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Applied and Environmental Microbiology May 2024Studying how phylogeny influences the composition and functions of microbiotas within animal hosts is essential for gaining insights into the connection between...
Studying how phylogeny influences the composition and functions of microbiotas within animal hosts is essential for gaining insights into the connection between genetics, ecology, and health in the animal kingdom. However, due to limited comprehensive studies, this influence remains unclear for many wild mammals, including Mexican pinnipeds. We employed 16S rRNA gene deep-sequencing to investigate the impact of phylogeny on the gut microbiota of four pinniped species inhabiting Mexican shores: the Pacific harbor seal (), the northern elephant seal (), the California sea lion (), and the Guadalupe fur seal (). Our results indicated that factors such as diets and shared life histories exerted more influence on microbiota composition than phylogeny alone. Notably, otariid species sharing similar life histories displayed greater microbiota similarity than phocids, which have distinct life histories and fewer microbiota similarities. Furthermore, harbor seals have more microbial similarities with the two otariid species than with elephant seals. Of particular concern, we observed a higher abundance of potentially pathogenic bacteria (e.g., and ) in harbor seals and Guadalupe fur seals compared to other pinnipeds. This finding could pose health threats to these species and nearby human populations.IMPORTANCEPinnipeds in Mexico host microbial communities that remain understudied. While several factors can influence microbiota composition, the role of phylogenetic relationships among these pinnipeds remains unclear due to limited knowledge of the microbiota in certain species. This study aimed to fill this gap by characterizing the composition and function of the gut microbiota in the four pinniped species that occur in Mexico. Our analysis reveals that shared diets and life histories contribute to similarities in the composition of gut microbial communities. This study also highlights the potential differences in the metabolic capabilities and adaptations within the gut microbiota of pinnipeds. Understanding how phylogeny impacts microbial communities enhances our insights into the evolutionary dynamics of marine mammals.
PubMed: 38771055
DOI: 10.1128/aem.02030-23 -
BioRxiv : the Preprint Server For... May 2024Marine bacteria experience fluctuations in osmolarity that they must adapt to, and most bacteria respond to high osmolarity by accumulating compatible solutes also known...
UNLABELLED
Marine bacteria experience fluctuations in osmolarity that they must adapt to, and most bacteria respond to high osmolarity by accumulating compatible solutes also known as osmolytes. The osmotic stress response and compatible solutes used by the coral and oyster pathogen were unknown. In this study, we showed that to alleviate osmotic stress biosynthesized glycine betaine (GB) and transported into the cell choline, GB, ectoine, dimethylglycine, and dimethylsulfoniopropionate, but not -inositol. -inositol is a stress protectant and a signaling molecule that is biosynthesized and used by algae. Bioinformatics identified -inositol ( ) catabolism clusters in and other and species. Growth pattern analysis demonstrated that utilized -inositol as a sole carbon source, with a short lag time of 3 h. An deletion mutant, which encodes an inositol dehydrogenase, was unable to grow on -inositol. Within the clusters were an MFS-type ( and an ABC-type ( transporter and analyses showed that both transported -inositol. IolG and IolA phylogeny among species showed different evolutionary histories indicating multiple acquisition events. Outside of , IolG was most closely related to IolG from a small group of fish and human pathogens and species. However, IolG from hypervirulent strains clustered with IolG from and divergently from and plant pathogens. The cluster was also present within and of which many species were associated with marine flora and fauna.
IMPORTANCE
Host associated bacteria such as encounter competition for nutrients and have evolved metabolic strategies to better compete for food. Emerging studies show that -inositol is exchanged in the coral-algae symbiosis, is likely involved in signaling, but is also an osmolyte in algae. The bacterial consumption of -inositol could contribute to a breakdown of the coral-algae symbiosis during thermal stress or disrupt the coral microbiome. Phylogenetic analyses showed that the evolutionary history of -inositol metabolism is complex, acquired multiple times in but acquired once in many bacterial plant pathogens. Further analysis also showed that a conserved cluster is prevalent among many marine species (commensals, mutualists, and pathogens) associated with marine flora and fauna, algae, sponges, corals, molluscs, crustaceans, and fish.
PubMed: 38766061
DOI: 10.1101/2024.01.16.575920 -
Foods (Basel, Switzerland) Apr 2024A novel storage technique that combines the low-frequency electric field (LFEF) and ice temperature was used to extend the shelf life of Pacific white shrimp (). The...
A novel storage technique that combines the low-frequency electric field (LFEF) and ice temperature was used to extend the shelf life of Pacific white shrimp (). The study investigated the effect of LFEF treatment on the quality and microbial composition of during storage at ice temperature. The results showed that the LFEF treatment significantly extended the shelf life of shrimp during storage at ice temperature. The total volatile base nitrogen (TVB-N) and pH of samples increased over time, while the total viable count (TVC) showed a trend of first decreasing and then increasing. Obviously, shrimp samples treated with LFEF had a lower pH, TVB-N and TVC values than the untreated samples ( < 0.05) at the middle and late stages of storage. LFEF treatment increased the diversity and altered the composition of the microbial communities in . Additionally, the treatment led to a decrease in the relative abundance of dominant spoilage bacteria, including , and , in stored at ice temperature for 11 days. Furthermore, correlation analysis indicated that TVB-N and pH had a significant and positive correlation with , suggesting that had a greater impact on shrimp quality. This study supports the practical application of accelerated low-frequency electric field-assisted shrimp preservation as an effective means of maintaining shrimp meat quality.
PubMed: 38672816
DOI: 10.3390/foods13081143 -
Microorganisms Feb 2024Spotted sea bass () is a high-economic-value aquacultural fish widely distributed in the coastal and estuarine areas of East Asia. In August 2020, a sudden outbreak of...
Spotted sea bass () is a high-economic-value aquacultural fish widely distributed in the coastal and estuarine areas of East Asia. In August 2020, a sudden outbreak of disease accompanied by significant mortality was documented in reared in marine cage cultures located in Nanhuang island, Yantai, China. Two coinfected bacterial strains, namely, NH-LM1 and NH-LM2, were isolated from the diseased for the first time. Through phylogenetic tree analysis, biochemical characterization, and genomic investigation, the isolated bacterial strains were identified as and subsp. , respectively. The genomic analysis revealed that possesses two circular chromosomes and six plasmids, while subsp. possesses two circular chromosomes and two plasmids. Furthermore, pathogenic genes analysis identified 587 and 484 genes in and subsp. , respectively. Additionally, drug-sensitivity testing demonstrated both and subsp. exhibited sensitivity to chloramphenicol, ciprofloxacin, ofloxacin, orfloxacin, minocycline, doxycycline, tetracycline, and ceftriaxone. Moreover, antibiotic resistance genes were detected in the plasmids of both strains. Extracellular product (ECP) analysis demonstrated that both and subsp. can produce hemolysin and amylase, while additionally can produce caseinase and esterase. Furthermore, infected fish displayed severe histopathological alterations, including infiltration of lymphocytes, cellular degeneration and necrosis, and loose aggregation of cells. Artificial infection assays determined that the LD of subsp. was 3 × 10 CFU/g, while the LD of was too low to be accurately evaluated. Furthermore, the dual infection of and subsp. elicits a more rapid and pronounced mortality rate compared to single challenge, thereby potentially exacerbating the severity of the disease through synergistic effects. Ultimately, our findings offer compelling evidence for the occurrence of coinfections involving and subsp. in , thereby contributing to the advancement of diagnostic and preventative measures for the associated disease.
PubMed: 38543554
DOI: 10.3390/microorganisms12030503 -
Frontiers in Immunology 2024Modern fish farming faces challenges in sourcing feed ingredients, most related with their prices, 21 availability, and specifically for plant protein sources,...
INTRODUCTION
Modern fish farming faces challenges in sourcing feed ingredients, most related with their prices, 21 availability, and specifically for plant protein sources, competition for the limited cultivation space for 22 vegetable crops. In that sense, halophytes have the added value of being rich in valuable bioactive compounds and salt tolerant. This study assessed the inclusion of non-food fractions of in European seabass diets.
METHODS
Different levels (2.5%, 5%, and 10%) were incorporated into seabass diets, replacing wheat meal (diets ST2.5, ST5, and ST10) or without inclusion (CTRL). Experimental diets were administered to seabass juveniles (8.62 ± 0.63 g) for 34 and 62 days and subsequent inflammatory responses to a heat-inactivated subsp. () were evaluated in a time-course manner (4, 24, 48, and 72 h after the challenge). At each sampling point, seabass haematological profile, plasma immune parameters, and head-kidney immune-related gene expression were evaluated.
RESULTS
After both feeding periods, most parameters remained unaltered by inclusion; nonetheless, seabass fed ST10 showed an upregulation of macrophage colony-stimulating factor 1 receptor 1 ( and cluster of differentiation 8 ( compared with those fed CTRL after 62 days of feeding. Regarding the inflammatory response, seabass fed ST10 showed lower plasma lysozyme levels than their counterparts fed ST2.5 and ST5 at 24 h following injection, while 4 h after the inflammatory stimulus, seabass fed ST10 presented higher numbers of peritoneal leucocytes than fish fed CTRL. Moreover, at 4 h, fish fed ST2.5, ST5, and ST10 showed a higher expression of interleukin 1β (), while fish fed ST5 showed higher levels of ornithine decarboxylase ( than those fed CTRL. An upregulation of macrophage colony-stimulating factor 1 receptor 1 () and glutathione peroxidase () was also observed at 72 h in fish fed ST10 or ST5 and ST10 compared with CTRL, respectively.
DISCUSSION
In conclusion, incorporating up to 10% of the non-food fraction in feed did not compromise seabass growth or immune status after 62 days, aligning with circular economy principles. However, inclusion improved the leucocyte response and upregulated key immune-related genes in seabass challenged with an inactivated pathogen.
Topics: Animals; Bass; Interleukin-1 Receptor-Like 1 Protein; Macrophage Colony-Stimulating Factor; Diet; Photobacterium
PubMed: 38500885
DOI: 10.3389/fimmu.2024.1342144 -
Vavilovskii Zhurnal Genetiki I Selektsii Dec 2023At the beginning of the paper, the level of necessary phenomenology of complex models is discussed. When working with complex systems, which of course include living...
At the beginning of the paper, the level of necessary phenomenology of complex models is discussed. When working with complex systems, which of course include living organisms and ecological systems, it is necessary to use a phenomenological description. An illustration of the phenomenological approach is given, which captures the most significant general principles or patterns of interactions; the specific values of the parameters cannot be calculated from the first principles, but are determined empirically. An appropriate interpretation is also chosen empirically and pragmatically. However, in order to simulate a wider range of situations, it becomes necessary to lower the level of phenomenology, switch to a more detailed description of the system, introducing interaction between selected elements of the system. The requirements for a system model combining ecological, metabolic and genetic levels of cell culture description are formulated. A mathematical model of quorum sensing dynamics during the growth of batch culture of luminescent bacteria at different concentrations of the nutrient substrate has been developed. The model contains four blocks describing ecological, energy, quorum and luminescent aspects of bacterial culture growth. The model demonstrated good agreement with the experimental data obtained. When analyzing the model, three oddities in the behavior of the culture were noted, which presumably can change the idea of some processes taking place during the development of a culture of luminescent bacteria. The results obtained suggest the presence of some additional control system for the luminescent reaction via the synthesis pathways of FMN · Н2 or aliphatic aldehyde. In this case, the generalized description of the contribution of energy metabolism to luminescence only through ATP is too strong a simplification. As a result of comparing the model dynamics with the experiment, a discrepancy arose between the concentration of the substrate (peptone) measured in the experiment and its effective influence on the bacterial population growth. This discrepancy seems to indicate peptone is not the leading substrate, and growth is limited by nutrients contained in the yeast extract, the concentration of which did not change in these experiments. The discrepancies noted between the expectations and the results of experimental data processing, together with the assumptions about the causes of these discrepancies, set the direction for further experimental and theoretical studies of quorum sensing mechanisms in a culture of luminescent bacteria.
PubMed: 38500739
DOI: 10.18699/VJGB-23-100 -
Scientific Reports Mar 2024It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume....
It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume. Sashimi is a type of popular raw seafood cuisine. Its microbiome, however, remained to be thoroughly explored. The objective of this study is to explore the microbiome composition in sashimi at the time when it is served and ready to be eaten. Specifically, our tasks include investigating the diversity and characteristics of microbial profiles in sashimi with respect to the fish types. We utilized the Sanger-sequencing based DNA barcoding technology for fish species authentication and next-generation sequencing for sashimi microbiome profiling. We investigated the microbiome profiles of amberjack, cobia, salmon, tuna and tilapia sashimi, which were all identified using the MT-CO1 DNA sequences regardless of their menu offering names. Chao1 and Shannon indexes, as well as Bray-Curtis dissimilarity index were used to evaluate the alpha and beta diversities of sashimi microbiome. We successfully validated our previous observation that tilapia sashimi has a significantly higher proportions of Pseudomonas compared to other fish sashimi, using independent samples (P = 0.0010). Salmon sashimi exhibited a notably higher Chao1 index in its microbiome in contrast to other fish species (P = 0.0031), indicating a richer and more diverse microbial ecosystem. Non-Metric Multidimensional Scaling (NMDS) based on Bray-Curtis dissimilarity index revealed distinct clusters of microbiome profiles with respect to fish types. Microbiome similarity was notably observed between amberjack and tuna, as well as cobia and salmon. The relationship of microbiome similarity can be depicted as a tree which resembles partly the phylogenetic tree of host species, emphasizing the close relationship between host evolution and microbial composition. Moreover, salmon exhibited a pronounced relative abundance of the Photobacterium genus, significantly surpassing tuna (P = 0.0079), observed consistently across various restaurant sources. In conclusion, microbiome composition of Pseudomonas is significantly higher in tilapia sashimi than in other fish sashimi. Salmon sashimi has the highest diversity of microbiome among all fish sashimi that we analyzed. The level of Photobacterium is significantly higher in salmon than in tuna across all the restaurants we surveyed. These findings provide critical insights into the intricate relationship between the host evolution and the microbial composition. These discoveries deepen our understanding of sashimi microbiota, facilitating our decision in selecting raw seafood.
Topics: Animals; Phylogeny; Microbiota; Gastrointestinal Microbiome; Salmon; Tuna; Seafood; Photobacterium; Pseudomonas
PubMed: 38443405
DOI: 10.1038/s41598-024-55938-1 -
International Journal of Food... Apr 2024The commercialization of processed fish products is rising in restaurants and small to medium enterprises. However, there is a lack of data related to the...
The commercialization of processed fish products is rising in restaurants and small to medium enterprises. However, there is a lack of data related to the microbiological safety of such products. In this study total aerobic colony count and Enterobacteriaceae, as proxy of process hygiene criteria, and detection of Listeria monocytogenes and concentration of histamine, as food safety criteria, were investigated in Salmo salar (salmon), Xiphias gladius (swordfish) and Thunnus albacares (yellowfin tuna), before, during, and at the end of a dry-curing process, performed in a dedicated cabinet, at controlled temperature, relative humidity and ventilation, up to 240 h. The microbiological parameters were investigated in the tested fish products by culture methods and shotgun metagenomic, while the presence of histamine, and other biogenic amines, was quantified by High Performance Liquid Chromatography. In the raw material, and up to the end of the dry curing process, the concentration of Enterobacteriaceae was always lower than 10 CFU/g, while total aerobic colony counts ranged between 3.9 and 5.4 Log CFU/g in salmon; 5.5 and 5.9 Log CFU/g in swordfish; 4.4 and 4.8 Log CFU/g in tuna. The pH values were significantly different between fish species, in the raw materials and during processing except for T4, occurring 70 h after the start of the process for salmon and after 114 h for swordfish and tuna. Water activity was different at specific sampling points and at the end of processing. Overall, 79 % of the sequences identified in the tested fish samples were assigned to y bacteria. The most abundant phyla were Pseudomonadota, Bacillota and Mycoplasmatota. The microbial populations identified by shotgun metagenomic in the tested fish species clustered well separated one from the other. Moreover, the microbial richness was significantly higher in salmon and tuna in comparison to swordfish. Listeria monocytogenes was not detected in the raw material by using the reference cultural method and very few reads (relative abundance <0.007) were detected in swordfish and tuna by shotgun metagenomic. Histamine producing bacteria, belonging to the genera Vibrio, Morganella, Photobacterium and Klebsiella, were identified primarily in swordfish. However, histamine and other biogenic amines were not detected in any sample. To the best of our knowledge this is the first paper reporting time point determinations of microbiological quality and safety parameters in salmon, swordfish and tuna, before, during and at the end of a dry-curing process. The data collected in this paper can help to predict the risk profile of ready to eat dry-cured fish products during storage before consumption.
Topics: Animals; Histamine; Food Microbiology; Seafood; Biogenic Amines; Enterobacteriaceae; Fishes; Bacteria; Tuna; Colony Count, Microbial
PubMed: 38432054
DOI: 10.1016/j.ijfoodmicro.2024.110641 -
Journal of Food Protection Apr 2024Developing countries such as Ecuador carry a heavy food safety burden but reports on the microbiological quality of their foods are scarce. In this investigation, the...
Developing countries such as Ecuador carry a heavy food safety burden but reports on the microbiological quality of their foods are scarce. In this investigation, the microbial diversity of 10 high-risk and mass-consumption street-vended foods including bolones, encebollado, food dressings, ceviche, chopped fruits, fruit juices, fruit salads, cheese, raw chicken, and ground beef in Quito, Guayaquil, and Cuenca, three major population centers in Ecuador, were evaluated using 16S rRNA gene High Throughput Sequencing. In total, 1,840 amplicon sequence variants (ASVs) were classified into 23 phyla, 253 families, 645 genera, and 829 species. In the tested food samples, Proteobacteria and Firmicutes were the most abundant phyla accounting for 97.41% of relative abundance (RA). At genus level, 10 dominant genera were identified: Acinetobacter (12.61% RA), Lactococcus (12.08% RA), Vibrio (8.23% RA), Weissella (7.43% RA), Aeromonas (6.18% RA), Photobacterium (6.32% RA), Pseudomonas (3.92% RA), Leuconostoc (3.51% RA), Klebsiella (3.49% RA), and Cupriavidus (2.86% RA). The highest microbial diversity indices were found in raw chicken, encebollados, fruit salads, and fruit juices from Guayaquil and Cuenca. From sampled foods, 29 species were classified as food spoilage bacteria and 24 as opportunistic pathogenic bacteria. Two groups associated with human diseases were identified, including 11 enteric species and 26 species of fecal bacteria. The occurrence of recognized and opportunistic pathogenic bacteria, as well as enteric and fecal microorganisms, in the street-vended foods indicated extensive risks for the consumers' health. This study demonstrated the application of culture-independent amplicon sequencing in providing a more comprehensive view of microbial safety for street-vended food, which could be a useful tool to facilitate the control of foodborne diseases.
Topics: Animals; Cattle; Humans; Food Microbiology; RNA, Ribosomal, 16S; Ecuador; Food Safety; Vibrio
PubMed: 38369192
DOI: 10.1016/j.jfp.2024.100247 -
FEMS Microbiology Ecology Feb 2024The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient...
The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes. Here, we examined 1922 fish skin microbiomes from 36 studies that included 98 species and nine rearing conditions to investigate associations between fish skin microbiome, fish species, and water physiochemical factors. Proteobacteria, particularly the class Gammaproteobacteria, were present in all marine and freshwater fish skin microbiomes. Acinetobacter, Aeromonas, Ralstonia, Sphingomonas and Flavobacterium were the most abundant genera within freshwater fish skin microbiomes, and Alteromonas, Photobacterium, Pseudoalteromonas, Psychrobacter and Vibrio were the most abundant in saltwater fish. Our results show that different culturing (rearing) environments have a small but significant effect on the skin bacterial community compositions. Water temperature, pH, dissolved oxygen concentration, and salinity significantly correlated with differences in beta-diversity but not necessarily alpha-diversity. To improve study comparability on fish skin microbiomes, we provide recommendations for approaches to the analyses of sequencing data and improve study reproducibility.
Topics: Animals; Water; Phylogeny; Reproducibility of Results; Skin; Microbiota
PubMed: 38366921
DOI: 10.1093/femsec/fiae021