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Frontiers in Microbiology 2021Chondroitin sulfate (CS)/dermatan sulfate (DS) is a kind of sulfated polyanionic, linear polysaccharide belonging to glycosaminoglycan. CS/DS sulfatases, which...
Chondroitin sulfate (CS)/dermatan sulfate (DS) is a kind of sulfated polyanionic, linear polysaccharide belonging to glycosaminoglycan. CS/DS sulfatases, which specifically hydrolyze sulfate groups from CS/DS oligo-/polysaccharides, are potential tools for structural and functional studies of CD/DS. However, only a few sulfatases have been reported and characterized in detail to date. In this study, two CS/DS sulfatases, PB_3262 and PB_3285, were identified from the marine bacterium sp. QA16 and their action patterns were studied in detail. PB_3262 was characterized as a novel 4--endosulfatase that can effectively and specifically hydrolyze the 4--sulfate group of disaccharide GlcUAβ1-3GalNAc(4--sulfate) but not GlcUAβ1-3GalNAc(4,6--sulfate) and IdoUAα1-3GalNAc(4--sulfate) in CS/DS oligo-/polysaccharides, which is very different from the identified 4--endosulfatases in the substrate profile. In contrast, PB_3285 specifically hydrolyzes the 6--sulfate groups of GalNAc(6--sulfate) residues located at the reducing ends of the CS chains and is the first recombinantly expressed 6--exosulfatase to effectively act on CS oligosaccharides.
PubMed: 35140691
DOI: 10.3389/fmicb.2021.775124 -
Genes Jun 2022Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity...
Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity of a marine biofilm community is a challenging task due to the high complexity in comparison with seawater. Here, we compared the resolution of full-length 16S rRNA gene sequencing technique of a PacBio platform for microbe identification in marine biofilms with the results of partial 16S rRNA gene sequencing of traditional Illumina PE250 platform. At the same time, the microbial richness, diversity, and composition of adjacent seawater communities in the same batch of samples were analyzed. Both techniques revealed higher species richness, as reflected by the Chao1 index, in the biofilms than that in the seawater communities. Moreover, compared with Illumina sequencing, PacBio sequencing detected more specific species for biofilms and less specific species for seawater. Members of , , , , and were significantly enriched in the biofilms, which is consistent with the previous understanding of species adapted to a surface-associated lifestyle and validates the taxonomic analyses in the current study. To conclude, the full-length sequencing of 16S rRNA genes has probably a stronger ability to analyze more complex microbial communities, such as marine biofilms, the species richness of which has probably been under-estimated in previous studies.
Topics: Biofilms; Genes, rRNA; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 35741812
DOI: 10.3390/genes13061050 -
Microbiology Spectrum Mar 2023Emerging evidence confirms using probiotics in promoting growth and immunity of farmed fish. However, the molecular mechanisms underlying the host-microbiome...
Emerging evidence confirms using probiotics in promoting growth and immunity of farmed fish. However, the molecular mechanisms underlying the host-microbiome interactions mediated by probiotics are not fully understood. In this study, we used rainbow trout (Oncorhynchus mykiss) as a model to investigate the internal mechanisms of host-microbiome interactions influenced by two probiotic bacteria, Bacillus velezensis and Lactobacillus sakei. We carried out experiments, including intestinal histology, serum physiology, and transcriptome and combined intestinal microbiome and metabolite profiling. Our results showed that both probiotics had a positive effect on growth, immunity, serum enzyme activity, the gut microbiome, and resistance to Aeromonas salmonicida in rainbow trout. Moreover, the intestinal microbial structure was reshaped with increased relative abundance of potential beneficial bacteria, such as , , , Bacillus coagulans, , , and in the group and and Eubacterium hallii in the group. Metabolomic profiling and transcriptome analysis revealed upregulated metabolites as biomarkers, i.e., sucrose and l-malic acid in the group, and -acetyl-l-phenylalanine, -acetylneuraminic acid, and hydroxyproline in the group. Additionally, a multiomics combined analysis illustrated significant positive correlations between the relative abundance of microflora, metabolites, and gene expression associated with immunity and growth. This study highlights the significant role of probiotics as effectors of intestinal microbial activity and shows that different probiotics can have a species-specific effect on the physiological regulation of the host. These findings contribute to a better understanding of the complex host-microbiome interactions in rainbow trout and may have implications for the use of probiotics in aquaculture. Probiotics are kinds of beneficial live microbes that impart beneficial effects on the host. Recent studies have proven that when given supplementation with probiotics, farmed fish showed improved disease prevention and growth promotion. However, the underlying metabolic functions regarding their involvement in regulating growth phenotypes, nutrient utilization, and immune response are not yet well understood in the aquaculture field. Given the active interactions between the gut microbiota and fish immune and growth performance, we conducted the supplementation experiments with the probiotics Bacillus velezensis and Lactobacillus sakei. The results showed that probiotics mediated intestinal microbiome- and microbiota-derived metabolites regulating the growth and immunity of fish, and different probiotics participated in the species-specific physiological regulation of the host. This study contributed to a better understanding of the functional interactions associated with host health and gut microbiota species.
PubMed: 36916965
DOI: 10.1128/spectrum.03980-22 -
Applied and Environmental Microbiology Jul 2022Photobacterium damselae comprises two subspecies, P. damselae subsp. damselae and P. damselae subsp. , that contrast remarkably despite their taxonomic relationship. The...
Photobacterium damselae comprises two subspecies, P. damselae subsp. damselae and P. damselae subsp. , that contrast remarkably despite their taxonomic relationship. The former is opportunistic and free-living but can cause disease in compromised individuals from a broad diversity of taxa, while the latter is a highly specialized, primary fish pathogen. Here, we employ new closed curated genome assemblies from Australia to estimate the global phylogenetic structure of the species P. damselae. We identify genes responsible for the shift from an opportunist to a host-adapted fish pathogen, potentially via an arthropod vector as fish-to-fish transmission was not achieved in repeated cohabitation challenges despite high virulence for . Acquisition of ShdA adhesin and of thiol peroxidase may have allowed the environmental, generalist ancestor to colonize zooplankton and to occasionally enter in fish host sentinel cells. As dependence on the host has increased, P. damselae has lost nonessential genes, such as those related to nitrite and sulfite reduction, urea degradation, a type 6 secretion system (T6SS) and several toxin-antitoxin (TA) systems. Similar to the evolution of Yersinia pestis, the loss of urease may be the crucial event that allowed the pathogen to stably colonize zooplankton vectors. Acquisition of host-specific genes, such as those required to form a sialic acid capsule, was likely necessary for the emergent P. damselae subsp. to become a highly specialized, facultative intracellular fish pathogen. Processes that have shaped P. damselae subsp. from subsp. damselae are similar to those underlying evolution of Yersinia pestis from Y. pseudotuberculosis. Photobacterium damselae subsp. damselae is a ubiquitous marine bacterium and opportunistic pathogen of compromised hosts of diverse taxa. In contrast, its sister subspecies P. damselae subsp. () is highly virulent in fish. has evolved from a single subclade of through gene loss and acquisition. We show that fish-to-fish transmission does not occur in repeated infection models in the primary host and present genomic evidence for vector-borne transmission, potentially via zooplankton. The broad genomic changes from generalist to specialist parallel those of the environmental opportunist Yersinia pseudotuberculosis to vector-borne plague bacterium Y. pestis and demonstrate that evolutionary processes in bacterial pathogens are universal between the terrestrial and marine biosphere.
Topics: Animals; Fish Diseases; Fishes; Gram-Negative Bacterial Infections; Photobacterium; Phylogeny
PubMed: 35862683
DOI: 10.1128/aem.00222-22 -
International Journal of Molecular... Mar 2023Lumazine protein from marine luminescent bacteria of species bind with very high affinity to the fluorescent chromophore 6,7-dimethyl-8-ribitylumazine. The light...
Lumazine protein from marine luminescent bacteria of species bind with very high affinity to the fluorescent chromophore 6,7-dimethyl-8-ribitylumazine. The light emission of bacterial luminescent systems is used as a sensitive, rapid, and safe assay for an ever-increasing number of biological systems. Plasmid pRFN4, containing the genes encoding riboflavin from the operon of , was designed for the overproduction of lumazine. To construct fluorescent bacteria for use as microbial sensors, novel recombinant plasmids (pRFN4-Pp N-P and pRFN4-Pp LP N-P) were constructed by amplifying the DNA encoding the N-P gene (L) from and the promoter region (LP) present upstream of the operon of the gene by PCR and ligating into the pRFN4-Pp N-P plasmid. A new recombinant plasmid, pRFN4-Pp LP-N-P, was constructed with the expectation that the fluorescence intensity would be further increased when transformed into . When this plasmid was transformed into 43R, the fluorescence intensity of transformants was 500 times greater than that of alone. As a result, the recombinant plasmid in which the gene encoding N-LumP and DNA containing the promoter exhibited expression that was so high as to show fluorescence in single cells. The fluorescent bacterial systems developed in the present study using and riboflavin genes can be utilized in the future as biosensors with high sensitivity and rapid analysis times.
Topics: Escherichia coli; Riboflavin; Plasmids; Promoter Regions, Genetic; Operon; Luminescent Measurements; Bacterial Proteins
PubMed: 36982169
DOI: 10.3390/ijms24065096 -
Foods (Basel, Switzerland) Jul 2021Improved quality control and prolonged shelf life are important actions in preventing food waste. To get an overview of the bacterial diversity of fillets from live...
Improved quality control and prolonged shelf life are important actions in preventing food waste. To get an overview of the bacterial diversity of fillets from live stored mature Atlantic cod, bacterial isolates were identified before and after storage (air and vacuum) and freezing/thawing. Based on the load of dominating bacteria, the effect of different packaging methods and a short freezing/thawing process on prolonged shelf-life was evaluated (total viable counts, bacteriota, sensory attributes, and volatile components). Hand filleted (strict hygiene) cod fillets had a low initial bacterial load dominated by the spoilage organism , whereas industrially produced fillets had higher bacterial loads and diversity (, , , ). The identified bacteria after storage in vacuum or air were similar to the initially identified bacteria. Bacteriota analysis showed that a short time freezing/thawing process reduced while modified atmosphere packaging (MAP; 60% CO/40% O or 60% CO/40% N) inhibited the growth of important spoilage bacteria () and allowed the growth of / and Despite being dominated by fresh fillets stored in MAP 60% CO/40% N demonstrated better sensory quality after 13 days of storage than fillets stored in MAP 60% CO/40% O (dominated by ). spp. or other members of may therefore be potential spoilage organisms in cod when other spoilage bacteria are reduced or inhibited.
PubMed: 34441531
DOI: 10.3390/foods10081754 -
Journal of Food Protection Aug 2017Precooking of tuna is a potential critical control point (CCP) in the commercial manufacturing of canned tuna. To assess the efficacy of precooking as a CCP, an...
Precooking of tuna is a potential critical control point (CCP) in the commercial manufacturing of canned tuna. To assess the efficacy of precooking as a CCP, an understanding of the thermal properties of histamine-producing bacteria (HPB) and their histidine decarboxylase (HDC) enzymes is required. The thermal properties of many HPB have been determined, but the thermal resistances of the HDC enzymes are unknown. The purpose of this study was to determine the D- and z-values of selected HDC enzymes to evaluate the CCP of precooking during the canning process and provide scientific data to support U.S. Food and Drug Administration guidelines. HDC (hdc) genes from three strains each of Morganella morganii, Enterobacter aerogenes, Raoultella planticola, and Photobacterium damselae were cloned, expressed, and purified using the Champion pET Directional TOPO Expression System, pET100 cloning vector, and HisPur Cobalt resin. The heat resistances of all enzymes were compared at 50°C, and the D- and z-values from one strain of each HPB were determined at 50 to 60°C. To evaluate the heat inactivation of HDC enzymes during canned tuna processing, tuna tissue was inoculated with HDCs and heated to 60°C in a water bath set at 65 and 100°C. The D-values for the HDC enzymes from M. morganii, E. aerogenes, R. planticola, and P. damselae ranged from 1.6 to 4.1, 1.6 to 6.3, 1.9 to 4.3, and 1.6 to 2.9 min, respectively, at 50 to 60°C. The z-values for M. morganii, E. aerogenes, R. planticola, and P. damselae were 19.2, 18.0, 22.0, and 13.3°C, respectively. The HDCs from all HPB except E. aerogenes showed no significant activity after being heated to 60°C. The data generated in this study will help refine current guidelines for the thermal destruction of the HDC enzymes.
Topics: Animals; Bacteria; Histamine; Histidine Decarboxylase; Hot Temperature; Seafood
PubMed: 28696146
DOI: 10.4315/0362-028X.JFP-17-008 -
Foods (Basel, Switzerland) Jul 2023Broomcorn millet Huangjiu brewing is usually divided into primary fermentation and post-fermentation. Microbial succession is the major factor influencing the...
Broomcorn millet Huangjiu brewing is usually divided into primary fermentation and post-fermentation. Microbial succession is the major factor influencing the development of the typical Huangjiu flavor. Here, we report the changes in flavor substances and microbial community during the primary fermentation of broomcorn millet Huangjiu. Results indicated that a total of 161 volatile flavor compounds were measured during primary fermentation, and estragole was detected for the first time in broomcorn millet Huangjiu. A total of 82 bacteria genera were identified. , , and were the dominant genera. and were dominant among the 30 fungal genera. Correlation analysis showed that 102 microorganisms were involved in major flavor substance production during primary fermentation, , , , , , , , and were most associated with flavoring substances. Four bacteria, (R1), (R2), (R3), and (R4), were isolated and identified from wheat Qu, which were added to wine Qu to prepare four kinds of fortified Qu (QR1, QR2, QR3, QR4). QR1 and QR2 fermentation can enhance the quality of Huangjiu. This work reveals the correlation between microorganisms and volatile flavor compounds and is beneficial for regulating the micro-ecosystem and flavor of the broomcorn millet Huangjiu.
PubMed: 37509772
DOI: 10.3390/foods12142680 -
Jundishapur Journal of Microbiology Jul 2015There are 4 different genera (i.e. Vibrio, Aliivibrio, Photobacterium, and Shewanella) in the new classification of bioluminescent bacteria. The mechanism of...
BACKGROUND
There are 4 different genera (i.e. Vibrio, Aliivibrio, Photobacterium, and Shewanella) in the new classification of bioluminescent bacteria. The mechanism of bioluminescence has yet to be fully elucidated. Therefore, the determination of physiological and genetic characteristics of bioluminescent bacteria isolated from different sources is very important. Pulsed-Field Gel Electrophoresis (PFGE) has the highest discriminatory power among the different molecular typing methods for the investigation of the clonal relationships between bacteria. For the PFGE analysis of bioluminescent bacteria, the NotI-HF™ is the method of choice among the restriction enzymes.
OBJECTIVES
The present study aimed to determine genetic relatedness via PFGE in 41 bioluminescent bacteria (belonging to 10 different species) isolated and identified from various marine sources.
MATERIALS AND METHODS
Different bioluminescent bacteria (i.e. Vibrio gigantis, V. azureus, V. harveyi, V. lentus, V. crassostreae, V. orientalis, Aliivibrio logei, A. fischeri, Shewanella woodyi, and Photobacterium kishitanii) were analyzed by PFGE using the NotI-HF™ restriction enzyme. The whole DNA of the strains embedded into the agarose plugs was digested with enzyme at 37°C for 30 minutes. CHEF-Mapper PFGE system was used for electrophoresis and band profile of the strains for the NotI-HF™ restriction enzyme were analyzed by Bio-Profil-1D++ software (Vilber Lourmat) at 10% homology coefficient.
RESULTS
Although all experiments were performed three times, four of forty-one bioluminescent strains (V. gigantis E-16, H-16 and S3W46 strains and A. fischeri E-4 strain) could not be typed by PFGE technique with NotI-HF™ enzyme. While only two strains (V. crassostreae H-12 and H-19 strains) were exhibiting same band pattern profiles (100% genome homology), thirty-six different PFGE band patterns were obtained. Pattern homologies changed between 66% - 92%, 73% - 83% and 49% - 100% for V. gigantis, V. harveyi and other strains, respectively.
CONCLUSIONS
The obtained results revealed that there has been a high rate of genetic diversity in bioluminescent strains isolated from Gulf of Izmir and V. lentus and V. crassostreae strains could be also bioluminescent for the first report. At the same time, PFGE analysis of bioluminescent bacteria including four different genera and ten different species were shown for the first time by this study. It is considered that data acquired by this study will contribute evolution and mechanism of bioluminescence to further works to be done.
PubMed: 26421141
DOI: 10.5812/jjm.28378v2 -
Microorganisms Jun 2022The gut microbiome is a unique marker for cetaceans' health status, and the microbiome composition of their skin wounds can indicate a potential infection from their...
The gut microbiome is a unique marker for cetaceans' health status, and the microbiome composition of their skin wounds can indicate a potential infection from their habitat. Our study provides the first comparative analysis of the microbial communities from gut regions and skin wounds of an individual Indo-Pacific finless porpoise (). Microbial richness increased from the foregut to the hindgut with variation in the composition of microbes. (67.51% ± 5.10%), (22.00% ± 2.60%), and (10.47% ± 5.49%) were the dominant phyla in the gastrointestinal tract, while Proteobacteria (76.11% ± 0.54%), (22.00% ± 2.60%), and (10.13% ± 0.49%) were the dominant phyla in the skin wounds. The genera , , , , , and , considered potential pathogens for mammals, were identified in the gut and skin wounds of the stranded Indo-Pacific finless porpoise. A comparison of the gut microbiome in the Indo-Pacific finless porpoise and other cetaceans revealed a possible species-specific gut microbiome in the Indo-Pacific finless porpoise. There was a significant difference between the skin wound microbiomes in terrestrial and marine mammals, probably due to habitat-specific differences. Our results show potential species specificity in the microbiome structure and a potential threat posed by environmental pathogens to cetaceans.
PubMed: 35889014
DOI: 10.3390/microorganisms10071295