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Cho GS, Stein M, Fiedler G, Igbinosa EO, Koll LP, Brinks E, Rathje J, Neve H, Franz CMAP. Polyphasic study of antibiotic-resistant enterobacteria isolated from fresh produce in Germany and description of Enterobacter vonholyi sp. nov. isolated from marjoram and Enterobacter dykesii sp. nov. isolated from mung bean sprout. Syst Appl Microbiol 2020; 44:126174. [PMID: 33370657 DOI: 10.1016/j.syapm.2020.126174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/29/2022]
Abstract
Forty-two antibiotic-resistant enterobacteria strains were isolated from fresh produce obtained from the northern German retail market. A polyphasic characterization based on both phenotypic and genotypic methods was used to identify predominant strains as Citrobacter (C.) gillenii, C. portucalensis, Enterobacter (En.) ludwigii, Escherichia (E.) coli and Klebsiella (K.) pneumoniae. 38.1% of the enterobacteria strains were resistant to tetracycline, while 23.8% and 9.5% of strains were resistant to streptomycin and chloramphenicol, respectively. A high percentage of Klebsiella (100%), Enterobacter (57.1%) and Citrobacter (42.9%) strains were also resistant to ampicillin, with some strains showing multiple resistances. For unequivocal species identification, the genomes of thirty strains were sequenced. Multilocus sequence analysis, average nucleotide identity and digital DNA-DNA hybridization showed that Enterobacter strains E1 and E13 were clearly clustered apart from Enterobacter species type strains below the species delineation cutoff values. Thus, strains E1T (=DSM 111347T, LMG 31875T) represents a novel species proposed as Enterobacter dykesii sp. nov., while strain E13T (=DSM 110788T, LMG 31764T) represent a novel species proposed as Enterobacter vonholyi sp. nov. Strains often possessed different serine β-lactamase genes, tet(A) and tet(D) tetracycline resistance genes and other acquired antibiotic resistance genes. Typical plasmid replicon types were determined. This study thus accurately identified the enterobacteria from fresh produce as species belonging to the genera Citrobacter, Enterobacter, Escherichia and Klebsiella, but also showed that these can carry potentially transferable antibiotic resistance genes and may thus contribute to the spread of these via the food route.
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Luzzi G, Brinks E, Fritsche J, Franz CMAP. Microbial composition of sweetness-enhanced yoghurt during fermentation and storage. AMB Express 2020; 10:131. [PMID: 32710182 PMCID: PMC7381539 DOI: 10.1186/s13568-020-01069-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/18/2020] [Indexed: 12/30/2022] Open
Abstract
The reformulation of dairy products to contain less added sugar can contribute to reducing sugar consumption, thereby reducing the risk of non-communicable diseases. The objective of this study was to investigate the microbial ecology of reformulated yoghurt, which was produced using bi-enzymatic modification of lactose to increase its sweetness by a factor of 2–3. Ultimately, this reformulation strategy could reduce the amount of added sugar needed for equal sweetness of the end product. The bi-enzymatic modification relied on utilisation of a β-galactosidase enzyme to convert the milk sugar lactose to galactose and glucose, followed by the enzymatic conversion of the glucose moiety to fructose using a glucose isomerase. The microbial ecology of reformulated yoghurt produced with two mixed starter culture preparations containing either Streptococcus (S.) thermophilus and Lactobacillus (Lb.) delbrueckii or S. thermophilus, Lb. acidophilus and Bifidobacterium sp. strains, was analysed during fermentation and cool storage using 16S rRNA based metagenomics. None of the yoghurt samples showed a significant difference in microbial composition between sweetness-enhanced and regular milk at all sampling time points during manufacture and storage of yoghurt. However, a significant difference between the microbiota of inoculated milk before and after fermentation was observed. In both types of yoghurt, the starter culture genera dominated the microbial ecology at the end of fermentation as expected, reducing the possibility of growth of potentially pathogenic or spoilage bacteria possibly resulting from a changed carbohydrate spectrum.
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Hylling O, Carstens AB, Kot W, Hansen M, Neve H, Franz CMAP, Johansen A, Ellegaard-Jensen L, Hansen LH. Two novel bacteriophage genera from a groundwater reservoir highlight subsurface environments as underexplored biotopes in bacteriophage ecology. Sci Rep 2020; 10:11879. [PMID: 32681144 PMCID: PMC7368026 DOI: 10.1038/s41598-020-68389-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 06/12/2020] [Indexed: 11/09/2022] Open
Abstract
Although bacteriophages are central entities in bacterial ecology and population dynamics, there is currently no literature on the genomes of bacteriophages isolated from groundwater. Using a collection of bacterial isolates from an aquifer as hosts, this study isolated, sequenced and characterised two bacteriophages native to the groundwater reservoir. Host phylogenetic analyses revealed that the phages targeted B. mycoides and a novel Pseudomonas species. These results suggest that both bacteriophages represent new genera, highlighting that groundwater reservoirs, and probably other subsurface environments as well, are underexplored biotopes in terms of the presence and ecology of bacteriophages.
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Kyrkou I, Carstens AB, Ellegaard-Jensen L, Kot W, Zervas A, Djurhuus AM, Neve H, Franz CMAP, Hansen M, Hansen LH. Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, "Silenusvirus". Sci Rep 2020; 10:8763. [PMID: 32472049 PMCID: PMC7260188 DOI: 10.1038/s41598-020-65366-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 05/04/2020] [Indexed: 11/10/2022] Open
Abstract
Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database, but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus "Silenusvirus".
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Fusco V, Chieffi D, Fanelli F, Logrieco AF, Cho G, Kabisch J, Böhnlein C, Franz CMAP. Microbial quality and safety of milk and milk products in the 21st century. Compr Rev Food Sci Food Saf 2020; 19:2013-2049. [DOI: 10.1111/1541-4337.12568] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 12/11/2022]
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Cho GS, Stein M, Brinks E, Rathje J, Lee W, Suh SH, Franz CMAP. Corrigendum to 'Serratia nevei sp. nov. and Serratia bockelmannii sp. nov., isolated from fresh produce in Germany and reclassification of Serratia marcescens subsp. sakuensis Ajithkumar et al. 2003 as a later heterotypic synonym of Serratia marcescens subsp. marcescens' [Syst. Appl. Microbiol. 43 (2020) 126055]. Syst Appl Microbiol 2020; 43:126082. [PMID: 32336497 DOI: 10.1016/j.syapm.2020.126082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, O'Toole PW, Pot B, Vandamme P, Walter J, Watanabe K, Wuyts S, Felis GE, Gänzle MG, Lebeer S. 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. Int J Syst Evol Microbiol 2020; 70:2782-2858. [PMID: 32293557 DOI: 10.1099/ijsem.0.004107] [Citation(s) in RCA: 1448] [Impact Index Per Article: 362.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic 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, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).
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Mattarelli P, Felis GE, Pot B, Holzapfel WH, Franz CMAP. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms Minutes of the closed meeting, 20 June 2019, Prague, Czech Republic. Int J Syst Evol Microbiol 2020; 70:2949-2951. [PMID: 32202991 DOI: 10.1099/ijsem.0.004104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Chieffi D, Fanelli F, Cho GS, Schubert J, Blaiotta G, Franz CMAP, Bania J, Fusco V. Novel insights into the enterotoxigenic potential and genomic background of Staphylococcus aureus isolated from raw milk. Food Microbiol 2020; 90:103482. [PMID: 32336356 DOI: 10.1016/j.fm.2020.103482] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 11/17/2022]
Abstract
In this study, 53 Staphylococcus (S.) aureus strains were typed by 16S-23S rDNA intergenic spacer region (ISR) typing and staphylococcal enterotoxin gene (SEg) typing for all the staphylococcal enterotoxin (se) and staphylococcal enterotoxin-like toxin (sel) genes known to date, revealing a higher discriminatory power than that of multi locus sequence typing. Six strains, one of each ISR- and SEg-type, were genome sequenced and the ability to produce some classical and new SEs when growing in milk was investigated. The manual analysis of the six genomes allowed us to confirm, correct and expand the results of common available genomic data pipelines such as VirulenceFinder. Moreover, it enabled us to (i) investigate the actual location of se and sel genes, even for genes such as selY, whose location (in the core genome) was so far unknown, (ii) find novel allelic variants of se and sel genes and pseudogenes, (iii) correctly annotate se and sel genes and pseudogenes, and (iv) discover a novel type of enterotoxin gene cluster (egc), i.e. the egc type 5 in strains 356P and 364P, while S. argenteus MSHR1132 harbored the egc type 6. Four of the six S. aureus strains produced sufficient amounts of SEA, SEC, SED and SEH in milk to cause staphylococcal food poisoning (SFP), with S. aureus 372 P being the highest producer of SED in milk found to date, producing as much as ca. 47,300 ng/mL and 49,200 ng/mL of SED, after 24 and 48 h of incubation in milk at 37 °C, respectively. S. aureus 372 P released a low amount of SER in milk, most likely because the seR gene was present as a pseudogene, putatively encoding only 51 amino acids. These findings confirm that not only the classical SEs, but also the new ones can represent a potential hazard for the consumers' health if produced in foods in sufficient amounts. Therefore, the detection of SEs in foods, especially if involved in SFP cases, should focus not only on classical, but also on all the new SEs and SEls known to date. Where reference methods are unavailable, the presence of the relevant genes, by using the conventional and real time PCR protocols we exhaustively provided herein, and their nucleotide sequences, should be investigated.
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Luzzi G, Steffens M, Clawin‐Rädecker I, Hoffmann W, Franz CMAP, Fritsche J, Lorenzen PC. Enhancing the sweetening power of lactose by enzymatic modification in the reformulation of dairy products. INT J DAIRY TECHNOL 2020. [DOI: 10.1111/1471-0307.12681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Hoffmann W, Luzzi G, Steffens M, Clawin‐Rädecker I, Franz CMAP, Fritsche J. Salt reduction in film‐ripened, semihard Edam cheese. INT J DAIRY TECHNOL 2019. [DOI: 10.1111/1471-0307.12675] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Fiedler G, Schneider C, Igbinosa EO, Kabisch J, Brinks E, Becker B, Stoll DA, Cho GS, Huch M, Franz CMAP. Antibiotics resistance and toxin profiles of Bacillus cereus-group isolates from fresh vegetables from German retail markets. BMC Microbiol 2019; 19:250. [PMID: 31706266 PMCID: PMC6842220 DOI: 10.1186/s12866-019-1632-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 10/29/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND This study aimed to evaluate the safety of raw vegetable products present on the German market regarding toxin-producing Bacillus cereus sensu lato (s.l.) group bacteria. RESULTS A total of 147 B. cereus s.l. group strains isolated from cucumbers, carrots, herbs, salad leaves and ready-to-eat mixed salad leaves were analyzed. Their toxinogenic potential was assessed by multiplex PCR targeting the hemolysin BL (hbl) component D (hblD), non-hemolytic enterotoxin (nhe) component A (nheA), cytotoxin K-2 (cytK-2) and the cereulide (ces) toxin genes. In addition, a serological test was used to detect Hbl and Nhe toxins. On the basis of PCR and serological results, none of the strains were positive for the cereulide protein/genes, while 91.2, 83.0 and 37.4% were positive for the Hbl, Nhe and CytK toxins or their genes, respectively. Numerous strains produced multiple toxins. Generally, strains showed resistance against the β-lactam antibiotics such as penicillin G and cefotaxim (100%), as well as amoxicillin/clavulanic acid combination and ampicillin (99.3%). Most strains were susceptible to ciprofloxacin (99.3%), chloramphenicol (98.6%), amikacin (98.0%), imipenem (93.9%), erythromycin (91.8%), gentamicin (88.4%), tetracycline (76.2%) and trimethoprim/sulfamethoxazole combination (52.4%). The genomes of eight selected strains were sequenced. The toxin gene profiles detected by PCR and serological test mostly agreed with those from whole-genome sequence data. CONCLUSIONS Our study showed that B. cereus s.l. strains encoding toxin genes occur in products sold on the German market and that these may pose a health risk to the consumer if present at elevated levels. Furthermore, a small percentage of these strains harbor antibiotic resistance genes. The presence of these bacteria in fresh produce should, therefore, be monitored to guarantee their safety.
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Tofalo R, Fusco V, Böhnlein C, Kabisch J, Logrieco AF, Habermann D, Cho GS, Benomar N, Abriouel H, Schmidt-Heydt M, Neve H, Bockelmann W, Franz CMAP. The life and times of yeasts in traditional food fermentations. Crit Rev Food Sci Nutr 2019; 60:3103-3132. [PMID: 31656083 DOI: 10.1080/10408398.2019.1677553] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Yeasts are eukaryotic microorganisms which have a long history in the biotechnology of food production, as they have been used since centuries in bread-making or in the production of alcoholic beverages such as wines or beers. Relative to this importance, a lot of research has been devoted to the study of yeasts involved in making these important products. The role of yeasts in other fermentations in association with other microorganisms - mainly lactic acid bacteria - has been relatively less studied, and often it is not clear if yeasts occurring in such fermentations are contaminants with no role in the fermentation, spoilage microorganisms or whether they actually serve a technological or functional purpose. Some knowledge is available for yeasts used as starter cultures in fermented raw sausages or in the production of acid curd cheeses. This review aimed to summarize the current knowledge on the taxonomy, the presence and potential functional or technological roles of yeasts in traditional fermented plant, dairy, fish and meat fermentations.
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Feyereisen M, Mahony J, Neve H, Franz CMAP, Noben JP, O’Sullivan T, Boer V, van Sinderen D. Biodiversity and Classification of Phages Infecting Lactobacillus brevis. Front Microbiol 2019; 10:2396. [PMID: 31681247 PMCID: PMC6805780 DOI: 10.3389/fmicb.2019.02396] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/03/2019] [Indexed: 11/13/2022] Open
Abstract
Lactobacillus brevis is a lactic acid bacterium that is known as a food and beverage spoilage organism, and more specifically as a beer-spoiler. Phages of L. brevis have been described, but very limited data is available regarding temperate phages of L. brevis. Temperate phages may exert benefits to the host, while they may also be employed to combat beer spoilage. The current study reports on the incidence of prophage sequences present in nineteen distinct L. brevis genomes. Prophage induction was evaluated using mitomycin C exposure followed by genome targeted-PCR, electron microscopy and structural proteome analysis. The morphological and genome sequence analyses revealed significant diversity among L. brevis prophages, which appear to be dominated by members of the Myoviridae phage family. Based on this analysis, we propose a classification of L. brevis phages into five groups.
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Cho GS, Cappello C, Schrader K, Fagbemigum O, Oguntoyinbo FA, Csovcsics C, Rösch N, Kabisch J, Neve H, Bockelmann W, Briviba K, Modesto M, Cilli E, Mattarelli P, Franz CMAP. Isolation and Characterization of Lactic Acid Bacteria from Fermented Goat Milk in Tajikistan. J Microbiol Biotechnol 2019; 28:1834-1845. [PMID: 30562882 DOI: 10.4014/jmb.1807.08011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The lactobacilli associated with a fermented goat milk product from Tajikistan were isolated to characterize their technological properties and antibiotic resistances in order to assess their suitability for development as starter cultures. In this study, twenty three strains were identified by 16S rRNA sequencing as typical dairy-associated lactic acid bacterial strains, i.e. L. plantarum, L. pentosus, L. delbrueckii, L. helveticus and L. paracasei. These strains were generally susceptible to most antibiotics tested in this study and this allowed a selection of strains as safe starters. The draft genomes of four representative strains were sequenced and the number of contigs of the four assembled genomes ranged from 51 to 245 and the genome sizes ranged from 1.75 to 3.24 Mbp. These representative strains showed differences in their growth behavior and pH-reducing abilities in in vitro studies. The co-inoculation of these Lactobacillus spp. strains together with a yeast Kluyveromyces marxianus MBT-5698, or together with the yeast and an additional Streptococcus thermophilus MBT-2, led to a pH reduction to 3.4 after 48 h. Only in the case of fermentation inoculated with the co-culture, the viscosity of the milk increased noticeably. In contrast, fermentations with single strains did not lead to gelation of the milk or to a decrease in the pH after 24h. The results of this study provide a comprehensive understanding of the predominant lactobacilli related to Tajikistani fermented milk products.
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Feyereisen M, Mahony J, Lugli GA, Ventura M, Neve H, Franz CMAP, Noben JP, O'Sullivan T, Sinderen DV. Isolation and Characterization of Lactobacillus brevis Phages. Viruses 2019; 11:v11050393. [PMID: 31035495 PMCID: PMC6563214 DOI: 10.3390/v11050393] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 11/22/2022] Open
Abstract
Lactobacillus brevis has been widely used in industry for fermentation purposes. However, it is also associated with the spoilage of foods and beverages, in particular, beer. There is an increasing demand for natural food preservation methods, and in this context, bacteriophages possess the potential to control such spoilage bacteria. Just a few studies on phages infecting Lactobacillus brevis have been performed to date and in the present study, we report the isolation and characterization of five virulent phages capable of infecting Lb. brevis strains. The analysis reveals a high diversity among the isolates, with members belonging to both, the Myoviridae and Siphoviridae families. One isolate, designated phage 3-521, possesses a genome of 140.8 kb, thus representing the largest Lb. brevis phage genome sequenced to date. While the isolated phages do not propagate on Lb. brevis beer-spoiling strains, phages showed activity against these strains, impairing the growth of some Lb. brevis strains. The results highlight the potential of bacteriophage-based treatments as an effective approach to prevent bacterial spoilage of beer.
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Beer F, Urbat F, Franz CMAP, Huch M, Kulling SE, Bunzel M, Bunzel D. The Human Fecal Microbiota Metabolizes Foodborne Heterocyclic Aromatic Amines by Reuterin Conjugation and Further Transformations. Mol Nutr Food Res 2019; 63:e1801177. [PMID: 30815965 DOI: 10.1002/mnfr.201801177] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/01/2019] [Indexed: 01/16/2023]
Abstract
SCOPE Heterocyclic aromatic amines (HAAs) are process-induced food contaminants with high mutagenic and/or carcinogenic potential. Although the human gut microbiota is known to affect the metabolism of dietary constituents, its impact on HAA metabolism and toxicity has been little studied. Here, the glycerol-dependent metabolism of seven foodborne HAAs (AαC, Trp-P-1, harman, norharman, PhIP, MeIQx, and MeIQ) by the human fecal microbiota is investigated. METHODS AND RESULTS As analyzed by HPLC-DAD/FLD, the extent of conversion is strongly dependent on glycerol supplementation and HAA structure. AαC (60-100%) and the 2-aminoimidazoazarenes (up to 58%) are especially prone to microbial conversion. Based on high-resolution MS and/or NMR spectroscopy data, 70 fecal metabolites are identified in total, mainly formed by chemical reactions with one or two molecules of microbially derived reuterin. Moreover, it has been demonstrated that the human fecal microbiota can further transform reuterin adducts by reduction and/or hydroxylation reactions. Upon isolation, some reuterin-induced HAA metabolites appear to be partially unstable, complicating structural identification. CONCLUSION The formation of microbial metabolites needs to be incorporated into risk assessment considerations for HAAs in human health. In this study, several HAA metabolites, mainly reuterin-dependent, are identified in vitro, providing the basis for future human studies investigating microbial HAA metabolism.
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Mattarelli P, Felis GE, Holzapfel WH, Franz CMAP. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of closed and open meetings, 3 September 2018, Berlin, Germany. Int J Syst Evol Microbiol 2019; 69:1521-1523. [PMID: 30896384 DOI: 10.1099/ijsem.0.003352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The meeting of International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Bifidobacterium,Lactobacillus and related organisms was held within the frame of the FoodMicro 2018 Congress (FoodMicro 2018, 3-6 September 2018, Berlin, Germany). The meeting comprised an open session with a workshop entitled 'Modern approaches of LAB identification and conservation' and a closed session on issues related to ICSP Subcommittee activities.
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Mattarelli P, Felis GE, Holzapfel WH, Franz CMAP. International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms. Minutes of open and closed meetings, 19 July 2016, Dublin, Ireland. Int J Syst Evol Microbiol 2019; 69:2172-2173. [PMID: 30896387 DOI: 10.1099/ijsem.0.003351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The meeting of International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Bifidobacterium, Lactobacillus and related organisms was held within the frame of the FoodMicro 2016 Congress in Dublin (FoodMicro 2016, 19-22 July 2016, Dublin, Ireland). The meeting comprised an open session with a workshop entitled 'Research and networking taxonomy in food with an emphasis on LAB' and a closed session on issues related to ICSP Subcommittee activities.
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Kupczok A, Neve H, Huang KD, Hoeppner MP, Heller KJ, Franz CMAP, Dagan T. Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades. Mol Biol Evol 2019; 35:1147-1159. [PMID: 29688542 PMCID: PMC5913663 DOI: 10.1093/molbev/msy027] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is quantified by the ratio of recombination to mutation. These rates have been estimated for bacteria; however, no estimates have been reported for phages. Here, we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We analyzed 34 isolates of the 936 group of Siphoviridae phages using a Lactococcus lactis strain from a single dairy over 29 years. We estimate a constant substitution rate of 1.9 × 10−4 substitutions per site per year due to mutation that is within the range of estimates for eukaryotic RNA and DNA viruses. The reconstruction of recombination events reveals a constant rate of five recombination events per year and 4.5 × 10−3 nucleotide alterations due to recombination per site per year. Thus, the recombination rate exceeds the substitution rate, resulting in a relative effect of recombination to mutation (r/m) of ∼24 that is homogenous over time. Especially in the early transcriptional region, we detect frequent gene loss and regain due to recombination with phages of the 936 group, demonstrating the role of the 936 group pangenome as a reservoir of genetic variation. The observed substitution rate homogeneity conforms to the neutral theory of evolution; hence, the neutral theory can be applied to phage genome evolution and also to genetic variation brought about by recombination.
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Hayes S, Duhoo Y, Neve H, Murphy J, Noben JP, Franz CMAP, Cambillau C, Mahony J, Nauta A, van Sinderen D. Identification of Dual Receptor Binding Protein Systems in Lactococcal 936 Group Phages. Viruses 2018; 10:v10120668. [PMID: 30486343 PMCID: PMC6315561 DOI: 10.3390/v10120668] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/14/2023] Open
Abstract
Siphoviridae of the lactococcal 936 group are the most commonly encountered bacteriophages in the dairy processing environment. The 936 group phages possess a discrete baseplate at the tip of their tail—a complex harbouring the Receptor Binding Protein (RBP) which is responsible for host recognition and attachment. The baseplate-encoding region is highly conserved amongst 936 phages, with 112 of 115 publicly available phages exhibiting complete synteny. Here, we detail the three exceptions (Phi4.2, Phi4R15L, and Phi4R16L), which differ from this genomic architecture in possessing an apparent second RBP-encoding gene upstream of the “classical” rbp gene. The newly identified RBP possesses an elongated neck region relative to currently defined 936 phage RBPs and is genetically distinct from defined 936 group RBPs. Through detailed characterisation of the representative phage Phi4.2 using a wide range of complementary techniques, we demonstrated that the above-mentioned three phages possess a complex and atypical baseplate structure. Furthermore, the presence of both RBPs in the tail tip of the mature virion was confirmed, while the anticipated host-binding capabilities of both proteins were also verified.
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Buttimer C, Lucid A, Neve H, Franz CMAP, O'Mahony J, Turner D, Lavigne R, Coffey A. Pectobacterium atrosepticum Phage vB_PatP_CB5: A Member of the Proposed Genus ' Phimunavirus'. Viruses 2018; 10:E394. [PMID: 30050020 PMCID: PMC6115819 DOI: 10.3390/v10080394] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 11/23/2022] Open
Abstract
Pectobacterium atrosepticum is a phytopathogen of economic importance as it is the causative agent of potato blackleg and soft rot. Here we describe the Pectobacterium phage vB_PatP_CB5 (abbreviated as CB5), which specifically infects the bacterium. The bacteriophage is characterized in detail and TEM micrographs indicate that it belongs to the Podoviridae family. CB5 shares significant pairwise nucleotide identity (≥80%) with P. atrosepticum phages φM1, Peat1, and PP90 and also shares common genome organization. Phylograms constructed using conserved proteins and whole-genome comparison-based amino acid sequences show that these phages form a distinct clade within the Autographivirinae. They also possess conserved RNA polymerase recognition and specificity loop sequences. Their lysis cassette resembles that of KP34virus, containing in sequential order a U-spanin, a holin, and a signal⁻arrest⁻release (SAR) endolysin. However, they share low pairwise nucleotide identity with the type phage of the KP34virus genus, Klebsiella phage KP34. In addition, phage KP34 does not possess several conserved proteins associated with these P. atrosepticum phages. As such, we propose the allocation of phages CB5, Peat1, φM1, and PP90 to a separate new genus designated Phimunavirus.
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Koberg S, Gieschler S, Brinks E, Wenning M, Neve H, Franz CMAP. Genome sequence of the novel virulent bacteriophage PMBT14 with lytic activity against Pseudomonas fluorescens DSM 50090 R. Arch Virol 2018; 163:2575-2577. [PMID: 29786121 DOI: 10.1007/s00705-018-3882-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/09/2018] [Indexed: 11/24/2022]
Abstract
Psychrotrophic gram-negative Pseudomonas spp. represent a serious problem in the dairy industry as they can cause spoilage of milk and dairy products. Bacteriophages have moved into focus as promising biocontrol agents for such food spoilage bacteria. The virulent Siphoviridae phage PMBT14 was isolated on a mutant variant of P. fluorescens DSM 50090 challenged with an unrelated virulent P. fluorescens DSM 50090 Podoviridae phage (i.e., mutant strain DSM 50090R). PMBT14 has a 47,820-bp dsDNA genome with 76 predicted open reading frames (ORFs). Its genome shows no significant sequence similarity to that of known phages, suggesting that PMBT14 represents a novel phage. Phage PMBT14 could be a promising biocontrol agent for P. fluorescens in milk or dairy foods.
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O'Sullivan L, Lucid A, Neve H, Franz CMAP, Bolton D, McAuliffe O, Paul Ross R, Coffey A. Comparative genomics of Cp8viruses with special reference to Campylobacter phage vB_CjeM_los1, isolated from a slaughterhouse in Ireland. Arch Virol 2018; 163:2139-2154. [PMID: 29687158 DOI: 10.1007/s00705-018-3845-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 03/10/2018] [Indexed: 01/08/2023]
Abstract
Campylobacter phage vB_CjeM_Los1 was recently isolated from a slaughterhouse in the Republic of Ireland using the host Campylobacter jejuni subsp. jejuni PT14, and full-genome sequencing and annotation were performed. The genome was found to be 134,073 bp in length and to contain 169 predicted open reading frames. Transmission electron microscopy images of vB_CjeM_Los1 revealed that it belongs to the family Myoviridae, with tail fibres observed in both extended and folded conformations, as seen in T4. The genome size and morphology of vB_CjeM_Los1 suggest that it belongs to the genus Cp8virus, and seven other Campylobacter phages with similar size characteristics have also been fully sequenced. In this work, comparative studies were performed in relation to genomic rearrangements and conservation within each of the eight genomes. None of the eight genomes were found to have undergone internal rearrangements, and their sequences retained more than 98% identity with one another despite the widespread geographical distribution of each phage. Whole-genome phylogenetics were also performed, and clades were shown to be representative of the differing number of tRNAs present in each phage. This may be an indication of lineages within the genus, despite their striking homology.
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Cho GS, Li B, Rostalsky A, Fiedler G, Rösch N, Igbinosa E, Kabisch J, Bockelmann W, Hammer P, Huys G, Franz CMAP. Diversity and Antibiotic Susceptibility of Acinetobacter Strains From Milk Powder Produced in Germany. Front Microbiol 2018; 9:536. [PMID: 29636733 PMCID: PMC5880893 DOI: 10.3389/fmicb.2018.00536] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/08/2018] [Indexed: 12/23/2022] Open
Abstract
Forty-seven Acinetobacter spp. isolates from milk powder obtained from a powdered milk producer in Germany were investigated for their antibiotic resistance susceptibilities, in order to assess whether strains from food harbor multiple antibiotic resistances and whether the food route is important for dissemination of resistance genes. The strains were identified by 16S rRNA and rpoB gene sequencing, as well as by whole genome sequencing of selected isolates and their in silico DNA-DNA hybridization (DDH). Furthermore, they were genotyped by rep-PCR together with reference strains of pan-European groups I, II, and III strains of Acinetobacter baumannii. Of the 47 strains, 42 were identified as A. baumannii, 4 as Acinetobacter Pittii, and 1 as Acinetobacter calcoaceticus based on 16S rRNA gene sequencing. In silico DDH with the genome sequence data of selected strains and rpoB gene sequencing data suggested that the five non-A. baumannii strains all belonged to A. pittii, suggesting that the rpoB gene is more reliable than the 16S rRNA gene for species level identification in this genus. Rep-PCR genotyping of the A. baumannii strains showed that these could be grouped into four groups, and that some strains clustered together with reference strains of pan-European clinical group II and III strains. All strains in this study were intrinsically resistant toward chloramphenicol and oxacillin, but susceptible toward tetracycline, tobramycin, erythromycin, and ciprofloxacin. For cefotaxime, 43 strains (91.5%) were intermediate and 3 strains (6.4%) resistant, while 3 (6.4%) and 21 (44.7%) strains exhibited resistance to cefepime and streptomycin, respectively. Forty-six (97.9%) strains were susceptible to amikacin and ampicillin-sulbactam. Therefore, the strains in this study were generally not resistant to the clinically relevant antibiotics, especially tobramycin, ciprofloxacin, cefepime, and meropenem, suggesting that the food route probably poses only a low risk for multidrug resistant Acinetobacter strains or resistance genes.
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