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Frontiers in Microbiology 2023Recirculating aquaculture systems (RAS) pose unique challenges in microbial community management since they rely on a stable community with key target groups, both in...
Recirculating aquaculture systems (RAS) pose unique challenges in microbial community management since they rely on a stable community with key target groups, both in the RAS environment and in the host (in this case, ). Our goal was to determine how much of the sole microbiome is inherited from the egg stage, and how much is acquired during the remainder of the sole life cycle in an aquaculture production batch, especially regarding potentially probiotic and pathogenic groups. Our work comprises sole tissue samples from 2 days before hatching and up to 146 days after hatching (-2 to 146 DAH), encompassing the egg, larval, weaning, and pre-ongrowing stages. Total DNA was isolated from the different sole tissues, as well as from live feed introduced in the first stages, and 16S rRNA gene was sequenced (V6-V8 region) using the Illumina MiSeq platform. The output was analysed with the DADA2 pipeline, and taxonomic attribution with SILVAngs version 138.1. Using the Bray-Curtis dissimilarity index, both age and life cycle stage appeared to be drivers of bacterial community dissimilarity. To try to distinguish the inherited (present since the egg stage) from the acquired community (detected at later stages), different tissues were analysed at 49, 119 and 146 DAH (gill, intestine, fin and mucus). Only a few genera were inherited, but those that were inherited accompany the sole microbiome throughout the life cycle. Two genera of potentially probiotic bacteria ( and ) were already present in the eggs, while others were acquired later, in particularly, forty days after live feed was introduced. The potentially pathogenic genera and were inherited from the eggs, while and seemed to be acquired at 49 and 119 DAH, respectively. Significant co-occurrence was found between and both and . On the other hand, significantly negative correlations were detected between and , , and . Our work reinforces the importance of life cycle studies, which can contribute to improve production husbandry strategies. However, we still need more information on this topic as repetition of patterns in different settings is essential to confirm our findings.
PubMed: 37434707
DOI: 10.3389/fmicb.2023.1188876 -
PloS One 2020Vermicompost application has been shown to promote plant growth, alter the rhizosphere microbiome, and suppress plant pathogens. These beneficial properties are often...
Vermicompost application has been shown to promote plant growth, alter the rhizosphere microbiome, and suppress plant pathogens. These beneficial properties are often attributed to the activity of vermicompost-associated microorganisms. However, little is known about the microbial shifts that occur in the rhizosphere after vermicompost application. To better understand the impact of vermicompost treatments on the assembly of rhizosphere bacterial communities, 16S rDNA communities of vermicompost and rhizospheres of each peat- and soil-grown tomatoes were profiled after conventional fertigation, irrigation without additional nutrients, and addition of three different vermicompost-extracts. The full dataset consisted of 412 identified genera, of which 317 remained following stringent quality filtration. Tomato rhizosphere microbiome responses to treatments were complex and unique between peat and soil growth substrates. Direct colonization of vermicompost-origin taxa into rhizospheres was limited, with genera Photobacterium and Luteimonas colonizing peat rhizospheres, genera Truepera, Phenylobacterium, and Lysinibacillus colonizing soil rhizospheres, and genus Pelagibius appearing in both soil and peat rhizospheres. Further patterns of differential abundance and presence/absence between treatments highlight vermicompost-mediated effects on rhizosphere microbiome assembly as an interplay of rhizosphere medium, direct colonization of vermicompost-origin taxa and vermicompost-induced shifts in the rhizosphere microbial community. This exploratory analysis is intended to provide an initial look at 16S community composition of vermicompost and the effects of vermicompost treatment on the rhizosphere microbiome assembly to highlight interactions of potential merit for subsequent investigations.
Topics: Bacteria; Composting; Solanum lycopersicum; Rhizosphere
PubMed: 32251438
DOI: 10.1371/journal.pone.0230577 -
Animal Microbiome May 2022Invertebrates are a very attractive subject for studying host-microbe interactions because of their simple gut microbial community and host diversity. Studying the...
BACKGROUND
Invertebrates are a very attractive subject for studying host-microbe interactions because of their simple gut microbial community and host diversity. Studying the composition of invertebrate gut microbiota and the determining factors is essential for understanding their symbiotic mechanism. Cephalopods are invertebrates that have similar biological properties to vertebrates such as closed circulation system, an advanced nervous system, and a well-differentiated digestive system. However, it is not currently known whether their microbiomes have more in common with vertebrates or invertebrates. This study reports on the microbial composition of six cephalopod species and compares them with other mollusk and marine fish microbiomes to investigate the factors that shape the gut microbiota.
RESULTS
Each cephalopod gut consisted of a distinct consortium of microbes, with Photobacterium and Mycoplasma identified as core taxa. The gut microbial composition of cephalopod reflected their host phylogeny, the importance of which was supported by a detailed oligotype-level analysis of operational taxonomic units assigned to Photobacterium and Mycoplasma. Photobacterium typically inhabited multiple hosts, whereas Mycoplasma tended to show host-specific colonization. Furthermore, we showed that class Cephalopoda has a distinct gut microbial community from those of other mollusk groups or marine fish. We also showed that the gut microbiota of phylum Mollusca was determined by host phylogeny, habitat, and diet.
CONCLUSION
We have provided the first comparative analysis of cephalopod and mollusk gut microbial communities. The gut microbial community of cephalopods is composed of distinctive microbes and is strongly associated with their phylogeny. The Photobacterium and Mycoplasma genera are core taxa within the cephalopod gut microbiota. Collectively, our findings provide evidence that cephalopod and mollusk gut microbiomes reflect host phylogeny, habitat, and diet. It is hoped that these data can contribute to future studies on invertebrate-microbe interactions.
PubMed: 35527289
DOI: 10.1186/s42523-022-00184-x -
The Journal of Hand Surgery Sep 2022Photobacterium damsela is a gram-negative bacterium that is known to cause infection, most commonly in marine animals and rarely in humans. Photobacterium damsela...
Photobacterium damsela is a gram-negative bacterium that is known to cause infection, most commonly in marine animals and rarely in humans. Photobacterium damsela typically results in skin and soft tissue infections in humans and has been associated with necrotizing fasciitis in several case reports. After an initially benign presentation, P damsela necrotizing fasciitis often progresses rapidly to multiorgan failure and death. Here, we present a fatal case of P damsela necrotizing fasciitis after a minor cut while scaling a fish with a discussion of current literature and treatment strategies.
Topics: Animals; Arm; Fasciitis, Necrotizing; Humans; Photobacterium; Soft Tissue Infections
PubMed: 34602337
DOI: 10.1016/j.jhsa.2021.07.033 -
Fish & Shellfish Immunology Mar 2024Immunonutrition is a promising and viable strategy for the development of prophylactic measures in aquaculture. Ulvan, a sulphated marine polysaccharide from green...
Immunonutrition is a promising and viable strategy for the development of prophylactic measures in aquaculture. Ulvan, a sulphated marine polysaccharide from green seaweeds, has many biological activities including the immunomodulatory ones. The aim of this study was to assess the short and long-term effects of an ulvan-rich extract obtained from U. ohnoi as immunonutrient in Senegalese sole juveniles. In this work, an ulvan-rich extract from Ulva ohnoi has been obtained by the hot water method and isolated by ethanol precipitation. The FTIR analysis revealed that the ulvan-rich extact had very similar characteristics to previously published ulvan spectra. The total sulfate and protein content was 24.85 ± 3.98 and 0.91 ± 0.04 %, respectively. In vitro assays performed in Senegalese sole (Solea senegalensis) macrophages showed that the ulvan obtained in this study did not compromise the cell viability at concentrations up to 1 mg ml and expression levels of lyg, irf1, il6, il10, c7, tf and txn were significantly upregulated in a concentration dependent-manner. Finally, S. senegalensis juveniles were fed basal diets and diets supplemented with the ulvan-rich extract at ratios 1 and 2 % for 30 days and then, challenged with Photobacterium damselae subsp. piscicida (Phdp). Thereafter, ulvan was withdrawn from the diet and all juveniles were fed the basal diet for 30 days. At 30 days post withdrawal (dpw), juveniles were challenged with Phdp. The expression profiles of a set of genes related to the immune system in spleen were evaluated as well as the lysozyme, peroxidase and bactericidal activity in plasma. Dietary effects of 1 % ulvan resulted in a boost of the immune response and increased disease resistance at short-term whereas juveniles fed diets supplemented with 2 % ulvan showed a significant decrease in the bactericidal activity and lack of protection against Phdp. At long-term (30 days after the withdrawal of ulvan), an improved response was observed in juveniles previously fed 1 % ulvan.
Topics: Animals; Fish Diseases; Gram-Negative Bacterial Infections; Polysaccharides; Flatfishes; Photobacterium
PubMed: 38296005
DOI: 10.1016/j.fsi.2024.109399 -
Journal of Applied Microbiology Jul 2020This review summarizes the current knowledge about iron uptake systems in bacterial fish pathogens and their involvement in the infective process. Like most animal... (Review)
Review
This review summarizes the current knowledge about iron uptake systems in bacterial fish pathogens and their involvement in the infective process. Like most animal pathogens, fish pathogens have evolved sophisticated iron uptake mechanisms some of which are key virulence factors for colonization of the host. Among these systems, siderophore production and heme uptake systems are the best studied in fish pathogenic bacteria. Siderophores like anguibactin or piscibactin, have been described in Vibrio and Photobacterium pathogens as key virulence factors to cause disease in fish. In many other bacterial fish pathogens production of siderophores was demonstrated but the compounds were not yet chemically characterized and their role in virulence was not determined. The role of heme uptake in virulence was not yet clearly elucidated in fish pathogens although there exist evidence that these systems are expressed in fish tissues during infection. The relationship of other systems, like Fe(II) transporters or the use of citrate as iron carrier, with virulence is also unclear. Future trends of research on all these iron uptake mechanisms in bacterial fish pathogens are also discussed.
Topics: Animals; Bacteria; Bacterial Proteins; Biological Transport; Fish Diseases; Heme; Iron; Siderophores; Virulence; Virulence Factors
PubMed: 31994331
DOI: 10.1111/jam.14595 -
Journal of Clinical Microbiology Feb 2023Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness... (Review)
Review
Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum ) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the , , and genera. Valid and effectively published novel members of the Streptococcus, , and genera are additionally described from disease pathogenesis perspectives.
Topics: Humans; Planctomycetes; Bacteria; Gram-Negative Bacteria; Phylogeny
PubMed: 36719221
DOI: 10.1128/jcm.01426-22 -
British Poultry Science Jun 20221. The goals of this study were to analyse the changes in microbiota composition of chilled chicken during storage and identify microbial biomarkers related to meat...
1. The goals of this study were to analyse the changes in microbiota composition of chilled chicken during storage and identify microbial biomarkers related to meat freshness.2. The study used 16S rDNA sequencing to track the microbiota shift in chilled chicken during storage. Associations between microbiota composition and storage time were analysed and microbial biomarkers were identified.3. The results showed that microbial diversity of chilled chicken decreased with the storage time. A total of 27 and 24 microbial biomarkers were identified by using orthogonal partial least squares (OPLS) and the random forest regression approach, respectively. The receiver operating characteristic (ROC) curve analysis indicated that the OPLS regression approach had better performance in identifying freshness-related biomarkers. The multiple stepwise regression analysis identified four key microbial biomarkers, including and genera and constructed a predictive model.4. The study provided microbial biomarkers and a model related to the freshness of chilled chicken. These findings provide a basis for developing detection methods of the freshness of chilled chicken.
Topics: Animals; Biomarkers; Chickens; Food Microbiology; Food Storage; Meat; Microbiota
PubMed: 34747672
DOI: 10.1080/00071668.2021.2003753 -
Environmental Research Dec 2022This study explored the microbial nitrogen transformation and removal potential in the plant rhizosphere of seven artificial tidal wetlands under different salinity...
This study explored the microbial nitrogen transformation and removal potential in the plant rhizosphere of seven artificial tidal wetlands under different salinity gradients (0-30‰). Molecular biological and stable isotopic analyses revealed the existence of simultaneous anammox (anaerobic ammonium oxidation), nitrification, DNRA (dissimilatory nitrate reduction to ammonium) and denitrification processes, contributing to nitrogen loss in rhizosphere soil. The microbial abundances were 2.87 × 10-9.12 × 10 (nitrogen functional genes) and 1.24 × 10-8.43 × 10 copies/g (16S rRNA gene), and the relative abundances of dissimilatory nitrate reduction and nitrification genera ranged from 6.75% to 24.41% and from 0.77% to 1.81%, respectively. The bacterial 16S rRNA high-throughput sequencing indicated that Bacillus, Zobellella and Paracoccus had obvious effects on nitrogen removal by heterotrophic nitrifying/aerobic denitrifying process (HN-AD), and autotrophic nitrification (Nitrosomonas, Nitrospira and Nitrospina), conventional denitrification (Bradyrhizobium, Burkholderia and Flavobacterium), anammox (Candidatus Brocadia and Candidatus Scalindua) and DNRA (Clostridium, Desulfovibrio and Photobacterium) organisms co-existed with HN-AD bacteria. The potential activities of DNRA, nitrification, anammox and denitrification were 1.23-9.23, 400.03-755.91, 3.12-35.24 and 30.51-300.04 nmolN·g·d, respectively. The denitrification process contributed to 73.59-88.65% of NO reduction, compared to 0.71-13.20% and 8.20-15.42% via DNRA and anammox, as 83.83-90.74% of N production was conducted by denitrification, with the rest through anammox. Meanwhile, the nitrification pathway accounted for 95.28-99.23% of NH oxidation, with the rest completed by anammox bacteria. Collectively, these findings improved our understanding on global nitrogen cycles, and provided a new idea for the removal of contaminants in saline water treatment.
Topics: Ammonium Compounds; Bacteria; Denitrification; Nitrates; Nitrogen; Oxidation-Reduction; RNA, Ribosomal, 16S; Rhizosphere; Salinity; Soil; Wetlands
PubMed: 36055394
DOI: 10.1016/j.envres.2022.114235 -
Environmental Pollution (Barking, Essex... Feb 2023Nodularin (NOD) is a harmful cyanotoxin that affects shrimp farming. The hepatopancreas and intestine of shrimp are the main target organs of cyanotoxins. In this study,...
Nodularin (NOD) is a harmful cyanotoxin that affects shrimp farming. The hepatopancreas and intestine of shrimp are the main target organs of cyanotoxins. In this study, we exposed Litopenaeus vannamei to NOD at 0.1 and 1 μg/L for 72 h, respectively, and changes in histology, oxidative stress, gene transcription, metabolism, and intestinal microbiota were investigated. After NOD exposure, the hepatopancreas and intestine showed obvious histopathological damage and elevated oxidative stress response. Transcription patterns of immune genes related to detoxification, prophenoloxidase and coagulation system were altered in the hepatopancreas. Furthermore, metabolic patterns, especially amino acid metabolism and arachidonic acid related metabolites, were also disturbed. The integration of differential genes and metabolites revealed that the functions of "alanine, aspartic acid and glutamate metabolism" and "aminoacyl-tRNA biosynthesis" were highly affected. Alternatively, NOD exposure induced the variation of the diversity and composition of intestinal microbiota, especially the abundance of potentially beneficial bacteria (Demequina, Phyllobacterium and Pseudoalteromonas) and pathogenic bacteria (Photobacterium and Vibrio). Several intestinal bacteria were correlated with the changes of host the metabolic function and immune factors. These results revealed the toxic effects of NOD on shrimp, and identified some biomarkers.
Topics: Animals; Intestines; Gastrointestinal Microbiome; Peptides, Cyclic; Penaeidae; Cyanobacteria Toxins; Immunity, Innate
PubMed: 36574809
DOI: 10.1016/j.envpol.2022.120950