sensitive. In this study, we focused on the targeted isolation of Dellaglioa spp. from HiOx-MAP meat samples and the characterization of our isolates regarding their adaption to HiOx-MAP conditions, their spoilage potential, as well as food safety aspects. We used a medium recently developed specifically for strains of this genus and investigated ten meat batches from seven different suppliers. Our study confirms that the occurrence of Dellaglioa spp. on HiOx-MAP meat is non-sporadic, reaching cell counts ranging from log10 5.8-7.1 CFU/cm2 at a late stage of chilled storage. Autochthonous Dellaglioa spp. and Leuconostoc (L.) gasicomitatum dominated the microbiota of the beef steaks with similar growth behavior. Our results suggest that Dellaglioa spp. benefits from the heme-dependent respiration of oxygen by L. gasicomitatum. Furthermore, whole genome analysis revealed the presence of genes predictively involved in oxidative stress defense, survival, and adaptation in meat environments. Moreover, we predict a weak aminogenic potential of D. algida strains. Tyramine production from tyrosine seems to be a species-specific characteristic of D. carnosa. The extent to which D. algida and D. carnosa occurrence is influenced by or even dependent on the composition of the entire microbiota remains to be investigated.
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Affiliation(s)
- Victoria Werum
- Lehrstuhl für Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354, Freising, Germany
| | - Matthias Ehrmann
- Lehrstuhl für Mikrobiologie, Technische Universität München, Gregor-Mendel-Straße 4, 85354, Freising, Germany.
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Bucka-Kolendo J, Kiousi DE, Wojtczak A, Doulgeraki AI, Galanis A, Sokołowska B. Depiction of the In Vitro and Genomic Basis of Resistance to Hop and High Hydrostatic Pressure of Lactiplantibacillus plantarum Isolated from Spoiled Beer. Genes (Basel) 2023; 14:1710. [PMID: 37761850 PMCID: PMC10530735 DOI: 10.3390/genes14091710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Among the beer-spoiling microorganisms, the dominant ones belong to the genera Lactobacillus, Leuconostoc, Oenococcus, and Pediococcus. It is assumed that resistance to hop bitters correlates with resistance to other factors and can significantly impact the brewing industry. Beer preservation with high hydrostatic pressure eliminates the spoiling microorganisms while preserving all desired properties of the beer. Here, we present comprehensive in vitro and genomic analysis of the beer-spoiling Lactiplantibacillus plantarum KKP 3573 capacity to resist hop and high hydrostatic pressure. Lp. plantarum KKP 3573 is a strain isolated from spoiled beer. Our finding suggests that the growth rate of the strain depends on the medium variant, where a small concentration of beer (5 IBU) stimulates the growth, suggesting that the limited concentration has a positive effect on cell growth. At the same time, increased concentrations of 20 IBU, 30 IBU, and pure beer 43.6 IBU decreased the growth rate of the KKP 3573 strain. We observed that higher extract content in the pressurized beer increased microbial survivability. The wort and Vienna Lager beer can stimulate the baroprotective effect. The taxonomy of the novel strain was confirmed after whole genome sequencing (WGS) and comparative genomic analysis. More specifically, it contains a chromosome of 3.3 Mb with a GC content of 44.4%, indicative of the Lp. plantarum species. Accordingly, it possesses high genomic similarity (>98%) with other species members. Annotation algorithms revealed that the strain carries several genes involved in resistance to stress, including extreme temperature, hop bitters and high pressure, and adaptation to the brewing environment. Lastly, the strain does not code for toxins and virulence proteins and cannot produce biogenic amines.
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Affiliation(s)
- Joanna Bucka-Kolendo
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.W.); (B.S.)
| | - Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (A.G.)
| | - Adrian Wojtczak
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.W.); (B.S.)
| | - Agapi I. Doulgeraki
- Laboratory of Food Microbiology and Hygiene, Department of Food Science & Technology, Faculty of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (D.E.K.); (A.G.)
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland; (A.W.); (B.S.)
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Saldarriaga-Córdoba M, Araya-León H, Irgang R, Avendaño-Herrera R. Development of a PCR assay for the specific identification of the fish pathogen Tenacibaculum piscium. JOURNAL OF FISH DISEASES 2023; 46:517-526. [PMID: 36727560 DOI: 10.1111/jfd.13764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Tenacibaculosis is an emerging disease that severely affects salmonid farming in Chile, producing high mortalities and causing great economic losses. This work describes a novel PCR assay for the specific detection of Tenacibaculum piscium, a species recently described and identified in tenacibaculosis outbreaks in Norway and Chile. The designed primers amplified a 678-bp fragment of the peptidase gene (peptidase M23 family) from T. piscium. This method is specific for T. piscium; no other chromosomal DNA amplification products were obtained for other Tenacibaculum species. In pure cultures, the PCR assay detected up to 500 pg of DNA, or the equivalent of 2.44 ± 0.06 × 104 CFU/ml. For seeded fish samples (i.e., gills, liver, kidney, and mucus), the sensitivity limit was 4.88 ± 0.11 × 106 CFU/g, sufficient to detect T. piscium in acute infections in fish. Notably, this sensitivity level was 100-fold lower for DNA extracted from mucus samples. As compared to other existing methodologies (e.g., gene sequencing), the PCR approach described in this work allowed for the easiest detection of T. piscium in mucus samples obtained from challenged fish, an important outcome considering that the identification of this bacterium is difficult. Our results indicate that the designed specific primers and PCR method provide a rapid and specific diagnosis of T. piscium.
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Affiliation(s)
- Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Santiago, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Henry Araya-León
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
| | - Rute Irgang
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile
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Kiousi DE, Bucka-Kolendo J, Wojtczak A, Sokołowska B, Doulgeraki AI, Galanis A. Genomic Analysis and In Vitro Investigation of the Hop Resistance Phenotype of Two Novel Loigolactobacillus backii Strains, Isolated from Spoiled Beer. Microorganisms 2023; 11:microorganisms11020280. [PMID: 36838246 PMCID: PMC9967799 DOI: 10.3390/microorganisms11020280] [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: 12/20/2022] [Revised: 01/15/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Loigolactobacillus backii is an important beer-spoiling species, exhibiting high hop tolerance. Here, we present the annotated whole genome sequence of two recently isolated strains, Lg. backii KKP 3565 and KKP 3566. Firstly, to study the genetic basis of the persistence of the two isolates in beer, a comprehensive bioinformatic analysis ensued. Their chromosome map was constructed, using whole-genome sequencing and assembly, revealing that the two strains carry genomes with a length of 2.79 Mb with a GC content of 40.68%. An average nucleotide identity (ANI) analysis demonstrated that the novel strains possess unique genomic sequences, also confirming their classification into the Lg. backii species. Their genome harbors numerous insertion sequences and plasmids, originating from other beer-spoiling species. Regarding their adaptation in brewery environment, homologous genes that confer resistance to hop were spotted, while the impact of hop bitters and pure beer on bacterial growth was investigated, in vitro. In brief, low hop concentrations were found to induce the proliferation of strains, while a higher concentration negatively affected their growth. Nonetheless, their ability to survive in pure beer indicated their tolerance to high hop concentrations. These results offer insight into the capacity of Lg. backii KKP 3566 and Lg. backii KKP 3566 to tolerate the extreme conditions prevalent in the brewery environment.
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Affiliation(s)
- Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Joanna Bucka-Kolendo
- Culture Collection of Industrial Microorganisms, Microbiological Resources Center, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Adrian Wojtczak
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology, State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Agapi I. Doulgeraki
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization—DIMITRA, Sofokli Venizelou 1, 14123 Lycovrissi, Attica, Greece
- Correspondence: (A.I.D.); (A.G.); Tel.: +30-21028-45940 (A.I.D.); +30-25510-30634 (A.G.)
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
- Correspondence: (A.I.D.); (A.G.); Tel.: +30-21028-45940 (A.I.D.); +30-25510-30634 (A.G.)
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ZHAO Y, WU X, SIEGUMFELDT H. Comparative gene analysis of beer tolerant and sensitive Lactobacillus brevis. FOOD SCIENCE AND TECHNOLOGY 2023. [DOI: 10.1590/fst.126422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Affiliation(s)
- Yu ZHAO
- Shaanxi Normal University, China
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7
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Schiffer CJ, Grätz C, Pfaffl MW, Vogel RF, Ehrmann MA. Characterization of the Staphylococcus xylosus methylome reveals a new variant of type I restriction modification system in staphylococci. Front Microbiol 2023; 14:946189. [PMID: 36970683 PMCID: PMC10030836 DOI: 10.3389/fmicb.2023.946189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restriction modification (RM) systems are known to provide a strong barrier to the exchange of DNA between and within bacterial species. Likewise, DNA methylation is known to have an important function in bacterial epigenetics regulating essential pathways such as DNA replication and the phase variable expression of prokaryotic phenotypes. To date, research on staphylococcal DNA methylation focused mainly on the two species Staphylococcus aureus and S. epidermidis. Less is known about other members of the genus such as S. xylosus, a coagulase-negative commensal of mammalian skin. The species is commonly used as starter organism in food fermentations but is also increasingly considered to have an as yet elusive function in bovine mastitis infections. We analyzed the methylomes of 14 S. xylosus strains using single-molecular, real-time (SMRT) sequencing. Subsequent in silico sequence analysis allowed identification of the RM systems and assignment of the respective enzymes to the discovered modification patterns. Hereby the presence of type I, II, III and IV RM systems in varying numbers and combinations among the different strains was revealed, clearly distinguishing the species from what is known for other members of the genus so far. In addition, the study characterizes a newly discovered type I RM system, encoded by S. xylosus but also by a variety of other staphylococcal species, with a hitherto unknown gene arrangement that involves two specificity units instead of one (hsdRSMS). Expression of different versions of the operon in E. coli showed proper base modification only when genes encoding both hsdS subunits were present. This study provides new insights into the general understanding of the versatility and function of RM systems as well as the distribution and variations in the genus Staphylococcus.
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Affiliation(s)
- Carolin J. Schiffer
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- *Correspondence: Carolin J. Schiffer,
| | - Christian Grätz
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Michael W. Pfaffl
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Rudi F. Vogel
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthias A. Ehrmann
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Comparative Genomics of Acetic Acid Bacteria within the Genus Bombella in Light of Beehive Habitat Adaptation. Microorganisms 2022; 10:microorganisms10051058. [PMID: 35630502 PMCID: PMC9147383 DOI: 10.3390/microorganisms10051058] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/10/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
It is known that the bacterial microbiota in beehives is essential for keeping bees healthy. Acetic acid bacteria of the genus Bombella colonize several niches in beehives and are associated with larvae protection against microbial pathogens. We have analyzed the genomes of 22 Bombella strains of different species isolated in eight different countries for taxonomic affiliation, central metabolism, prophages, bacteriocins and tetracycline resistance to further elucidate the symbiotic lifestyle and to identify typical traits of acetic acid bacteria. The genomes can be assigned to four different species. Three genomes show ANIb values and DDH values below species demarcation values to any validly described species, which identifies them as two potentially new species. All Bombella spp. lack genes in the Embden–Meyerhof–Parnas pathway and the tricarboxylic acid cycle, indicating a focus of intracellular carbohydrate metabolism on the pentose phosphate pathway or the Entner–Doudoroff pathway for which all genes were identified within the genomes. Five membrane-bound dehydrogenases were identified that catalyze oxidative fermentation reactions in the periplasm, yielding oxidative energy. Several complete prophages, but no bacteriocins, were identified. Resistance to tetracycline, used to prevent bacterial infections in beehives, was only found in Bombella apis MRM1T. Bombella strains exhibit increased osmotolerance in high glucose concentrations compared to Gluconobacter oxydans, indicating adaption to high sugar environments such as beehives.
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Werum V, Ehrmann M, Vogel R, Hilgarth M. Comparative genome analysis, predicted lifestyle and antimicrobial strategies of Lactococcus carnosus and Lactococcus paracarnosus isolated from meat. Microbiol Res 2022; 258:126982. [DOI: 10.1016/j.micres.2022.126982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022]
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Xu Z, Wang K, Liu Z, Soteyome T, Deng Y, Chen L, Seneviratne G, Hong W, Liu J, Harro JM, Kjellerup BV. A novel procedure in combination of genomic sequencing, flow cytometry and routine culturing for confirmation of beer spoilage caused by Pediococcus damnosus in viable but nonculturable state. Lebensm Wiss Technol 2022; 154:112623. [DOI: 10.1016/j.lwt.2021.112623] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Zhenbo Xu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, 510640, China
- State Key Laboratory of Applied Microbiology China Southern, Insititue of Microbiology, Guangdong Academy of Sciences, 510070, China
- Center for Translational Medicine, the Second Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong, China
Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
Research Institute for Food Nutrition and Human Health, Guangzhou, China
| | | | | | | | | | | | | | - Wei Hong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Junyan Liu
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, 20742, USA
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Fuertes-Perez S, Vogel RF, Hilgarth M. Comparative genomics of Photobacterium species from terrestrial and marine habitats. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100087. [PMID: 34950912 PMCID: PMC8671102 DOI: 10.1016/j.crmicr.2021.100087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 11/26/2021] [Indexed: 11/28/2022] Open
Abstract
Photobacterium (P.) is a genus widely studied in regards to its association with and ubiquitous presence in marine environments. However, certain species (P. phosphoreum, P. carnosum, P. iliopiscarium) have been recently described to colonize and spoil raw meats without a marine link. We have studied 27 strains from meat as well as 26 strains from marine environments in order to probe for intraspecies marine/terrestrial subpopulations and identify distinct genomic features acquired by environmental adaptation. We have conducted phylogenetic analysis (MLSA, ANI, fur, codon usage), search of plasmids (plasmidSPADES), phages (PHASTER), CRISPR-cas operons (CRISPR-finder) and secondary metabolites gene clusters (antiSMASH, BAGEL), in addition to a targeted gene search for specific pathways (e.g. TCA cycle, pentose phosphate, respiratory chain) and elements relevant for growth, adaptation and competition (substrate utilization, motility, bioluminescence, sodium and iron transport). P. carnosum appears as a conserved single clade, with one isolate from MAP fish clustering apart that doesn't, however, show distinct features that could indicate different adaptation. The species harbors genes for a wide carbon source utilization (glycogen/starch, maltose, pullulan, fucose) for colonization of diverse niches in its genome. P. phosphoreum is represented by two different clades on the phylogenetic analyses not correlating to their origin or distribution of other features analyzed that can be divided into two novel subspecies based on genome-wide values. A more diverse antimicrobial activity (sactipeptides, microcins), production of secondary metabolites (siderophores and arylpolyenes), stress response and adaptation (bioluminescence, sodium transporters, catalase, high affinity for oxygen cytochrome cbb3 oxidase, DMSO reductase and proton translocating NADH dehydrogenase) is predicted compared to the other species. P. iliopiscarium was divided into two clades based on source of isolation correlating with phylogeny and distribution of several traits. The species shows traits common to the other two species, similar carbon utilization/transport gene conservation as P. carnosum for the meat-isolated strains, and predicted utilization of marine-common DMSO and flagellar cluster for the sea-isolated strains. Results additionally suggest that photobacteria are highly prone to horizontal acquisition/loss of genetic material and genetic transduction, and that it might be a strategy for increasing the frequency of strain- or species-specific features that offers a growth/competition advantage.
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Affiliation(s)
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Germany
| | - Maik Hilgarth
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Germany
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Link T, Vogel RF, Ehrmann MA. The diversity among the species Tetragenococcus halophilus including new isolates from a lupine seed fermentation. BMC Microbiol 2021; 21:320. [PMID: 34798831 PMCID: PMC8605565 DOI: 10.1186/s12866-021-02381-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/03/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Tetragenococcus (T.) halophilus can be isolated from a variety of fermented foods, such as soy sauce, different soy pastes, salted fish sauce and from cheese brine or degraded sugar beet thick juice. This species contributes by the formation of short chain acids to the flavor of the product. Recently, T. halophilus has been identified as a dominant species in a seasoning sauce fermentation based on koji made with lupine seeds. RESULTS In this study we characterized six strains of T. halophilus isolated from lupine moromi fermentations in terms of their adaptation towards this fermentation environment, salt tolerance and production of biogenic amines. Phylogenic and genomic analysis revealed three distinctive lineages within the species T. halophilus with no relation to their isolation source, besides the lineage of T. halophilus subsp. flandriensis. All isolated strains from lupine moromi belong to one lineage in that any of the type strains are absent. The strains form lupine moromi could not convincingly be assigned to one of the current subspecies. Taken together with strain specific differences in the carbohydrate metabolism (arabinose, mannitol, melibiose, gluconate, galactonate) and amino acid degradation pathways such as arginine deiminase pathway (ADI) and the agmatine deiminase pathway (AgDI) the biodiversity in the species of T. halophilus is greater than expected. Among the new strains, some strains have a favorable combination of traits wanted in a starter culture. CONCLUSIONS Our study characterized T. halophilus strains that were isolated from lupine fermentation. The lupine moromi environment appears to select strains with specific traits as all of the strains are phylogenetically closely related, which potentially can be used as a starter culture for lupine moromi. We also found that the strains can be clearly distinguished phylogenetically and phenotypically from the type strains of both subspecies T. halophilus subsp. halophilus and T. halophilus subsp. flandriensis.
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Affiliation(s)
- Tobias Link
- Lehrstuhl für Mikrobiologie, Technische Universität München, 85354, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Mikrobiologie, Technische Universität München, 85354, Freising, Germany
| | - Matthias A Ehrmann
- Lehrstuhl für Mikrobiologie, Technische Universität München, 85354, Freising, Germany.
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Kurniawan YN, Shinohara Y, Sakai H, Magarifuchi T, Suzuki K. Applications of the Third-Generation DNA Sequencing Technology to the Detection of Hop Tolerance Genes and Discrimination of Saccharomyces Yeast Strains. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2021. [DOI: 10.1080/03610470.2021.1939606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yohanes Novi Kurniawan
- Analytical Science Laboratories, Asahi Quality and Innovations, Ltd, Moriya, Ibaraki, Japan
| | - Yuji Shinohara
- Analytical Science Laboratories, Asahi Quality and Innovations, Ltd, Moriya, Ibaraki, Japan
| | - Hiroaki Sakai
- Analytical Science Laboratories, Asahi Quality and Innovations, Ltd, Moriya, Ibaraki, Japan
| | - Tetsuro Magarifuchi
- Analytical Science Laboratories, Asahi Quality and Innovations, Ltd, Moriya, Ibaraki, Japan
| | - Koji Suzuki
- Asahi Quality and Innovations, Ltd, Moriya, Ibaraki, Japan
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Artavia G, Cortés-Herrera C, Granados-Chinchilla F. Selected Instrumental Techniques Applied in Food and Feed: Quality, Safety and Adulteration Analysis. Foods 2021; 10:1081. [PMID: 34068197 PMCID: PMC8152966 DOI: 10.3390/foods10051081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/13/2021] [Accepted: 03/19/2021] [Indexed: 12/28/2022] Open
Abstract
This review presents an overall glance at selected instrumental analytical techniques and methods used in food analysis, focusing on their primary food science research applications. The methods described represent approaches that have already been developed or are currently being implemented in our laboratories. Some techniques are widespread and well known and hence we will focus only in very specific examples, whilst the relatively less common techniques applied in food science are covered in a wider fashion. We made a particular emphasis on the works published on this topic in the last five years. When appropriate, we referred the reader to specialized reports highlighting each technique's principle and focused on said technologies' applications in the food analysis field. Each example forwarded will consider the advantages and limitations of the application. Certain study cases will typify that several of the techniques mentioned are used simultaneously to resolve an issue, support novel data, or gather further information from the food sample.
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Affiliation(s)
- Graciela Artavia
- Centro Nacional de Ciencia y Tecnología de Alimentos, Sede Rodrigo Facio, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
| | - Carolina Cortés-Herrera
- Centro Nacional de Ciencia y Tecnología de Alimentos, Sede Rodrigo Facio, Universidad de Costa Rica, San José 11501-2060, Costa Rica;
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Suzuki K, Shinohara Y, Kurniawan YN. Role of Plasmids in Beer Spoilage Lactic Acid Bacteria: A Review. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2020. [DOI: 10.1080/03610470.2020.1843899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Koji Suzuki
- Asahi Quality and Innovations, Ltd., Moriya, Japan
| | - Yuji Shinohara
- Department of Safety Technology Development, Analytical Science Laboratories, Asahi Quality and Innovations, Ltd., Moriya, Japan
| | - Yohanes Novi Kurniawan
- Department of Safety Technology Development, Analytical Science Laboratories, Asahi Quality and Innovations, Ltd., Moriya, Japan
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16
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Hauschild P, Hilgarth M, Vogel RF. Hydrostatic pressure- and halotolerance of Photobacterium phosphoreum and P. carnosum isolated from spoiled meat and salmon. Food Microbiol 2020; 99:103679. [PMID: 34119089 DOI: 10.1016/j.fm.2020.103679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 11/02/2020] [Accepted: 11/08/2020] [Indexed: 10/23/2022]
Abstract
Photobacterium spp. occur frequently in marine environments but have been recently also found as common spoilers on chilled meats. The environmental conditions in these ecological niches differ especially regarding salinity and ambient pressure. Linking the occurrence of photobacteria in different niches may elucidate its ecology and bring insights for the food industry. We investigated tolerance of Photobacterium (P.) phosphoreum and P. carnosum strains to high hydrostatic pressure and salinity and aligned our observations with presence of relevant genes. The strains were isolated from packaged meats and salmon (or the sea) to identify adaptations to marine and terrestrial habitats. Growth of all P. carnosum strains was reduced by 40 MPa hydrostatic pressure and >3% sodium chloride, suggesting loss of traits associated with marine habitats. In contrast, P. phosphoreum strains were only slightly affected, suggesting general adaptation to marine habitats. In accordance, these strains had gene clusters associated with marine niches, e.g. flagellar and lux-operons, being incomplete in P. carnosum. Occurrence of P. carnosum strains on packaged salmon and P. phosphoreum strains on meats therefore likely results from cross-contamination in meat and fish processing. Still, these strains showed intermediate traits regarding pressure- and halotolerance, suggesting developing adaptation to their respective environment.
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Affiliation(s)
- Philippa Hauschild
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, 85354, Freising, Germany.
| | - Maik Hilgarth
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, 85354, Freising, Germany.
| | - Rudi F Vogel
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, 85354, Freising, Germany.
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17
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Rogalski E, Ehrmann MA, Vogel RF. Intraspecies diversity and genome-phenotype-associations in Fructilactobacillus sanfranciscensis. Microbiol Res 2020; 243:126625. [PMID: 33129664 DOI: 10.1016/j.micres.2020.126625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 10/09/2020] [Indexed: 02/04/2023]
Abstract
In this study the intraspecies diversity of Fructilactobacillus (F.) sanfranciscensis (formerly Lactobacillus sanfranciscensis) was characterized by comparative genomics supported by physiological data. Twenty-four strains of F. sanfranciscensis were analyzed and sorted into six different genomic clusters. The core genome comprised only 43,14 % of the pan genome, i.e. 0.87 Mbp of 2.04 Mbp. The main annotated genomic differences reside in maltose, fructose and sucrose as well as nucleotide metabolism, use of electron acceptors, and exopolysacchride formation. Furthermore, all strains are well equipped to cope with oxidative stress via NADH oxidase and a distinct thiol metabolism. Only ten of 24 genomes contain two maltose phosphorylase genes (mapA and mapB). In F. sanfranciscensis TMW 1.897 only mapA was found. All strains except those from genomic cluster 2 contained the mannitol dehydrogenase and should therefore be able to use fructose as external electron acceptor. Moreover, six strains were able to grow on fructose as sole carbon source, as they contained a functional fructokinase gene. No growth was observed on pentoses, i.e. xylose, arabinose or ribose, as sole carbon source. This can be referred to the absence of ribose pyranase rbsD in all genomes, and absence of or mutations in numerous other genes, which are essential for arabinose and xylose metabolism. Seven strains were able to produce exopolysaccharides (EPS) from sucrose. In addition, the strains containing levS were able to grow on sucrose as sole carbon source. Strains of one cluster exhibit auxotrophies for purine nucleotides. The physiological and genomic analyses suggest that the biodiversity of F. sanfranciscensis is larger than anticipated. Consequently, "original" habitats and lifestyles of F. sanfranciscensis may vary but can generally be referred to an adaptation to sugary (maltose/sucrose/fructose-rich) and aerobic environments as found in plants and insects. It can dominate sourdoughs as a result of reductive evolution and cooperation with fructose-delivering, acetate-tolerant yeasts.
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Affiliation(s)
- Esther Rogalski
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Matthias A Ehrmann
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Technische Universität München, Freising, Germany.
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18
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Genomic and physiological insights into the lifestyle of Bifidobacterium species from water kefir. Arch Microbiol 2020; 202:1627-1637. [PMID: 32266422 DOI: 10.1007/s00203-020-01870-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/26/2020] [Accepted: 03/20/2020] [Indexed: 12/13/2022]
Abstract
Water kefir is a fermented beverage employing a natural microbial consortium, which harbours bifidobacteria, namely Bifidobacterium aquikefiri and Bifidobacterium tibiigranuli. However, little information is available on their metabolic properties or role in the consortium. In this study, we combined genomic and physiologic investigations to predict and characterize the properties of these organisms and their possible role in the consortium. When comparing the genomes of these psychrotrophic organisms with that of the three selected mesophilic probiotic Bifidobacterium strains, we could find 143 genes shared by the 3 known isolates of bifidobacteria from water kefir that do not occur in the probiotic strains. These include genes involved in acid and oxygen tolerance. In addition, their genomically predicted carbohydrate usage and transport suggest adaptation to sucrose and other plant-related sugars. Furthermore, they proved prototrophic for all amino acids in vitro, which enables them to cope with the strong amino acid limitation in water kefir.
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Kramer T, Kelleher P, van der Meer J, O'Sullivan T, Geertman JMA, Duncan SH, Flint HJ, Louis P. Comparative genetic and physiological characterisation of Pectinatus species reveals shared tolerance to beer-associated stressors but halotolerance specific to pickle-associated strains. Food Microbiol 2020; 90:103462. [PMID: 32336380 DOI: 10.1016/j.fm.2020.103462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/09/2020] [Accepted: 02/17/2020] [Indexed: 11/19/2022]
Abstract
Obligate anaerobic bacteria from the genus Pectinatus have been known to cause beer spoilage for over 40 years. Whole genome sequencing was performed on eleven beer spoilage strains (nine Pectinatus frisingensis, one Pectinatus cerevisiiphilus and one Pectinatus haikarae isolate), as well as two pickle spoilage species (Pectinatus brassicae MB591 and Pectinatus sottacetonis MB620) and the tolerance of all species to a range of environmental conditions was tested. Exploration of metabolic pathways for carbohydrates, amino acids and vitamins showed little difference between beer spoilage- and pickle spoilage-associated strains. However, genes for certain carbohydrate- and sulphur-containing amino acid-associated enzymes were only present in the beer spoilage group and genes for specific transporters and regulatory genes were uniquely found in the pickle spoilage group. Transporters for compatible solutes, only present in pickle-associated strains, likely explain their experimentally observed higher halotolerance compared to the beer spoilers. Genes involved in biofilm formation and ATP Binding Cassette (ABC) transporters potentially capable of exporting hop-derived antimicrobial compounds were found in all strains. All species grew in the presence of alcohol up to 5% alcohol by volume (ABV) and hops extract up to 80 ppm of iso-α-acids. Therefore, the species isolated from pickle processes may pose novel hazards in brewing.
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Affiliation(s)
- Timo Kramer
- University of Aberdeen, The Rowett Institute, Foresterhill, AB25 2ZD, Aberdeen, United Kingdom
| | - Philip Kelleher
- APC Microbiome Ireland, Food Science & Technology Building, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | | | - Tadhg O'Sullivan
- Heineken Supply Chain B.V., Burgemeester Smeetsweg 1, 2382 PH, Zoeterwoude, the Netherlands
| | - Jan-Maarten A Geertman
- Heineken Supply Chain B.V., Burgemeester Smeetsweg 1, 2382 PH, Zoeterwoude, the Netherlands
| | - Sylvia H Duncan
- University of Aberdeen, The Rowett Institute, Foresterhill, AB25 2ZD, Aberdeen, United Kingdom
| | - Harry J Flint
- University of Aberdeen, The Rowett Institute, Foresterhill, AB25 2ZD, Aberdeen, United Kingdom
| | - Petra Louis
- University of Aberdeen, The Rowett Institute, Foresterhill, AB25 2ZD, Aberdeen, United Kingdom.
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A Plasmid-Encoded Putative Glycosyltransferase Is Involved in Hop Tolerance and Beer Spoilage in Lactobacillus brevis. Appl Environ Microbiol 2020; 86:AEM.02268-19. [PMID: 31757821 DOI: 10.1128/aem.02268-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/20/2019] [Indexed: 11/20/2022] Open
Abstract
Lactobacillus brevis beer-spoiling strains harbor plasmids that contain genes such as horA, horC, and hitA which are known to confer hop tolerance. The L. brevis beer-spoiling strain UCCLBBS124, which possesses four plasmids, was treated with novobiocin, resulting in the isolation of UCCLBBS124 derivatives exhibiting hop sensitivity and an inability to grow in beer. One selected derivative was shown to have lost a single plasmid, here designated UCCLBBS124_D, which harbors the UCCLBBS124_pD0015 gene, predicted to encode a glycosyltransferase. Hop tolerance and growth in beer were restored when UCCLBBS124_pD0015 was introduced in one of these hop-sensitive derivatives on a plasmid. We hypothesize that this gene modifies the surface composition of the polysaccharide cell wall, conferring protection against hop compounds. Furthermore, the introduction of this gene in trans in L. brevis UCCLB521, a strain that cannot grow in and spoil beer, was shown to furnish the resulting strain with the ability to grow in beer, while its expression also conferred phage resistance. This study underscores how the acquisition of certain mobile genetic elements plays a role in hop tolerance and beer spoilage for strains of this bacterial species.IMPORTANCE Lactobacillus brevis is a member of the lactic acid bacteria and is often reported as the causative agent of food or beverage spoilage, in particular, that of beer. Bacterial spoilage of beer may result in product withdrawal or recall, with concomitant economic losses for the brewing industry. A very limited number of genes involved in beer spoilage have been identified and primarily include those involved in hop resistance, such as horA, hitA, and horC However, since none of these genes are universal, it is clear that there are likely (many) other molecular players involved in beer spoilage. Here, we report on the importance of a plasmid-encoded glycosyltransferase associated with beer spoilage by L. brevis that is involved in hop tolerance. The study highlights the complexity of the genetic requirements to facilitate beer spoilage and the role of multiple key players in this process.
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21
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Comparative genomics of Lactobacillus sakei supports the development of starter strain combinations. Microbiol Res 2019; 221:1-9. [DOI: 10.1016/j.micres.2019.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 11/19/2022]
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Bechtner J, Xu D, Behr J, Ludwig C, Vogel RF. Proteomic Analysis of Lactobacillus nagelii in the Presence of Saccharomyces cerevisiae Isolated From Water Kefir and Comparison With Lactobacillus hordei. Front Microbiol 2019; 10:325. [PMID: 30891008 PMCID: PMC6413804 DOI: 10.3389/fmicb.2019.00325] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/07/2019] [Indexed: 12/21/2022] Open
Abstract
Water kefir is a slightly alcoholic and traditionally fermented beverage, which is prepared from sucrose, water, kefir grains, and dried or fresh fruits (e.g., figs). Lactobacillus (L.) nagelii, L. hordei, and Saccharomyces (S.) cerevisiae are predominant and stable lactic acid bacteria and yeasts, respectively, isolated from water kefir consortia. The growth of L. nagelii and L. hordei are improved in the presence of S. cerevisiae. In this work we demonstrate that quantitative comparative proteomics enables the investigation of interactions between LAB and yeast to predict real-time metabolic exchange in water kefir. It revealed 73 differentially expressed (DE) in L. nagelii TMW 1.1827 in the presence of S. cerevisiae. The presence of the yeast induced changes in the changes in the carbohydrate metabolism of L. nagelii and affected reactions involved in NAD+/NADH homeostasis. Furthermore, the DE enzymes involved in amino acid biosynthesis or catabolism predict that S. cerevisiae releases glutamine, histidine, methionine, and arginine, which are subsequently used by L. nagelii to ensure its survival in the water kefir consortium. In co-culture with S. cerevisiae, L. nagelii profits from riboflavin, most likely secreted by the yeast. The reaction of L. nagelii to the presence of S. cerevisiae differs from that one of the previously studied L. hordei, which displays 233 differentially expressed proteins, changes in citrate metabolism and an antidromic strategy for NAD+/NADH homeostasis. So far, aggregation promotion factors, i.e., formation of a specific glucan and bifunctional enzymes were only detected in L. hordei.
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Affiliation(s)
- Julia Bechtner
- Lehrstuhl für Technische Mikrobiologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Di Xu
- Lehrstuhl für Technische Mikrobiologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Jürgen Behr
- Lehrstuhl für Technische Mikrobiologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany.,Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany
| | - Rudi F Vogel
- Lehrstuhl für Technische Mikrobiologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
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Xu D, Bechtner J, Behr J, Eisenbach L, Geißler AJ, Vogel RF. Lifestyle of Lactobacillus hordei isolated from water kefir based on genomic, proteomic and physiological characterization. Int J Food Microbiol 2019; 290:141-149. [DOI: 10.1016/j.ijfoodmicro.2018.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/10/2018] [Accepted: 10/03/2018] [Indexed: 10/28/2022]
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24
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Comparative genomics of Lactobacillus curvatus enables prediction of traits relating to adaptation and strategies of assertiveness in sausage fermentation. Int J Food Microbiol 2018; 286:37-47. [DOI: 10.1016/j.ijfoodmicro.2018.06.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/12/2018] [Accepted: 06/29/2018] [Indexed: 11/23/2022]
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25
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Janßen D, Eisenbach L, Ehrmann MA, Vogel RF. Assertiveness of Lactobacillus sakei and Lactobacillus curvatus in a fermented sausage model. Int J Food Microbiol 2018; 285:188-197. [DOI: 10.1016/j.ijfoodmicro.2018.04.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 11/15/2022]
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Comparative Genomics of Lactobacillus brevis Reveals a Significant Plasmidome Overlap of Brewery and Insect Isolates. Curr Microbiol 2018; 76:37-47. [DOI: 10.1007/s00284-018-1581-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
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27
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Lauterbach A, Geissler AJ, Eisenbach L, Behr J, Vogel RF. Novel diagnostic marker genes differentiate Saccharomyces
with respect to their potential application. JOURNAL OF THE INSTITUTE OF BREWING 2018. [DOI: 10.1002/jib.525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alexander Lauterbach
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
| | - Andreas J. Geissler
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
| | - Lara Eisenbach
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
| | - Jürgen Behr
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
- Bavarian Center for Biomolecular Mass Spectrometry; Gregor-Mendel Str. 4 85354 Freising Germany
| | - Rudi F. Vogel
- Lehrstuhl für Technische Mikrobiologie; Technische Universität München; Gregor-Mendel Str. 4 85354 Freising Germany
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28
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Fraunhofer ME, Geissler AJ, Wefers D, Bunzel M, Jakob F, Vogel RF. Characterization of β-glucan formation by Lactobacillus brevis TMW 1.2112 isolated from slimy spoiled beer. Int J Biol Macromol 2018; 107:874-881. [DOI: 10.1016/j.ijbiomac.2017.09.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/01/2017] [Accepted: 09/17/2017] [Indexed: 10/18/2022]
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29
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Bergsveinson J, Ziola B. Comparative genomic and plasmid analysis of beer-spoiling and non-beer-spoiling Lactobacillus brevis isolates. Can J Microbiol 2017; 63:970-983. [PMID: 28977764 DOI: 10.1139/cjm-2017-0405] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.
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Affiliation(s)
- Jordyn Bergsveinson
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada.,Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada
| | - Barry Ziola
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada.,Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada
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30
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Abstract
We report here the genome sequences of four Lactobacillus plantarum strains which vary in surface hydrophobicity. Bioinformatic analysis, using additional genomes of Lactobacillus plantarum strains, revealed a possible correlation between the cell wall teichoic acid-type and cell surface hydrophobicity and provide the basis for consecutive analyses.
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31
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Bergsveinson J, Kajala I, Ziola B. Next-generation sequencing approaches for improvement of lactic acid bacteria-fermented plant-based beverages. AIMS Microbiol 2017; 3:8-24. [PMID: 31294146 PMCID: PMC6604971 DOI: 10.3934/microbiol.2017.1.8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/12/2017] [Indexed: 12/31/2022] Open
Abstract
Plant-based beverages and milk alternatives produced from cereals and legumes have grown in popularity in recent years due to a range of consumer concerns over dairy products. These plant-based products can often have undesirable physiochemical properties related to flavour, texture, and nutrient availability and/or deficiencies. Lactic acid bacteria (LAB) fermentation offers potential remediation for many of these issues, and allows consumers to retain their perception of the resultant products as natural and additive-free. Using next-generation sequencing (NGS) or omics approaches to characterize LAB isolates to find those that will improve properties of plant-based beverages is the most direct way to product improvement. Although NGS/omics approaches have been extensively used for selection of LAB for use in the dairy industry, a comparable effort has not occurred for selecting LAB for fermenting plant raw substrates, save those used in producing wine and certain types of beer. Here we review the few and recent applications of NGS/omics to profile and improve LAB fermentation of various plant-based substrates for beverage production. We also identify specific issues in the production of various LAB fermented plant-based beverages that such NGS/omics applications have the power to resolve.
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Affiliation(s)
- Jordyn Bergsveinson
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK Canada S7N 0W8
| | - Ilkka Kajala
- VTT Technical Research Centre of Finland Ltd., PL1000, 02044VTT, Espoo, Finland
| | - Barry Ziola
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 2841 Royal University Hospital, 103 Hospital Drive, Saskatoon, SK Canada S7N 0W8
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32
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Multiple Genome Sequences of Important Beer-Spoiling Lactic Acid Bacteria. GENOME ANNOUNCEMENTS 2016; 4:4/5/e01077-16. [PMID: 27795248 PMCID: PMC5054319 DOI: 10.1128/genomea.01077-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Seven strains of important beer-spoiling lactic acid bacteria were sequenced using single-molecule real-time sequencing. Complete genomes were obtained for strains of Lactobacillus paracollinoides, Lactobacillus lindneri, and Pediococcus claussenii. The analysis of these genomes emphasizes the role of plasmids as the genomic foundation of beer-spoiling ability.
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Multiple Genome Sequences of the Important Beer-Spoiling Species Lactobacillus backii. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00826-16. [PMID: 27563041 PMCID: PMC5000825 DOI: 10.1128/genomea.00826-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lactobacillus backii is an important beer-spoiling species. Five strains isolated from four different breweries were sequenced using single-molecule real-time sequencing. Five complete genomes were generated, which will help to understand niche adaptation to beer and provide the basis for consecutive analyses.
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