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Food Research International (Ottawa,... Jun 2024The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end...
The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.
Topics: Microbiota; Red Meat; Animals; Cattle; Food Microbiology; Food Handling; Bacteria; Metagenomics; Drug Resistance, Bacterial; Abattoirs; Anti-Bacterial Agents; Food Contamination; Drug Resistance, Microbial; Food Packaging
PubMed: 38729711
DOI: 10.1016/j.foodres.2024.114318 -
Food Research International (Ottawa,... Jan 2024Fresh fish is a highly perishable product and is easily spoiled by microbiological activity and chemical oxidation of lipids. However, microbial spoilage is the main...
Fresh fish is a highly perishable product and is easily spoiled by microbiological activity and chemical oxidation of lipids. However, microbial spoilage is the main factor linked with the rapid fish sensorial degradation due to the action of specific spoilage organisms (SSOs) that have the ability to dominate over other microorganisms and produce metabolites responsible for off-flavours. We explored the microbial dynamics in fresh anchovies stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) using shotgun metagenomics, highlighting the selection of different microbial species according to the packaging type. Indeed, Pseudoalteromonas nigrifaciens, Psychrobacter cryohalolentis and Ps. immobilis, Pseudomonas deceptionensis and Vibrio splendidus have been identified as the main SSOs in aerobically stored anchovies, while Shewanella baltica, Photobacterium iliopiscarium, Ps. cryohalolentis and Ps. immobilis prevailed in VP and MAP. In addition, we identified the presence of spoilage-associated genes, leading to the potential production of biogenic amines and different off-flavors (HS, TMA). In particular, the abundance of microbial genes leading to BA biosynthesis increased at higher storage temperature, while those related to HS and TMA production were enriched in aerobically and VP packed anchovies, suggesting that MAP could be an effective strategy in delaying the production of these compounds. Finally, we provided evidence of the presence of a wide range of antibiotic resistance genes conferring resistance to different classes of antibiotic (β-lactams, tetracyclines, polymyxins, trimethoprims and phenicols) and highlighted that storage at higher temperature (4 and 10 °C) boosted the abundance of ARG-carrying taxa, especially in aerobically and MAP packed fish.
Topics: Animals; Food Packaging; Anti-Bacterial Agents; Food Microbiology; Food Preservation; Genomics; Microbiota
PubMed: 38129066
DOI: 10.1016/j.foodres.2023.113788 -
BMC Genomics Dec 2014Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial...
BACKGROUND
Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned.
RESULTS
We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study.
CONCLUSIONS
Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods.
Topics: Bacteria; Cheese; Dairy Products; Databases, Genetic; Fermentation; Genome, Bacterial; Metagenomics; Microbiota; Sequence Analysis
PubMed: 25496341
DOI: 10.1186/1471-2164-15-1101 -
Journal of Clinical Immunology Jan 2014A 16-year old boy with chronic granulomatous disease (CGD) developed Psychrobacter immobilis septicemia during a course of fulminant hepatic failure. The patient died...
A 16-year old boy with chronic granulomatous disease (CGD) developed Psychrobacter immobilis septicemia during a course of fulminant hepatic failure. The patient died despite aggressive management with antimicrobials and corticosteroids. While Psychrobacter immobilis rarely affects humans, it should be considered an organism that can cause sepsis in patients with CGD.
Topics: Adolescent; Anti-Bacterial Agents; Autopsy; Bacteremia; Fatal Outcome; Granulomatous Disease, Chronic; Humans; Liver Failure, Acute; Male; Moraxellaceae Infections; Psychrobacter
PubMed: 24217814
DOI: 10.1007/s10875-013-9961-7 -
Food Microbiology Dec 2013The dominant microbiota of brown shrimp (Crangon crangon) were systematically identified during storage under different conditions. Freshly caught shrimp were processed... (Comparative Study)
Comparative Study
The dominant microbiota of brown shrimp (Crangon crangon) were systematically identified during storage under different conditions. Freshly caught shrimp were processed on board the fishing vessel under the best possible hygienic conditions (IDEAL), unpeeled and manually (sterile) peeled, then stored on ice and at 7.5 °C until microbiologically spoiled. Results were compared with industrially processed (INDUSTRIAL) shrimp. Isolates grown on various media were identified by 16S rRNA and gyrB gene sequencing. We examined the total microbiota and microbial population shifts of shrimp under various storage conditions using denaturant gradient gel electrophoresis (DGGE). The microbiota differed somewhat during storage and among the various storage conditions; however, members of the genera Psychrobacter and Pseudoalteromonas were found to dominate the microbiota of all shrimp samples regardless of processing procedures or storage conditions. Most isolates could be identified by gyrB gene sequencing as Psychrobacter immobilis or Psychrobacter cibarius. Also Pseudoalteromonas nigrifaciens, Pseudoalteromonas elyakovii or Pseudoalteromonas paragorgicola dominated the microbiota of brown shrimp during storage. Also species from the genera Planocuccus, Exiguobacterium, Carnobacterium, Pseudomonas, Chryseobacterium and Staphylococcus were detected during storage of brown shrimp. Culture-dependent and culture-independent DGGE analysis produced different results in band patterns. Both methods are therefore required to accurately identify the microbiota and bacterial population shifts on seafood during storage.
Topics: Animals; Bacteria; Colony Count, Microbial; Crangonidae; Denaturing Gradient Gel Electrophoresis; Food Contamination; Food Handling; Food Storage; Microbiota; Seafood
PubMed: 24010590
DOI: 10.1016/j.fm.2013.04.009 -
International Journal of Systematic and... Mar 2012Human Psychrobacter isolates, other than Psychrobacter phenylpyruvicus, are predominantly designated Psychrobacter immobilis. Phenotypic and genotypic testing of...
Psychrobacter isolates of human origin, other than Psychrobacter phenylpyruvicus, are predominantly Psychrobacter faecalis and Psychrobacter pulmonis, with emended description of P. faecalis.
Human Psychrobacter isolates, other than Psychrobacter phenylpyruvicus, are predominantly designated Psychrobacter immobilis. Phenotypic and genotypic testing of Psychrobacter isolates that have been deposited in different culture collections as P. immobilis indicates that most of these human isolates belong to the species Psychrobacter faecalis and Psychrobacter pulmonis.
Topics: Bacterial Typing Techniques; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Humans; Molecular Sequence Data; Moraxellaceae Infections; Phylogeny; Psychrobacter; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 21551328
DOI: 10.1099/ijs.0.032631-0 -
Biotechnology and Bioengineering Jun 2008Selective biocatalyzed synthesis of 2'-deoxyadenosine from 2'-deoxypyrimidine nucleosides was carried out using free or immobilized whole cells. The reaction was...
Selective biocatalyzed synthesis of 2'-deoxyadenosine from 2'-deoxypyrimidine nucleosides was carried out using free or immobilized whole cells. The reaction was performed at 57 degrees C without secondary reactions. Two psychrotrophic microorganisms, Bacillus psychrosaccharolyticus and Psychrobacter immobilis, are described for the first time as active and specific strains for the synthesis of 2'-deoxyadenosine. Adenosine deaminase activity was not detected. Whole cells were immobilized in different matrixes. Calcium alginate and calcium pectate gave the best biocatalysts. The synthesis of 2'-deoxyadenosine follows an apparent first order kinetic expression. External mass transfer control was negligible as deduced from k(s), N(A), and Omega values. Internal mass transfer was the rate controlling step according to eta(T) and phi values.
Topics: Bacillus; Cell Culture Techniques; Cell Proliferation; Cells, Immobilized; Cold Temperature; Deoxyadenosines; Psychrobacter
PubMed: 18098315
DOI: 10.1002/bit.21756 -
Journal of Bioscience and Bioengineering 2000The estA gene encoding the enzyme that catalyzes the production of (R)-beta-acetylmercaptoisobutyric acid from (R,S)-ester from Pseudomonas aeruginosa 1001, was cloned...
The estA gene encoding the enzyme that catalyzes the production of (R)-beta-acetylmercaptoisobutyric acid from (R,S)-ester from Pseudomonas aeruginosa 1001, was cloned in Escherichia coli and its nucleotide sequence was determined, revealing the presumed open reading frame encoding a polypeptide of 316 amino acid residues (948 nucleotides). The overall A + T and C + G compositions were 32.59% and 67.41%, respectively. The amino acid sequence of the estA gene product showed a significant similarity with that of the triacylglycerol lipase from Psychrobacter immobilis (38% identity), triacylglycerol lipase from Moraxella sp. (36% identity), and two forms of carboxyl esterases from Acinetobacter calcoaceticus (17% and 17% identities). The deduced amino acid sequences have a pentapeptide consensus sequence, G-X-S-X-G, having an active serine residue, and another active site, dipeptides H-G, located at 70-100 amino acids upstream of the G-X-S-X-G consensus sequence.
PubMed: 16232934
DOI: 10.1263/jbb.90.684 -
Journal of Medical Entomology Nov 2003The responses of Aedes albopictus to sources of oviposition attractants and stimulants were evaluated with a behavioral bioassay in which females attracted to odorants...
The responses of Aedes albopictus to sources of oviposition attractants and stimulants were evaluated with a behavioral bioassay in which females attracted to odorants emanating from water were trapped on screens coated with an adhesive. Gravid mosquitoes were attracted to volatiles from larval-rearing water and soil-contaminated cotton towels. Bacteria were isolated from these substrates and from an organic infusion made with oak leaves. Through fatty acid-methyl ester analyses, six bacterial isolates from larval-rearing water, two isolates from soil-contaminated cotton towels, and three isolates from oak leaf infusion were identified to species. The response of gravid mosquitoes to these isolates was also evaluated in behavioral bioassays. Water containing Psychrobacter immobilis (from larval-rearing water), Sphingobacterium multivorum (from soil-contaminated cotton towels), and an undetermined Bacillus species (from oak leaf infusion) elicited significantly higher oviposition than control water without bacteria. Only volatiles collected from larval rearing water elicited significant electroantennogram responses in females.
Topics: Aedes; Animals; Bacteria; Bacterial Physiological Phenomena; Female; Larva; Odorants; Oviposition; Plant Leaves; Quercus
PubMed: 14765661
DOI: 10.1603/0022-2585-40.6.841 -
International Journal of Systematic and... Nov 2003A facultatively psychrophilic bacterium, strain MD17(T), which hydrolyses lipids at 5 degrees C, was isolated from the Monbetsu coast of the Okhotsk Sea in Hokkaido,...
A facultatively psychrophilic bacterium, strain MD17(T), which hydrolyses lipids at 5 degrees C, was isolated from the Monbetsu coast of the Okhotsk Sea in Hokkaido, Japan, when ice carried by the cold current came to the area. The isolate is an aerobic, non-motile coccobacillus that reduces nitrate to nitrite and hydrolyses Tweens 20, 40, 60 and 80, but not gelatin, DNA or alginic acid. The isolate grows at 0 degrees C, but not at temperatures higher than 36 degrees C; its optimum growth temperature is 25 degrees C. It grows in the presence of 0-10 % NaCl. Its major isoprenoid quinone is ubiquinone-8 (Q-8) and its DNA G+C content is 46.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MD17(T) is closely related to Psychrobacter glacincola DSM 12194(T) (99.0 % similarity) and Psychrobacter immobilis DSM 7229(T) (98.7 % similarity). DNA-DNA hybridization revealed 45.9 % relatedness between strain MD17(T) and P. immobilis ATCC 43116(T) and 33.4 % between strain MD17(T) and P. glacincola ATCC 700754(T). Based on physiological and biochemical characteristics, phylogenetic position (as determined by 16S rRNA gene sequence analysis) and DNA-DNA relatedness, it is concluded that the isolate should be designated as a novel species, for which the name Psychrobacter okhotskensis sp. nov. is proposed. The type strain is MD17(T) (=NCIMB 13931(T)=JCM 11840(T)).
Topics: Base Composition; Base Sequence; DNA, Bacterial; Japan; Molecular Sequence Data; Moraxellaceae; Phylogeny; Seawater; Temperature
PubMed: 14657134
DOI: 10.1099/ijs.0.02686-0