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PloS One 2024This study aimed to investigate the cause of a foodborne disease outbreak in Huzhou on August 14, 2023. Multiple enteropathogens were detected using FilmArray, and the...
This study aimed to investigate the cause of a foodborne disease outbreak in Huzhou on August 14, 2023. Multiple enteropathogens were detected using FilmArray, and the pathogen was subsequently isolated and cultured from anal swabs of the cases and stream water. The isolated strains were identified using VITEK MS, and antimicrobial susceptibility test, pulsed field gel electrophoresis (PFGE) molecular typing, and whole genome sequencing (WGS) were performed on the isolates of Plesiomonas shigelloides. Gene annotation and sequence alignment were used to analyze the virulence genes and drug resistance genes of the strains. A phylogenetic tree was constructed based on single nucleotide polymorphism (SNP), and homology analysis was conducted to trace the origin of P. shigelloides. A total of 7 strains of P.shigelloides were isolated, with 3 from stream water and 4 from anal swabs. All 7 strains exhibited the same PFGE pattern and showed resistance to amikacin, trimethoprim-sulfamethoxazole, chloramphenicol, tetracycline, cefazolin, streptomycin, and florfenicol. The isolated strains carried the same resistance genes and virulence factors. In the sequences of the isolated strains from this outbreak, 11 mutation sites were detected. The phylogenetic tree based on SNP sites showed that these strains were homologous. This foodborne disease outbreak caused by P.shigelloides was the first reported in Huzhou. WGS can be used as a complementary method to PFGE for epidemiological investigations of disease outbreaks.
Topics: Humans; Plesiomonas; Rivers; Phylogeny; Diarrhea; Foodborne Diseases; Water
PubMed: 38574097
DOI: 10.1371/journal.pone.0301623 -
MicrobiologyOpen Dec 2019The Siamese crocodile (Crocodylus siamensis) is a freshwater, endangered crocodile with high economic value in the farming industry. Gut microflora plays an essential...
The Siamese crocodile (Crocodylus siamensis) is a freshwater, endangered crocodile with high economic value in the farming industry. Gut microflora plays an essential role in host physiological activity, and it contributes significantly to both the health and diseased states of animals. However, thus far, no study has focused on the correlation between diseases and intestinal bacterial communities in crocodilians. Here, we first compared the composition and function of gut microbial communities in captive juvenile C. siamensis suffering from anorexia and healthy crocodile controls using deep amplicon sequencing. The gut microbial diversity of anorexic crocodiles was much lower than the healthy individuals. Obvious changes in gut microbial composition were observed between sick and healthy crocodiles, except for Cetobacterium somerae of phylum Fusobacteria. In particular, the abundance of Bacteroides luti, Clostridium disporicum, Plesiomonas shigelloides, and Odoribacter sp. in the gut flora of healthy crocodiles was distinctly higher than the diseased group. Conversely, the species Edwardsiella tarda was overrepresented in the gut of anorexic crocodiles compared to the healthy group. Furthermore, in anorexic crocodiles, the predicted microbial functions that were related to amino acid metabolism, biosynthesis of other secondary metabolites, nucleotide metabolism, replication and repair, and translation were significantly reduced, while signal transduction was significantly enriched. These findings of the present study provide a reference to enrich the field of gut microorganism studies in crocodilians and suggest that alterations in the composition and function of gut bacteria in C. siamensis juveniles may be associated with anorexia in crocodiles.
Topics: Alligators and Crocodiles; Animals; Anorexia; Biodiversity; Feces; Gastrointestinal Microbiome; Phylogeny
PubMed: 31482690
DOI: 10.1002/mbo3.929 -
Veterinary Sciences Nov 2021A 7-year-old male gray wolf was found dead at a zoo during exhibition. To determine the cause of death, histological and gross necropsy diagnoses and a molecular...
A 7-year-old male gray wolf was found dead at a zoo during exhibition. To determine the cause of death, histological and gross necropsy diagnoses and a molecular analysis were performed. The gross necropsy revealed a swollen abdomen, hemorrhagic exudates around the mouth, splenomegaly, a discolored liver, a congested kidney, hemorrhagic ascites, and dark gray-colored membranes and air bubbles in the fundus of the stomach. Rod-shaped bacteria were found in the liver parenchyma and hemorrhagic ascites using Giemsa staining. The nucleotide sequencing of the cultured bacteria identified the causative agent as , which is rarely responsible for systemic infections. This study describes a rare case and the first reported systemic gastrointestinal infection due to in a zoo animal.
PubMed: 34822653
DOI: 10.3390/vetsci8110280 -
Animals : An Open Access Journal From... Jan 2023A 28 day feeding trial was conducted to investigate the growth performance, immune response and intestinal microbiota of laminarin (LAM) supplemented diets in juvenile...
A 28 day feeding trial was conducted to investigate the growth performance, immune response and intestinal microbiota of laminarin (LAM) supplemented diets in juvenile largemouth bass (). Four hundred and eighty fish (initial average weight: 0.72 ± 0.04 g) were randomly divided into four groups (40 fish per tank with three replicates in each group) Four diets were prepared with LAM supplementation at the doses of 0 (control), 5 g Kg (LL), 10 g Kg (ML) and 15 g Kg (HL), respectively. No significant difference in the specific growth rate (SGR) and hepatosomatic index (HSI) was observed in fish among the four groups, or in the lipid and ash content of fish flesh. In addition, fish in the LL group exhibited much higher antioxidant capacity ( < 0.05), while the diets with the inclusion of 5 and 10 g Kg LAM remarkably decreased the antioxidant capacity of fish ( > 0.05). Dietary LAM at the dose of 5 g Kg inhibited the transcription of interleukin-1β () and tumor necrosis factor-α (), while promoting the expression of transforming growth factor-β () in fish intestine. Moreover, the beneficial intestinal bacteria , and abundance significantly increased in fish from the LL group, while the content of opportunistic pathogens , and in fish of the HL group was substantially higher than the control group. Overall, the appropriate dose of supplemented LAM in the diet was 5 g Kg, while an excessive supplementation of LAM in the diet led to microbial community instability in largemouth bass.
PubMed: 36766348
DOI: 10.3390/ani13030459 -
Animals : An Open Access Journal From... Oct 2023This research aimed to examine the effects of dietary rutin supplementation on growth, body composition, serum biochemical indexes, liver enzyme activities and...
This research aimed to examine the effects of dietary rutin supplementation on growth, body composition, serum biochemical indexes, liver enzyme activities and antioxidant-related genes expression, intestinal morphology, and microbiota composition of juvenile yellow catfish (). Rutin was added to the basal diets at doses of 0 (control), 100 mg/kg, and 500 mg/kg. Each diet was fed randomly into three tanks, each tank containing 30 fish with an initial body mass of (10.27 ± 0.62) g. The feeding trial was conducted in an indoor recirculating aquiculture system at 28 °C for 56 days. According to the findings, the inclusion of 100 mg/kg rutin significantly improved the growth performance of yellow catfish and reduced the feed conversion ratio; however, the growth promotion effect was diminished when the diet was supplemented with 500 mg/kg of rutin. The inclusion of 500 mg/kg rutin in the diet significantly reduced the level of crude lipid and protein of the whole fish. Serum activities of alkaline phosphatase, albumin, and total protein were all significantly increased when fish were fed the diet supplemented with 500 mg/kg rutin, while serum glucose was significantly lower compared to the control group. Meanwhile, dietary rutin at a concentration of 500 mg/kg significantly induced the hepatic mRNA expressions of antioxidant-related genes (including , , , ) and inflammatory-associated genes (including , , ). Incorporating rutin at doses of 100 mg/kg and 500 mg/kg into the diets resulted in a notable increase in superoxide dismutase (SOD) activity, while simultaneously reducing malondiadehyde (MDA) content in the liver and intestine. Intestinal villus height, villus width, muscular thickness, and lumen diameter were significantly increased with the administration of 500 mg/kg of dietary rutin. Gut microbial diversity analysis indicated that supplementing diets with 100 mg/kg and 500 mg/kg rutin significantly enhanced the abundance of while decreasing richness. In conclusion, dietary rutin levels at 100 mg/kg could enhance the growth, antioxidant capability, and intestinal health of yellow catfish under present experimental conditions.
PubMed: 37958140
DOI: 10.3390/ani13213386 -
The Journal of Biological Chemistry Apr 2023N-acetyl-d-glucosamine (GlcNAc) is a major component of bacterial cell walls. Many organisms recycle GlcNAc from the cell wall or metabolize environmental GlcNAc. The...
N-acetyl-d-glucosamine (GlcNAc) is a major component of bacterial cell walls. Many organisms recycle GlcNAc from the cell wall or metabolize environmental GlcNAc. The first step in GlcNAc metabolism is phosphorylation to GlcNAc-6-phosphate. In bacteria, the ROK family kinase N-acetylglucosamine kinase (NagK) performs this activity. Although ROK kinases have been studied extensively, no ternary complex showing the two substrates has yet been observed. Here, we solved the structure of NagK from the human pathogen Plesiomonas shigelloides in complex with GlcNAc and the ATP analog AMP-PNP. Surprisingly, PsNagK showed distinct conformational changes associated with the binding of each substrate. Consistent with this, the enzyme showed a sequential random enzyme mechanism. This indicates that the enzyme acts as a coordinated unit responding to each interaction. Our molecular dynamics modeling of catalytic ion binding confirmed the location of the essential catalytic metal. Additionally, site-directed mutagenesis confirmed the catalytic base and that the metal-coordinating residue is essential. Together, this study provides the most comprehensive insight into the activity of a ROK kinase.
Topics: Humans; Acetylglucosamine; Glucosamine; Metals; Phosphotransferases (Alcohol Group Acceptor); rho-Associated Kinases; Plesiomonas
PubMed: 36806680
DOI: 10.1016/j.jbc.2023.103033 -
JMIR Infodemiology 2022Internet search volume for medical information, as tracked by Google Trends, has been used to demonstrate unexpected seasonality in the symptom burden of a variety of...
Confounding Effect of Undergraduate Semester-Driven "Academic" Internet Searches on the Ability to Detect True Disease Seasonality in Google Trends Data: Fourier Filter Method Development and Demonstration.
BACKGROUND
Internet search volume for medical information, as tracked by Google Trends, has been used to demonstrate unexpected seasonality in the symptom burden of a variety of medical conditions. However, when more technical medical language is used (eg, diagnoses), we believe that this technique is confounded by the cyclic, school year-driven internet search patterns of health care students.
OBJECTIVE
This study aimed to (1) demonstrate that artificial "academic cycling" of Google Trends' search volume is present in many health care terms, (2) demonstrate how signal processing techniques can be used to filter academic cycling out of Google Trends data, and (3) apply this filtering technique to some clinically relevant examples.
METHODS
We obtained the Google Trends search volume data for a variety of academic terms demonstrating strong academic cycling and used a Fourier analysis technique to (1) identify the frequency domain fingerprint of this modulating pattern in one particularly strong example, and (2) filter that pattern out of the original data. After this illustrative example, we then applied the same filtering technique to internet searches for information on 3 medical conditions believed to have true seasonal modulation (myocardial infarction, hypertension, and depression), and all bacterial genus terms within a common medical microbiology textbook.
RESULTS
Academic cycling explains much of the seasonal variation in internet search volume for many technically oriented search terms, including the bacterial genus term ["Staphylococcus"], for which academic cycling explained 73.8% of the variability in search volume (using the squared Spearman rank correlation coefficient, <.001). Of the 56 bacterial genus terms examined, 6 displayed sufficiently strong seasonality to warrant further examination post filtering. This included (1) ["Aeromonas" + "Plesiomonas"] (nosocomial infections that were searched for more frequently during the summer), (2) ["Ehrlichia"] (a tick-borne pathogen that was searched for more frequently during late spring), (3) ["Moraxella"] and ["Haemophilus"] (respiratory infections that were searched for more frequently during late winter), (4) ["Legionella"] (searched for more frequently during midsummer), and (5) ["Vibrio"] (which spiked for 2 months during midsummer). The terms ["myocardial infarction"] and ["hypertension"] lacked any obvious seasonal cycling after filtering, whereas ["depression"] maintained an annual cycling pattern.
CONCLUSIONS
Although it is reasonable to search for seasonal modulation of medical conditions using Google Trends' internet search volume and lay-appropriate search terms, the variation in more technical search terms may be driven by health care students whose search frequency varies with the academic school year. When this is the case, using Fourier analysis to filter out academic cycling is a potential means to establish whether additional seasonality is present.
PubMed: 37113451
DOI: 10.2196/34464 -
Antioxidants (Basel, Switzerland) Mar 2024Lipids are critical nutrients for aquatic animals, and excessive or insufficient lipid intake can lead to physiological disorders, which further affect fish growth and...
Lipids are critical nutrients for aquatic animals, and excessive or insufficient lipid intake can lead to physiological disorders, which further affect fish growth and health. In aquatic animals, the gut microbiota has an important regulatory role in lipid metabolism. However, the effects of a high-fat diet on physical health and microbiota diversity in the gut of freshwater drum () are unclear. Therefore, in the present study, a control group (Con, 6%) and a high-fat diet group (HFD, 12%) were established for a 16-week feeding experiment in freshwater drum to explore the physiological changes in the gut and the potential regulatory mechanisms of bacteria. The results indicated that a high-fat diet inhibited antioxidant and immune capacity while increasing inflammation, apoptosis and autophagy in gut cells. Transcriptome analysis revealed significant enrichment in immune-related, apoptosis-related and disease-related pathways. Through 16S rRNA analysis, a total of 31 genus-level differentially abundant bacterial taxa were identified. In addition, a high-fat diet reduced gut microbial diversity and disrupted the ecological balance of the gut microbiota (Ace, Chao, Shannon and Simpson indices). Integrated analysis of the gut microbiota combined with physiological indicators and the transcriptome revealed that gut microbial disorders were associated with intestinal antioxidants, immune and inflammatory responses, cell apoptosis and autophagy. Specifically, genus-level bacterial taxa in Proteobacteria (, , and ) could serve as potential targets controlling the response to high-fat-diet stimulation.
PubMed: 38539896
DOI: 10.3390/antiox13030363 -
Data in Brief Apr 2020This article describes the data on community structure and diversity of intestinal bacteria of Indonesian shortfin wild eel fingerling and elver (). The specimens were...
This article describes the data on community structure and diversity of intestinal bacteria of Indonesian shortfin wild eel fingerling and elver (). The specimens were obtained from Ci Kangean River, Alur Village, Cipatujah District, Tasikmalaya, West Java, Indonesia. The data were generated using DNA metagenomic approach on an Illumina paired-end platform by utilizing the V3-V4 region of the 16S rRNA gene. A total of 151,636 reads with 91.60% effective tags and 155,388 with 84.86% effective tags were generated from the intestine of wild eel fingerling (WF) and elver (WE), respectively. The total OTUs was 100 in WF and 358 in WE. The phyla Bacteroidetes (50%), Firmicutes (15%), Proteobacteria (13%), Fusobacteria (11%) and Verrucomicrobia (8%) were found in WF, and Proteobacteria (64%), Firmicutes (34%) and Fusobacteria (1%) were found in WE. The predominating families in WF were Porphyromonadaceae (50%), Clostridiaceae (12%), Fusobacteriaceae (10%), Verrucomicrobiaceae (8%), and in WE were Enterobacteriaceae (38%), Clostridiaceae (30%), Aeromonadaceae (17%), Moraxellaceae (7%). The predominating genera in WF were unassigned (48%), (10%), (sensu stricto) (9%), (8%), (4%), (4%), (4%), and in WE were (36%), (sensu stricto 1) (31%), (17%), (7%). The amount of lactic acid bacteria found in the intestine of WF was 0.0028% and WE was 0.1218%. The data provide baseline information on the changes in the community and bacterial composition in line with the stages of growth and development of wild Indonesian shortfin eels.
PubMed: 32181290
DOI: 10.1016/j.dib.2020.105299 -
PloS One 2024The field of fish microbiome research has rapidly been advancing, primarily focusing on farmed or laboratory fish species rather than natural or marine fish populations....
The field of fish microbiome research has rapidly been advancing, primarily focusing on farmed or laboratory fish species rather than natural or marine fish populations. This study sought to reveal the distinctive gut bacteriome composition and diversity within the anadromous fish species Tenualosa ilisha (hilsa), which holds the status of being the national fish of Bangladesh. We conducted an analysis on 15 gut samples obtained from 15 individual hilsa fishes collected from three primary habitats (e.g., freshwater = 5, brackish water = 5 and marine water = 5) in Bangladesh. The analysis utilized metagenomics based on 16S rRNA gene sequencing targeting the V3-V4 regions. Our comprehensive identification revealed a total of 258 operational taxonomic units (OTUs). The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our analysis unveiled considerable taxonomic differences among the habitats (freshwater, brackish water, and marine water) of hilsa fishes, as denoted by a higher level of shared microbiota (p = 0.007, Kruskal-Wallis test). Among the identified genera in the gut of hilsa fishes, including Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, and Hafnia, several are recognized as fish probiotics. Importantly, some bacterial genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella identified in the gut of hilsa identified in this study have not been reported in any aquatic or marine fish species. Significantly, we observed that 67.50% (27/40) of bacterial genera were found to be common among hilsa fishes across all three habitats. Our findings offer compelling evidence for the presence of both exclusive and communal bacteriomes within the gut of hilsa fishes, exhibiting potential probiotic properties. These observations could be crucial for guiding future microbiome investigations in this economically significant fish species.
Topics: Animals; Bangladesh; Gastrointestinal Microbiome; Fishes; RNA, Ribosomal, 16S; Bacteria; Biodiversity; Phylogeny
PubMed: 38691556
DOI: 10.1371/journal.pone.0303047