1
|
Gómez-Govea MA, Ramírez-Ahuja MDL, Contreras-Perera Y, Jiménez-Camacho AJ, Ruiz-Ayma G, Villanueva-Segura OK, Trujillo-Rodríguez GDJ, Delgado-Enciso I, Martínez-Fierro ML, Manrique-Saide P, Puerta-Guardo H, Flores-Suárez AE, Ponce-García G, Rodríguez-Sánchez IP. Suppression of Midgut Microbiota Impact Pyrethroid Susceptibility in Aedes aegypti. Front Microbiol 2022; 13:761459. [PMID: 35979482 PMCID: PMC9376455 DOI: 10.3389/fmicb.2022.761459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
Aedes aegypti is a mosquito that transmits viral diseases such as dengue, chikungunya, Zika, and yellow fever. The insect’s microbiota is recognized for regulating several biological processes, including digestion, metabolism, egg production, development, and immune response. However, the role of the bacteria involved in insecticide susceptibility has not been established. Therefore, the objective of this study was to characterize the resident microbiota in a field population of A. aegypti to evaluate its role associated with susceptibility to the insecticides permethrin and deltamethrin. Mosquitoes were fed 10% sucrose mixed with antibiotics and then exposed to insecticides using a diagnostic dose. DNA was extracted, and sequencing of bacterial 16S rRNA was carried out on Illumina® MiSeq™. Proteobacteria (92.4%) and Bacteroidetes (7.6%) were the phyla, which are most abundant in mosquitoes fed with sucrose 10%. After exposure to permethrin, the most abundant bacterial species were Pantoea agglomerans (38.4%) and Pseudomonas azotoformans-fluorescens-synxantha (14.2%). Elizabethkingia meningoseptica (38.4%) and Ps. azotoformans-fluorescens-synxantha (26.1%) were the most abundant after exposure to deltamethrin. Our results showed a decrease in mosquitoes’ survival when exposed to permethrin, while no difference in survival when exposed to deltamethrin when the microbiota was modified. We found that the change in microbiota modifies the response of mosquitoes to permethrin. These results are essential for a better understanding of mosquito physiology in response to insecticides.
Collapse
Affiliation(s)
- Mayra A. Gómez-Govea
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Laboratorio de Fisiología Molecular y Estructural, San Nicolás de los Garza, Mexico
| | - María de Lourdes Ramírez-Ahuja
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Laboratorio de Fisiología Molecular y Estructural, San Nicolás de los Garza, Mexico
| | - Yamili Contreras-Perera
- Unidad Colaborativa de Bioensayos Entomológicos (UCBE) y del Laboratorio de Control Biológico (LCB) para Ae. aegypti, Universidad Autónoma de Yucatán (UADY), Mérida, Mexico
| | - Armando J. Jiménez-Camacho
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Laboratorio de Fisiología Molecular y Estructural, San Nicolás de los Garza, Mexico
| | - Gabriel Ruiz-Ayma
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biologicas, Laboratorio de Biológía de la Conservación, San Nicolás de los Garza, Mexico
| | - Olga Karina Villanueva-Segura
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Laboratorio de Fisiología Molecular y Estructural, San Nicolás de los Garza, Mexico
| | - Gerardo de Jesús Trujillo-Rodríguez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Laboratorio de Fisiología Molecular y Estructural, San Nicolás de los Garza, Mexico
| | | | - Margarita L. Martínez-Fierro
- Universidad Autónoma de Zacatecas, Laboratorio de Medicina Molecular, Unidad Académica de Medicina Humana, Zacatecas, Mexico
| | - Pablo Manrique-Saide
- Unidad Colaborativa de Bioensayos Entomológicos (UCBE) y del Laboratorio de Control Biológico (LCB) para Ae. aegypti, Universidad Autónoma de Yucatán (UADY), Mérida, Mexico
| | - Henry Puerta-Guardo
- Unidad Colaborativa de Bioensayos Entomológicos (UCBE) y del Laboratorio de Control Biológico (LCB) para Ae. aegypti, Universidad Autónoma de Yucatán (UADY), Mérida, Mexico
| | - Adriana E. Flores-Suárez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Zoología de Invertebrados, San Nicolás de los Garza, Mexico
| | - Gustavo Ponce-García
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Zoología de Invertebrados, San Nicolás de los Garza, Mexico
| | - Iram P. Rodríguez-Sánchez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Laboratorio de Fisiología Molecular y Estructural, San Nicolás de los Garza, Mexico
- *Correspondence: Iram P. Rodríguez-Sánchez,
| |
Collapse
|
2
|
Lacorte GA, Cruvinel LA, de Paula Ávila M, Dias MF, de Abreu Pereira A, Nascimento AMA, de Melo Franco BDG. Investigating the influence of Food Safety Management Systems (FSMS) on microbial diversity of Canastra cheeses and their processing environments. Food Microbiol 2022; 105:104023. [DOI: 10.1016/j.fm.2022.104023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022]
|
3
|
Mjølnerød EB, Nilsen HK, Gulla S, Riborg A, Bottolfsen KL, Wiklund T, Christiansen D, López Romalde JÁ, Scholz F, Colquhoun DJ. Multilocus sequence analysis reveals different lineages of Pseudomonas anguilliseptica associated with disease in farmed lumpfish (Cyclopterus lumpus L.). PLoS One 2021; 16:e0259725. [PMID: 34807918 PMCID: PMC8608339 DOI: 10.1371/journal.pone.0259725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022] Open
Abstract
The bacterium Pseudomonas anguilliseptica has in recent years emerged as a serious threat to production of lumpfish in Norway. Little is known about the population structure of this bacterium despite its association with disease in a wide range of different fish species throughout the world. The phylogenetic relationships between 53 isolates, primarily derived from diseased lumpfish, but including a number of reference strains from diverse geographical origins and fish species, were reconstructed by Multi-Locus Sequence Analysis (MLSA) using nine housekeeping genes (rpoB, atpD, gyrB, rpoD, ileS, aroE, carA, glnS and recA). MLSA revealed a high degree of relatedness between the studied isolates, altough the seven genotypes identified formed three main phylogenetic lineages. While four genotypes were identified amongst Norwegian lumpfish isolates, a single genotype dominated, irrespective of geographic origin. This suggests the existence of a dominant genotype associated with disease in production of lumpfish in Norwegian aquaculture. Elucidation of the population structure of the bacterium has provided valuable information for potential future vaccine development.
Collapse
Affiliation(s)
| | | | - Snore Gulla
- Norwegian Veterinary Institute, Oslo, Norway
| | - Andreas Riborg
- Norwegian Veterinary Institute, Oslo, Norway
- Vaxxinova AS, Bergen, Norway
| | | | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Debes Christiansen
- Food and Veterinary Agency, National Reference Laboratory for Fish Diseases, Tórshavn, Faroe Islands
| | - Jesús Ángel López Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Duncan John Colquhoun
- University of Bergen, Institute of Biological Science, Bergen, Norway
- Norwegian Veterinary Institute, Oslo, Norway
- * E-mail:
| |
Collapse
|
4
|
Pseudomonas spp.: Are Food Grade Organic Acids Efficient against These Spoilage Microorganisms in Fresh Cheeses? Foods 2021; 10:foods10040891. [PMID: 33921594 PMCID: PMC8074068 DOI: 10.3390/foods10040891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/01/2021] [Accepted: 04/15/2021] [Indexed: 11/16/2022] Open
Abstract
Psychrotolerant Pseudomonas spp. are among the most common spoilage agents in fresh, soft and semi-soft cheeses; therefore, hurdles inhibiting their growth are in strong demand by producers. This study aimed to establish Minimal Inhibiting Concentrations (MICs) of lactic and acetic acid towards P. fluorescens and to evaluate the efficacy of a cheese surface treatment with these two organic acids. MICs were determined in Brain Heart Infusion broth at 30 °C: the inhibition was achieved at a concentration of 49.96 mM and 44.40 mM of acetic and lactic acid, respectively. Two series of inhibition tests were performed on fresh “Primo sale” cheese, inoculated with P. brenneri MGM3, then dipped into different acid solutions (acetic acid: 49.96, 99.92 and 149.88 mM; lactic acid: 44.40, 88.80 and 133.20 mM) and stored at 6 °C. P. brenneri MGM3 were enumerated, including a control series. A significantly lower growth was revealed at the highest concentrations tested, both for acetic (p < 0.01) and lactic acid (p < 0.05) if compared to control samples. A conditioning of “Primo sale” surface with organic acid solutions could be a useful hurdle for Pseudomonas inhibition and shelf-life extension; it should be applied in combination with other mild interventions to fight spoilage and maintain the original product characteristics.
Collapse
|
5
|
Carrascosa C, Martínez R, Sanjuán E, Millán R, Del Rosario-Quintana C, Acosta F, García A, Jaber JR. Identification of the Pseudomonas fluorescens group as being responsible for blue pigment on fresh cheese. J Dairy Sci 2021; 104:6548-6558. [PMID: 33838893 DOI: 10.3168/jds.2020-19517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022]
Abstract
New cases of blue cheese discoloration has led to recent research to identify the causal agent and factors that favor blue pigment appearing. Nonetheless, very few reports have described the source of contamination and the measurements to eradicate the microbiological source on cheese farms by determining the relation between blue discoloration on fresh cheese and the Pseudomonas fluorescens group. Thus, 60 samples from a cheese farm (cheese, equipment surfaces, tap water, and raw and pasteurized milk) were analyzed by phenotypical, MALDI-TOF, 16S rRNA sequencing and pulsed-field gel electrophoresis tests to determine the causal agent. The results obtained by pulsed-field gel electrophoresis with restriction enzymes XbaI and SpeI confirmed tap water as the initial contaminated source. The above-mentioned result was essential to avoid Pseudomonas contamination due to the most residual microorganisms being inactivated through a new disinfection program.
Collapse
Affiliation(s)
- Conrado Carrascosa
- Food Hygiene Unit, Department of Animal Pathology, Animal Production, Bromatology, and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Arucas, 35413 Las Palmas, Spain.
| | - Remigio Martínez
- Red de Grupos de Investigación en Recursos Faunísticos, Instituto de Biotecnología Ganadera y Cinegética (INBIO), Facultad de Veterinaria, Universidad de Extremadura, 10003 Cáceres, Spain
| | - Esther Sanjuán
- Food Hygiene Unit, Department of Animal Pathology, Animal Production, Bromatology, and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Arucas, 35413 Las Palmas, Spain
| | - Rafael Millán
- Food Hygiene Unit, Department of Animal Pathology, Animal Production, Bromatology, and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Arucas, 35413 Las Palmas, Spain
| | - Cristóbal Del Rosario-Quintana
- Microbiology Service, Complejo Hospitalario Materno-Insular de Gran Canaria, Canary Health Service, 35016, Las Palmas de Gran Canaria, Spain
| | - Félix Acosta
- Grupo de Investigación de Acuicultura (GIA), Instituto EcoAqua, Universidad de Las Palmas de Gran Canaria, Spain
| | - Alfredo García
- Department of Animal Production, CICYTEX-La Orden, 06187 Junta de Extremadura, Spain
| | - José R Jaber
- Department of Morphology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Arucas, 35413 Las Palmas, Spain
| |
Collapse
|
6
|
Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Kröckel L. Pseudomonas paracarnis sp. nov., isolated from refrigerated beef. Int J Syst Evol Microbiol 2021; 71. [PMID: 33480838 DOI: 10.1099/ijsem.0.004652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a project focusing on the diversity of meat microbiota associated with beef ripening, a Pseudomonas strain was isolated exhibiting high 16S rRNA gene sequence similarities (>99 %) to Pseudomonas carnis DSM 107652T, P. lactis DSM 29167T, P. paralactis DSM 29164T and P. azotoformans DSM 18862T. Phylogenetic analysis of the complete rpoB gene sequences of the isolate V5/DAB/2/5T indicated a separate branch with about 99.0 % nucleotide identities to the closest relatives P. carnis DSM 107652T, P. lactis DSM 29167T and P. paralactis DSM 29164T, while average nucleotide identities (ANIb) calculated from the draft genomes were 94.8, 94.2 and 90.2 %, respectively. Pairwise genome-to-genome distance calculations (GGDC) resulted in values of 67.7, 63.5 and 45.7 %, respectively, lying below the actual species demarcation line as well. A second isolate, UBT403, was detected some years later by using matrix-assisted laser desorption ionization-time of flight MS of the microbiota of minced beef. The fatty acid profile of V5/DAB/2/5T consisted of C16 : 0, summed feature C 16 : 1 ω7c/iso-C15 : 0 2-OH, C18 : 1 ω7c, C17 : 0 cyclo, C12 : 0, C12 : 0 3-OH, C10 : 0 3-OH and C12 : 0 2-OH. The major cellular lipids were aminopholipids, phospholipids, phosphatidylethanolamine and phosphatidylglycerol; the major quinone was Q9 with a minor proportion of Q8. Based on phenotypic and chemotaxonomic characterizations, the isolates can be considered as representing a novel species, for which the name Pseudomonas paracarnis sp. nov. is proposed. The type strain is V5/DAB/2/5T (=DSM 111363T=LMG 31846T); a second strain is UBT403 (=DSM 111362=LMG 31847).
Collapse
Affiliation(s)
- Sonja Lick
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann-Straße 20, D-95326 Kulmbach, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Annika Winkler
- Center for Biotechnology - CeBiTec, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Christina Grimmler
- Chair of Bioanalytical Sciences and Food Analysis, University Bayreuth, Universitätsstraße 30, D-95447 Bayreuth and Max Rubner-Institut, E.C.-Baumann Straße 20, D-95326 Kulmbach, Germany.,Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann-Straße 20, D-95326 Kulmbach, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Lothar Kröckel
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann-Straße 20, D-95326 Kulmbach, Germany
| |
Collapse
|
7
|
Reichler SJ, Murphy SI, Martin NH, Wiedmann M. Identification, subtyping, and tracking of dairy spoilage-associated Pseudomonas by sequencing the ileS gene. J Dairy Sci 2021; 104:2668-2683. [PMID: 33455773 DOI: 10.3168/jds.2020-19283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/25/2020] [Indexed: 11/19/2022]
Abstract
Pseudomonas spp. are important spoilage bacteria that negatively affect the quality of refrigerated fluid milk and uncultured cheese by generating unwanted odors, flavors, and pigments. They are frequently found in dairy plant environments and enter dairy products predominantly as postpasteurization contaminants. Current subtyping and characterization methods for dairy-associated Pseudomonas are often labor-intensive and expensive or provide limited and possibly unreliable classification information (e.g., to the species level). Our goal was to identify a single-copy gene that could be analyzed in dairy spoilage-associated Pseudomonas for preliminary species-level identification, subtyping, and phenotype prediction. We tested 7 genes previously targeted in a Pseudomonas fluorescens multilocus sequence typing scheme for their individual suitability in this application using a set of 113 Pseudomonas spp. isolates representing the diversity of typical pasteurized milk contamination. For each of the 7 candidate genes, we determined the success rate of PCR and sequencing for these 113 isolates as well as the level of discrimination for species identification and subtyping that the sequence data provided. Using these metrics, we selected a single gene, isoleucyl tRNA synthetase (ileS), which had the most suitable traits for simple and affordable single-gene Pseudomonas characterization. This was based on the number of isolates successfully sequenced for ileS (113/113), the number of unique allelic types assigned (83, compared with 50 for 16S rDNA), nucleotide and sequence diversity measures (e.g., number of unique SNP and Simpson index), and tests for genetic recombination. The discriminatory ability of ileS sequencing was confirmed by separation of 99 additional dairy Pseudomonas spp. isolates, which were indistinguishable by 16S rDNA sequencing, into 28 different ileS allelic types. Further, we used whole-genome sequencing data to demonstrate the similarities in ileS-based phylogenetic clustering to whole-genome-based clustering for 27 closely related dairy-associated Pseudomonas spp. isolates and for 178 Pseudomonas type strains. We also found that dairy-associated Pseudomonas within an ileS cluster typically shared the same proteolytic and lipolytic activities. Use of ileS sequencing provides a promising strategy for affordable initial characterization of Pseudomonas isolates, which will help the dairy industry identify, characterize, and track Pseudomonas in their facilities and products.
Collapse
Affiliation(s)
- S J Reichler
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - S I Murphy
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - N H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - M Wiedmann
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853.
| |
Collapse
|
8
|
Evaluation of bacterial communities of Grana Padano cheese by DNA metabarcoding and DNA fingerprinting analysis. Food Microbiol 2020; 93:103613. [PMID: 32912585 DOI: 10.1016/j.fm.2020.103613] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
The composition of the bacterial community of Grana Padano (GP) cheese was evaluated by an amplicon-based metagenomic approach (DNA metabarcoding) and RAPD-PCR fingerprinting. One hundred eighteen cheeses, which included 118 dairies located in the production area of GP, were collected. Two hundred fifty-four OTUs were detected, of which 82 were further discriminated between dominant (32 OTUs; > 1% total reads) and subdominant (50 OTUs; between 0.1% and 1% total reads) taxa. Lactobacillus (L.) delbrueckii, Lacticaseibacillus (Lact.) rhamnosus, Lact. casei, Limosilactobacillus fermentum, Lactococcus (Lc.) raffinolactis, L. helveticus, Streptococcus thermophilus, and Lc. lactis were the major dominant taxa ('core microbiota'). The origin of samples significantly impacted on both richness, evenness, and the relative abundance of bacterial species, with peculiar pattern distribution among the five GP production regions. A differential analysis allowed to find bacterial species significantly associated with specific region pairings. The analysis of pattern similarity among RAPD-PCR profiles highlighted the presence of a 'core' community banding pattern present in all the GP samples, which was strictly associated with the core microbiota highlighted by DNA metabarcoding. A trend to group samples according to the five production regions was also observed. This study widened our knowledge on the bacterial composition and ecology of Grana Padano cheese.
Collapse
|
9
|
Reichler S, Murphy S, Erickson A, Martin N, Snyder A, Wiedmann M. Interventions designed to control postpasteurization contamination in high-temperature, short-time-pasteurized fluid milk processing facilities: A case study on the effect of employee training, clean-in-place chemical modification, and preventive maintenance programs. J Dairy Sci 2020; 103:7569-7584. [DOI: 10.3168/jds.2020-18186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/26/2020] [Indexed: 01/21/2023]
|
10
|
Reichler SJ, Martin NH, Evanowski RL, Kovac J, Wiedmann M, Orsi RH. A century of gray: A genomic locus found in 2 distinct Pseudomonas spp. is associated with historical and contemporary color defects in dairy products worldwide. J Dairy Sci 2019; 102:5979-6000. [DOI: 10.3168/jds.2018-16192] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/23/2019] [Indexed: 11/19/2022]
|
11
|
A Novel Oligonucleotide Pair for Genotyping Members of the Pseudomonas Genus by Single-Round PCR Amplification of the gyrB Gene. Methods Protoc 2018. [PMCID: PMC6481054 DOI: 10.3390/mps1030024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas is a phylogenetically diverse bacterial genus which is broadly distributed in different ecological niches, and whose taxonomy is continuously under revision. For that purpose, gyrB is one of the housekeeping genes routinely used for multilocus sequence analysis (MLSA). As we noticed that there was not a single primer pair available in the literature suitable for direct sequencing of this gene, we decided to design a unique oligonucleotide pair and to set up a polymerase chain reaction (PCR) protocol to obtain a single amplicon for the entire Pseudomonas genus. Based on the available gyrB sequence from 148 Pseudomonas species, we identified highly conserved regions to design oligonucleotides without fully degenerate positions. We then set up cycling conditions for achieving high specificity and yield of the PCR protocol. Then, we showed that the amplicons produced with this procedure were appropriate for direct sequencing with both primers, obtaining more than 95% of amplicons coverage. Finally, we demonstrated that a PCR-RFLP (restriction fragment length polymorphism) approach served to differentiate among Pseudomonas species, and even between members of the same species.
Collapse
|
12
|
Reichler SJ, Trmčić A, Martin NH, Boor KJ, Wiedmann M. Pseudomonas fluorescens group bacterial strains are responsible for repeat and sporadic postpasteurization contamination and reduced fluid milk shelf life. J Dairy Sci 2018; 101:7780-7800. [PMID: 29960782 DOI: 10.3168/jds.2018-14438] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/11/2018] [Indexed: 01/18/2023]
Abstract
Postpasteurization contamination (PPC) of high temperature, short time-pasteurized fluid milk by gram-negative (GN) bacteria continues to be an issue for processors. To improve PPC control, a better understanding of PPC patterns in dairy processing facilities over time and across equipment is needed. We thus collected samples from 10 fluid milk processing facilities to (1) detect and characterize PPC patterns over time, (2) determine the efficacy of different media to detect PPC, and (3) characterize sensory defects associated with PPC. Specifically, we collected 280 samples of high temperature, short time-pasteurized milk representing different products (2%, skim, and chocolate) and different fillers over 4 samplings performed over 11 mo at each of the 10 facilities. Standard plate count (SPC) as well as total GN, coliform, and Enterobacteriaceae (EB) counts were performed upon receipt and after 7, 10, 14, 17, and 21 d of storage at 6°C. We used 16S rDNA sequencing to characterize representative bacterial isolates from (1) test days with SPC >20,000 cfu/mL and (2) all samples with presumptive GN, coliforms, or EB. Day-21 samples were also evaluated by a trained defect judging panel. By d 21, 226 samples had SPC >20,000 cfu/mL on at least 1 d of shelf life; GN bacteria were found in 132 of these 226 samples, indicating PPC. Crystal violet tetrazolium agar detected PPC with the greatest sensitivity. Spoilage due to PPC was predominantly associated with Pseudomonas (isolated from 101 of the 132 samples with PPC); coliforms and EB were found in 27 and 37 samples with spoilage due to PPC, respectively. Detection of Pseudomonas and Acinetobacter was associated with lower flavor scores; coagulated, fruity fermented, and unclean defects were more prevalent in d-21 samples with PPC. Repeat isolation of Pseudomonas fluorescens group strains with identical partial 16S rDNA sequence types was observed in 8 facilities. In several facilities, specific lines, products, or processing days were linked to repeat product contamination with Pseudomonas with identical sequence types. Our data show that PPC due to Pseudomonas remains a major challenge for fluid milk processors; the inability of coliform and EB tests to detect Pseudomonas may contribute to this. Our data also provide important initial insights into PPC patterns (e.g., line-specific contamination), supporting the importance of molecular subtyping methods for identification of PPC sources.
Collapse
Affiliation(s)
- S J Reichler
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - A Trmčić
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - N H Martin
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - K J Boor
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - M Wiedmann
- Milk Quality Improvement Program, Department of Food Science, Cornell University, Ithaca, NY 14853.
| |
Collapse
|
13
|
Stellato G, Utter DR, Voorhis A, De Angelis M, Eren AM, Ercolini D. A Few Pseudomonas Oligotypes Dominate in the Meat and Dairy Processing Environment. Front Microbiol 2017; 8:264. [PMID: 28303120 PMCID: PMC5332365 DOI: 10.3389/fmicb.2017.00264] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
The occurrence of bacteria in the food processing environments plays a key role in food contamination and development of spoilage. Species of the genus Pseudomonas are recognized as major food spoilers and the capability to actually determine spoilage can be species- as well as strain-dependent. In order to improve the taxonomic resolution of 16S rRNA gene amplicons, in this study we used oligotyping to investigate the diversity of Pseudomonas populations in meat and dairy processing environments. Sequences of the V1-V3 regions from previous studies were used, including environmental swabs and food samples from both meat and dairy processing plants. We showed that the most frequently found oligotypes belonged to Pseudomonas fragi and P. fluorescens, that the most abundant oligotypes co-occurred, and were shared between the meat and dairy datasets. All the oligotypes occurring in foods were also identified in the environmental samples of the corresponding plants, highlighting the important role of the environment as a source of strains for food contamination. Oligotypes of the same species showed different levels depending on food processing and type of sample, suggesting that different strains of the same species can have different adaptation efficiency, leading to resilient bacterial associations.
Collapse
Affiliation(s)
- Giuseppina Stellato
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico IIPortici, Italy
| | - Daniel R. Utter
- Department of Organismic and Evolutionary Biology, Harvard University, CambridgeMA, USA
| | - Andy Voorhis
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods HoleMA, USA
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo MoroBari, Italy
| | - A. Murat Eren
- Department of Medicine, University of Chicago, ChicagoIL, USA
| | - Danilo Ercolini
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico IIPortici, Italy
| |
Collapse
|
14
|
Puga CH, Orgaz B, SanJose C. Listeria monocytogenes Impact on Mature or Old Pseudomonas fluorescens Biofilms During Growth at 4 and 20°C. Front Microbiol 2016; 7:134. [PMID: 26913024 PMCID: PMC4753298 DOI: 10.3389/fmicb.2016.00134] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/25/2016] [Indexed: 12/11/2022] Open
Abstract
Changes in spatial organization, as observed by confocal laser scanning microscopy (CLSM), viable cell content, biovolume, and substratum surface coverage of the biofilms formed on glass by Pseudomonas fluorescens resulting from co-culture with Listeria monocytogenes, were examined. Two strains of L. monocytogenes, two culture temperatures and two biofilm developmental stages were investigated. Both L. monocytogenes strains, a persistently sampled isolate (collected repeatedly along 3 years from a meat factory) and Scott A, induced shrinkage in matrix volume, both at 20°C and 4°C, in mature or old biofilms, without loss of P. fluorescens cell count per surface unit. The nearly homogeneous pattern of surface coverage shown by mono-species P. fluorescens biofilms, turned into more irregular layouts in co-culture with L. monocytogenes. The upper layer of both mono and dual-species biofilms turned to predominantly consist of matrix, with plenty of viable cells underneath, in old biofilms cultured at 20°C, but not in those grown at 4°C. Between 15 and 56% of the substratum area was covered by biofilm, the extent depending on temperature, time and L. monocytogenes strain. Real biofilms in food-related surfaces may thus be very heterogeneous regarding their superficial components, i.e., those more accessible to disinfectants. It is therefore a hygienic challenge to choose an adequate agent to disrupt them.
Collapse
Affiliation(s)
| | - Belen Orgaz
- Department of Nutrition, Food Science and Technology, Faculty of Veterinary, Complutense University of MadridMadrid, Spain
| | | |
Collapse
|
15
|
Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment. Appl Environ Microbiol 2015; 81:7893-904. [PMID: 26341209 DOI: 10.1128/aem.02294-15] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/01/2015] [Indexed: 11/20/2022] Open
Abstract
Microbial contamination in food processing plants can play a fundamental role in food quality and safety. In this study, the microbiota in a dairy plant was studied by both 16S rRNA- and 26S rRNA-based culture-independent high-throughput amplicon sequencing. Environmental samples from surfaces and tools were studied along with the different types of cheese produced in the same plant. The microbiota of environmental swabs was very complex, including more than 200 operational taxonomic units with extremely variable relative abundances (0.01 to 99%) depending on the species and sample. A core microbiota shared by 70% of the samples indicated a coexistence of lactic acid bacteria with a remarkable level of Streptococcus thermophilus and possible spoilage-associated bacteria, including Pseudomonas, Acinetobacter, and Psychrobacter, with a relative abundance above 50%. The most abundant yeasts were Kluyveromyces marxianus, Yamadazyma triangularis, Trichosporon faecale, and Debaryomyces hansenii. Beta-diversity analyses showed a clear separation of environmental and cheese samples based on both yeast and bacterial community structure. In addition, predicted metagenomes also indicated differential distribution of metabolic pathways between the two categories of samples. Cooccurrence and coexclusion pattern analyses indicated that the occurrence of potential spoilers was excluded by lactic acid bacteria. In addition, their persistence in the environment can be helpful to counter the development of potential spoilers that may contaminate the cheeses, with possible negative effects on their microbiological quality.
Collapse
|
16
|
Alkema W, Boekhorst J, Wels M, van Hijum SAFT. Microbial bioinformatics for food safety and production. Brief Bioinform 2015; 17:283-92. [PMID: 26082168 PMCID: PMC4793891 DOI: 10.1093/bib/bbv034] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 12/14/2022] Open
Abstract
In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput 'omics' technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.
Collapse
|