Biogenic Amine Production by and Phylogenetic Analysis of 23 Photobacterium Species

Insight to the diversity of Photobacterium spp. isolated from European plaice (Pleuronectes platessa) based on phylogenetic analysis, phenotypic characterisation and spoilage potential

This study aimed to explore the diversity of fifty-four Photobacterium strains isolated from muscle tissue of European plaice (Pleuronectes platessa) caught at different fishing seasons and stored 14-days under various conditions. Single phylogenetic markers (16S rRNA, gapA, gyrB and recA) and multilocus sequence analysis (MLSA) were employed to classify isolates at species level. Furthermore, intra- and interspecies variability in the phenotypic traits, maximum specific growth rate (μmax) and spoilage potential of the Photobacterium isolates were investigated. The isolates were classified into the P. iliopiscarium (53.7 %), P. phosphoreum (40.7 %) and P. piscicola (5.6 %) clades using MLSA. Two housekeeping genes, gyrB and recA, exhibited a consistent phylogenetic relationship with MLSA, suggesting that they might be used as individual phylogenetic markers for the Photobacterium genus. Intra- and interspecies variability in the expression of phenotypic characteristics and the production of trimethylamine (TMA), inosine (HxR), and hypoxanthine (Hx) were observed. A growth optimum temperature for P. iliopiscarium was approximately 20 °C, while those for P. phosphoreum and P. piscicola were closer to 15 °C. All isolates exhibited the highest growth density at 1.5 % NaCl, followed by 0.5 %, 3 %, and 6 % NaCl. However, P. phosphoreum demonstrated a higher NaCl tolerance than the other two species. Although, the high CO2 atmosphere significantly inhibited the growth of all strains at 4 °C, P. phosphoreum and P. piscicola showed higher growth density at 15 °C than P. iliopiscarium. Notably, all strains demonstrated H2S production. The μmax varied considerably within each species, highlighting the significance of strain-level variability. This study demonstrates that P. iliopiscarium and P. piscicola, alongside P. phosphoreum, are efficient TMA-, HxR-, Hx-, and H2S-producers, suggesting their potential contribution to synergistic off-odour generation and spoilage. Moreover, the Photobacterium isolates seem to exhibit diverse adaptations to their environments, resulting in fluctuated growth and spoilage potential. Understanding intra- and interspecies variability will facilitate modelling seafood spoilage in microbial risk assessments and developing targeted hurdles to prolong products' shelf-life.

Microbiome dynamics, antibiotic resistance gene patterns and spoilage-associated genomic potential in fresh anchovies stored in different conditions

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 (H2S, TMA). In particular, the abundance of microbial genes leading to BA biosynthesis increased at higher storage temperature, while those related to H2S 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.

Deciphering the growth responses and genotypic diversity of bioluminescent Photobacterium phosphoreum on chicken meat during aerobic refrigerated storage

The advent of high-throughput sequencing technologies in recent years has revealed the unexpected presence of genus Photobacterium within the chicken meat spoilage ecosystem. This study was undertaken to decipher the occurrence, the growth patterns and the genotypic biodiversity of Photobacterium phosphoreum on chicken breast fillets stored aerobically at 4 °C through conventional microbiological methods and molecular techniques. Samples were periodically cultured on marine broth agar (MA; supplemented with meat extract and vancomycin) for the enumeration of presumptive bioluminescent Photobacterium spp. In total, 90 bioluminescent bacteria were recovered from the initial (time of first appearance), middle and end stages of storage. Concomitantly, 95 total psychrotrophic/psychrophilic bacteria were isolated from the same medium to assess the presence and diversity of non-luminous photobacteria. Genetic diversity between bioluminescent isolates was assessed with two PCR-based DNA fingerprinting methods, i.e. RAPD and rep-PCR. Moreover, the characterization of selected bacterial isolates at the genus and/or species level was performed by sequencing of the 16S rRNA and/or gyrB gene. Bioluminescent bacteria were scarcely encountered in fresh samples at population levels of ca. 2.0 log CFU/g, whilst total psychrotrophic/psychrophilic bacteria were found at levels of ca. 4.4 log CFU/g. As time proceeded and close to shelf-life end, bioluminescent bacteria were encountered at higher populations, and were found at levels of 5.3 and 7.0 log CFU/g in samples from the second and third batch, respectively. In the first batch their presence was occasional and at levels up to 3.9 log CFU/g. Accordingly, total psychrotrophic/psychrophilic bacteria exceeded 8.4 log CFU/g at the end of storage, suggesting the possible underestimation of bioluminescent populations following the specific cultivation conditions. Sequence analysis assigned bioluminescent isolates to Photobacterium phosphoreum, while genetic fingerprinting revealed high intra-species variability. Respectively, total psychrotrophs/psychrophiles were assigned to genera Pseudomonas, Shewanella, Psychrobacter, Acinetobacter, Vibrio and Photobacterium. Non-luminous photobacteria were not identified within the psychrotrophs/psychrophiles. Results of the present study reveal the intra- and inter-batch variability on the occurrence and growth responses of P. phosphoreum and highlight its potential role in the chicken meat spoilage consortium.

Detection, Identification, and Inactivation of Histamine-forming Bacteria in Seafood: A Mini-review

Seafood is one of the essential sources of nutrients for the human diet. However, they can be subject to contamination and can cause foodborne illnesses, including scombroid fish poisoning caused by histamine. Many microorganisms can produce enzymes that eventually decompose endogenous histidine to histamine in postmortem fish muscles and tissues. One of these is histamine-forming bacteria (HFB), primarily found in the gills, gut, and skin of fishes. Previous studies linked a plethora of Gram-negative HFB including Morganella spp. and Photobacterium spp. to scombroid fish poisoning from many types of seafood, especially the Scombridae family. These bacteria possess the hdc gene to produce histidine decarboxylase enzyme. It was reported that Gram-negative HFB produced 6345 ppm in tuna and 1223 ppm in Spanish mackerel. Interestingly, Gram-positive HFB have been isolated in the seafood samples with lower histamine levels. It suggests that Gram-negative HFB are the major contributor to the accumulation of histamine in seafood. Several analytical methods are available to detect and identify HFB and their histamine metabolites from seafood substrates. Rapid test kits can be used in food production settings for early detection of histamine to avoid food intoxication. Furthermore, high hydrostatic pressure and irradiation treatment could prevent the proliferation of HFB and inactivate the existing histidine decarboxylase (HDC) activity. As demonstrated in different seafood model systems, the HDC activity was deactivated at a maximum high hydrostatic pressure level of 400 MPa. The complete inactivation of HFB was achieved by gamma irradiation at a dose of 4.0 kGy. Other postharvest treatments, like enzymatic degradation and electrolyzed oxidizing water, were studied as sustainable methods for bacterial growth prevention and enzyme inactivation. However, other HFB react differently to these treatment conditions, and further studies are recommended.

Heterologous expression and activity verification of ornithine decarboxylase from a wild strain of Shewanella xiamenensis

Shewanella xiamenensis is widely found in spoilage fish, shrimp and other seafoods. Under suitable conditions, ornithine can be synthesized into putrescine, which may spoil food or endanger health. Our research used a wild strain of Shewanella xiamenensis isolated from "Yi Lu Xian" salted fish (a salting method for sea bass) as a research object. According to the database of National Center of Biotechnology Information (NCBI), the target ornithine decarboxylase (ODC) gene SpeF was successfully amplified using the wild strain of Shewanella xiamenensis as the template. Sequencing alignment showed that the SpeF of the wild strain had more than 98% homology compared with the standard strain. The amino acid substitution occurred in the residues of 343, 618, 705, and 708 in the wild strain. After optimizing the expression conditions, a heterologous expression system of ODC was constructed to achieve a high yield of expression. The amount of 253.38 mg of ODC per liter of LB broth was finally expressed. High performance liquid chromatography (HPLC) and subsequent ODC activity verification experiments showed that hetero-expressed ODC showed a certain enzyme activity for about 11.91 ± 0.38 U/mg. Our study gives a new way to the development of a low-cost and high-yield strategy to produce ODC, providing experimental materials for further research and elimination of putrescine in food hazards.

Tracking spoilage bacteria in the tuna microbiome

Like other seafood products, tuna is highly perishable and sensitive to microbial spoilage. Its consumption, whether fresh or canned, can lead to severe food poisoning due to the activity of specific microorganisms, including histamine-producing bacteria. Yet, many grey areas persist regarding their ecology, conditions of emergence, and proliferation in fish. In this study, we used 16S rRNA barcoding to investigate postmortem changes in the bacteriome of fresh and brine-frozen yellowfin tuna (Thunnus albacares), until late stages of decomposition (i.e. 120 h). The results revealed that despite standard refrigeration storage conditions (i.e. 4°C), a diverse and complex spoilage bacteriome developed in the gut and liver. The relative abundance of spoilage bacterial taxa increased rapidly in both organs, representing 82% of the bacterial communities in fresh yellowfin tuna, and less than 30% in brine-frozen tuna. Photobacterium was identified as one of the dominant bacterial genera, and its temporal dynamics were positively correlated with histamine concentration in both gut and liver samples, which ultimately exceeded the recommended sanitary threshold of 50 ppm in edible parts of tuna. The results from this study show that the sanitary risks associated with the consumption of this widely eaten fish are strongly influenced by postcapture storage conditions.

Fishing for the Microbiome of Tropical Tuna

Although tunas represent a significant part of the global fish economy and a major nutritional resource worldwide, their microbiome still remains poorly documented. Here, we conducted an analysis of the taxonomic composition of the bacterial communities inhabiting the gut, skin, and liver of two most consumed tropical tuna species (skipjack and yellowfin), from individuals caught in the Atlantic and Indian oceans. We hypothesized that each organ harbors a specific microbial assemblage whose composition might vary according to different biotic (sex, species) and/or abiotic (environmental) factors. Our results revealed that the composition of the tuna microbiome was totally independent of fish sex, regardless of the species and ocean considered. Instead, the main determinants of observed diversity were (i) tuna species for the gut and (ii) sampling site for the skin mucus layer and (iii) a combination of both parameters for the liver. Interestingly, 4.5% of all amplicon sequence variants (ASV) were shared by the three organs, highlighting the presence of a core-microbiota whose most abundant representatives belonged to the genera Mycoplasma, Cutibacterium, and Photobacterium. Our study also revealed the presence of a unique and diversified bacterial assemblage within the tuna liver, comprising a substantial proportion of potential histamine-producing bacteria, well known for their pathogenicity and their contribution to fish poisoning cases. These results indicate that this organ is an unexplored microbial niche whose role in the health of both the host and consumers remains to be elucidated.

Prevalence of Histamine-Forming Bacteria in Two Kinds of Salted Fish at Town Markets of Guangdong Province of South China

ABSTRACT

Histamine-forming bacteria (HFB) were isolated from the 70 salted fish samples bought from town markets of Guangdong Province of south China. In addition, the histamine-forming ability of HFB was analyzed. There were 31 strains of HFB isolated from 36 salted fish pickled overnight. They were identified as six bacteria species: Vibrio alginolyticus, Vibrio rumoiensis, Staphylococcus saprophyticus, Staphylococcus xylosus, Lactococcus lactis, and Morganella morganii. The rate of confirmation of V. alginolyticus was highest (23 of 31), exceeding 200 mg/kg histamine. In particular, M. morganii produced a histamine amount that exceeded 2,000 mg/kg, although it was only one isolate in this study. In addition, five bacteria species of HFB were isolated from 34 dried salted fish. Among them, S. saprophyticus was dominant in the dried salted fish but produced histamines below 200 mg/kg. However, Enterobacter aerogenes from dried salted fish formed a histamine amount exceeding 200 mg/kg. The study showed that the dominant strain of HFB was different in two kinds of salted fish. Both kinds of salted fish contained HFB whose histamine-forming capacity exceeded 200 mg/kg. As a result, the safety of salted fish should be of concern, especially salted fish pickled overnight.

HIGHLIGHTS

Comparative genomics of Photobacterium species from terrestrial and marine habitats

Photobacterium (P.) is a genus widely studied in regards to its association with and ubiquitous presence in marine environments. However, certain species (P. phosphoreum, P. carnosum, P. iliopiscarium) have been recently described to colonize and spoil raw meats without a marine link. We have studied 27 strains from meat as well as 26 strains from marine environments in order to probe for intraspecies marine/terrestrial subpopulations and identify distinct genomic features acquired by environmental adaptation. We have conducted phylogenetic analysis (MLSA, ANI, fur, codon usage), search of plasmids (plasmidSPADES), phages (PHASTER), CRISPR-cas operons (CRISPR-finder) and secondary metabolites gene clusters (antiSMASH, BAGEL), in addition to a targeted gene search for specific pathways (e.g. TCA cycle, pentose phosphate, respiratory chain) and elements relevant for growth, adaptation and competition (substrate utilization, motility, bioluminescence, sodium and iron transport). P. carnosum appears as a conserved single clade, with one isolate from MAP fish clustering apart that doesn't, however, show distinct features that could indicate different adaptation. The species harbors genes for a wide carbon source utilization (glycogen/starch, maltose, pullulan, fucose) for colonization of diverse niches in its genome. P. phosphoreum is represented by two different clades on the phylogenetic analyses not correlating to their origin or distribution of other features analyzed that can be divided into two novel subspecies based on genome-wide values. A more diverse antimicrobial activity (sactipeptides, microcins), production of secondary metabolites (siderophores and arylpolyenes), stress response and adaptation (bioluminescence, sodium transporters, catalase, high affinity for oxygen cytochrome cbb3 oxidase, DMSO reductase and proton translocating NADH dehydrogenase) is predicted compared to the other species. P. iliopiscarium was divided into two clades based on source of isolation correlating with phylogeny and distribution of several traits. The species shows traits common to the other two species, similar carbon utilization/transport gene conservation as P. carnosum for the meat-isolated strains, and predicted utilization of marine-common DMSO and flagellar cluster for the sea-isolated strains. Results additionally suggest that photobacteria are highly prone to horizontal acquisition/loss of genetic material and genetic transduction, and that it might be a strategy for increasing the frequency of strain- or species-specific features that offers a growth/competition advantage.

Histamine and Scombrotoxins

Histamine intoxications result when histamine-metabolizing enzymes are compromised or overwhelmed by dietary histamine in the human body. This can occur either due to metabolic enzyme deficiencies, such as in histamine intolerance to wines, aged cheese and other foods or from high concentrations of histamine following ingestion of decomposed fish. The presence of histamine in decomposed fish and fish products results from bacterial decarboxylation of free L-histidine following product mishandling. Consequently, histamine intoxications from mishandled fish, commonly referred to as scombrotoxin fish poisoning (SFP) or scombroid poisoning, require high levels of free L-histidine only found in certain species of pelagic fish. Differential diagnosis is required of clinicians since dietary histamine intoxications produce the same symptoms typical of release of endogenous histamine due to IgE -mediated seafood allergies or anisakiasis. Although high levels of dietary histamine are responsible for SFP, histamine has important physiological functions and tends to exert toxic effects only at doses beyond the physiological range. Endogenous histamine is essential to local immune responses, regulation of gastric acid secretion in the gut, and neurotransmission in the central nervous system. Scombrotoxins, postulated to explain histamine's augmented toxicity in scombrotoxic fish, are a milieu of histamine and other bioactives. Since time-and-temperature abuse is required to produce high levels of histamine in fish, management consists of ensuring proper handling by identifying hazards and critical control points (HACCP) and maintaining a "cold chain" from catch to consumption. Reference methods for detecting histamine have received increased attention and the European Commission has validated a popular precolumn dansylation-based HPLC method through inter-laboratory collaboration and studied method equivalence with the AOAC fluorescence method 977.13 recognized by Codex Alimentarius. Much progress has been made during the last decade in the development and validation of rapid screening methods for detecting histamine in food and especially in fish products. These include many innovative sensors and several validated commercial test kits, many of them based on a recombinant form of the enzyme histamine dehydrogenase (HD).

Three-in-one via syringe needle-based device: sampling, microextraction and peroxidase-like catalysis for colorimetric detection of the change of biogenic amines levels with time in meat

In this work, a syringe needle-based integrated method was designed for the detection of biogenic amines (BAs) in raw meat samples. Based on a sequential process, the needle-based sampling, micro liquid-phase extraction and peroxidase-like catalysis were adopted for the sample collection, target analytes extraction and colorimetric analysis, respectively. The proposed method exhibited high selectivity towards BAs (the total amount of histamine, putrescine and cadaverine was utilized to present the level of BAs), where the linear range is 5-50 μM and 50-1000 μM, and the limit of detection is 1.52 μM. Specifically, the whole process could be completed in a single syringe needle. In addition, due to the minimized sampling, the change of BAs levels with time in different area of real samples (fish) can be conveniently investigated. This method has the advantages of simplicity, low cost, high sensitivity and selectivity, endowing it a promising candidate for food analysis.

Development of a rapid detection method for Photobacterium spp. using Loop-mediated isothermal amplification (LAMP)

While the abundance of photobacteria has previously been exclusively associated with marine environments and spoilage of seafood, several recent studies have demonstrated their status as pervasive constituents of the microbiota on packaged meats. Since their ubiquitous nature has been revealed, detection of their presence on meat, their entry route into meat processing environments and prevention of their growth is a novel emerging challenge for the food industry. In this study, we have developed a highly sensitive and specific loop-mediated isothermal amplification (LAMP) assay for the detection of relevant species of photobacteria on foods, and tested its efficacy on meats. The gene encoding trimethylamine-N-oxide reductase (torA) was chosen as the target for this assay. Designed primers based on the gene sequence proved their specificity by testing 67 isolates of 5 species of photobacteria (positive) as well as 63 strains of 16 species of other common meat spoilers (negative). The optimized assay takes 2 h including sample preparation and has a detection limit of only 10-11 copies (50 fg/reaction) of the average Photobacterium (P.) genome per reaction. Its applicability could be successfully demonstrated on naturally and artificially contaminated chicken, beef and pork samples and evaluated by comparison with a culture-dependent approach using selective media and MALDI-TOF MS for identification. The developed LAMP assay revealed presence of photobacteria on one naturally contaminated chicken sample stored at 4 °C long before (3 days) confirmation by the culture-dependent approach. This study demonstrates that the developed LAMP assay represents a reliable and sensitive method for rapid detection of photobacteria on meats. However, its specificity would allow the applicability of the methodology to be extended to other foods, e.g. fish and seafood where presence of photobacteria is directly linked to their shelf life. The method has no requirement for specialized equipment or specially trained personal allowing an easy implementation within the quality control of the food industry. Considering the lot-to-lot variations observed on meats regarding the presence of photobacteria and the impracticality of implementing quantitative methods within the routine control, the LAMP method can simplify and reduce the workload for detection of photobacteria on high sample numbers. Consequently, producers can identify batches/plants that need more stringent control, and are provided with a tool to determine the entry route of photobacteria into the processing and distribution chain of raw meats.

Characterization of a novel enzyme from Photobacterium phosphoreum with histidine decarboxylase activity

Histamine or scombrotoxin fish poisoning is caused by ingestion of bacterially produced histamine in fish. Histamine-producing bacteria generally contain the histidine decarboxylase gene (hdc). However, some strains of Photobacterium phosphoreum are known to produce significant levels of histamine, although the hdc gene in these strains has not been recognized. The objective of this study was to investigate a previously unidentified mechanism of histamine production by P. phosphoreum. We identified a protein with histidine decarboxylase (HDC) activity comparable to activity of the pyridoxal-5-phosphate (PLP) dependent HDC from P. kishitanii and M. morganii. The newly identified protein (HDC2) in P. phosphoreum and P. kishitanii strains, was approximately 2× longer than the HDC protein from other Gram-negative bacteria and had 12% similarity to previously identified HDCs. In addition, the hdc2 gene cluster in P. phosphoreum was identical to the hdc gene cluster in P. kishitanii. HDC2 had optimal activity at 20-35 °C, at pH 4, and was not affected by 0-8% NaCl concentrations. Compared to the hdc gene from P. kishitanii, expression of the hdc2 gene was constitutive and not affected by pH or excess histidine. This newly identified protein explains possible mechanisms of histamine production in P. phosphoreum. Characterization of this protein will help in designing control measures to prevent or reduce histamine production in fish.

Biodiversity of Photobacterium spp. Isolated From Meats

Photobacteria are common psychrophilic bacteria found in marine environments. Recently, several studies revealed high numbers of Photobacterium (P.) spp. on packaged fresh meat. Their occurrence appears relevant for the spoilage of meat, since species of the genus are already known as potent fish spoilage organisms. Here we report on distribution, biodiversity, and specific traits of P. carnosum (n = 31), P. phosphoreum (n = 24), and P. iliopiscarium (n = 3) strains from different foods. Biodiversity was assessed by genomic fingerprinting, diversity index analysis, growth dynamics, comparison of metabolic activities, and antibiotic resistance. We observed a ubiquitous occurrence of the species on all common meats independent of packaging conditions and producer, suggesting contamination during an established processing or packaging step. Regarding biodiversity, the three species differed clearly in their growth properties and metabolic characteristics, with P. phosphoreum growing the fastest and showing the strongest alkalization of the media. On strain level we also recorded variations in enzymatic reactions, acid production, and antibiotic resistances not restricted to specific meat types. This depicts high biodiversity on species and strain level on each contaminated meat sample. Our analysis showed that meat-borne strains of P. phosphoreum and P. iliopiscarium clearly differ from their type strains from a marine habitat. Additionally, we report for the first time isolation of P. carnosum strains from packaged fish, which in contrast showed comparable phenotypic properties to meat-borne strains. This hints at different initial origins of P. phosphoreum/P. iliopiscarium (marine background) and P. carnosum (no demonstrated marine background) contaminations on fish and meat, respectively.