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BMC Microbiology Nov 2019In light of rampant childhood diarrhoea, this study investigated bacterial pathogens from human and non-human sources in an urban informal settlement. Meat from informal...
Prevalence and antibiotic susceptibility patterns of enteric bacterial pathogens in human and non-human sources in an urban informal settlement in Cape Town, South Africa.
BACKGROUND
In light of rampant childhood diarrhoea, this study investigated bacterial pathogens from human and non-human sources in an urban informal settlement. Meat from informal abattoirs (n = 85), river water (n = 64), and diarrheic stool (n = 66) were collected between September 2015 and May 2016. A duplex real-time PCR, gel-based PCR, and CHROMagar™STEC were used to screen Tryptic Soy Broth (TSB) for diarrheic E. coli. Standard methods were used to screen for other selected food and waterborne bacterial pathogens.
RESULTS
Pathogens isolated from stool, meat, and surface water included Salmonella enterica (6, 5, 0%), Plesiomonas shigelloides (9, 0, 17%), Aeromonas sobria (3, 3, 0%), Campylobacter jejuni (5, 5, 0%), Shigella flexneri (17, 5, 0%), Vibrio vulnificus (0, 0, 9%), and diarrheic E. coli (21, 3, 7%) respectively. All the isolates were resistant to trimethoprim-sulphamethoxazole.
CONCLUSIONS
There was a high burden of drug resistant diarrheal pathogens in the stool, surface water and meat from informal slaughter. Integrated control measures are needed to ensure food safety and to prevent the spread of drug resistant pathogens in similar settings.
Topics: Bacteria; Bacterial Infections; Child, Preschool; Diarrhea; Drug Resistance, Multiple, Bacterial; Feces; Female; Food Microbiology; Humans; Infant; Male; Meat; Population Surveillance; Prevalence; Rivers; South Africa; Trimethoprim, Sulfamethoxazole Drug Combination; Urban Renewal
PubMed: 31694551
DOI: 10.1186/s12866-019-1620-6 -
Frontiers in Immunology 2020In mammals, interleukin (IL)-17A and F are hallmark inflammatory cytokines that play key roles in protection against infection and intestinal mucosal immunity. In the...
In mammals, interleukin (IL)-17A and F are hallmark inflammatory cytokines that play key roles in protection against infection and intestinal mucosal immunity. In the gastrointestinal tract (GI), the induction of antimicrobial peptide (AMP) production via Paneth cells is a fundamental role of IL-17A and F in maintaining homeostasis of the GI microbiome and health. Although mammalian IL-17A and F homologs (referred to as IL-17A/F1-3) have been identified in several fish species, their function in the intestine is poorly understood. Additionally, the fish intestine lacks Paneth cells, and its GI structure is very different from that of mammals. Therefore, the GI microbiome modulatory mechanism via IL-17A/F genes has not been fully elucidated. In this study, Japanese medaka () were used as a teleost model, and IL-17A/F1-knockout (IL-17A/F1-KO) medaka were established using the CRISPR/Cas9 genome editing technique. Furthermore, two IL-17A/F1-deficient medaka strains were generated, including one strain containing a 7-bp deletion (-7) and another with an 11-bp addition (+11). After establishing F2 homozygous KO medaka, transcriptome analysis (RNA-seq) was conducted to elucidate IL-17A/F1-dependent gene induction in the intestine. Results of RNA-seq and real-time PCR (qPCR) demonstrated down-regulation of immune-related genes, including interleukin-1β (β), complement 1q subunit C (), transferrin a (), and G-type lysozyme (), in IL-17A/F1-KO medaka. Interestingly, protein and lipid digestive enzyme genes, including phospholipase A2, group IB (), and elastase-1-like (), were also downregulated in the intestines of IL-17A/F1-KO medaka. Furthermore, to reveal the influence of these downregulated genes on the gut microbiome in IL-17A/F1-KO, 16S rRNA-based metagenomic sequencing analysis was conducted to analyze the microbiome constitution. Under a non-exposed state, the intestinal microbiome of IL-17A/F1-KO medaka differed at the phylum level from wild-type, with significantly higher levels of Verrucomicrobia and Planctomycetes. Additionally, at the operational taxonomic unit (OTU) level of the human and fish pathogens, the Enterobacteriaceae was the dominant species in IL-17A/F1-KO medaka. These findings suggest that IL-17A/F1 is involved in the maintenance of a healthy gut microbiome.
Topics: Animals; Fish Proteins; Gastrointestinal Microbiome; Gene Expression; Immunity, Mucosal; Interleukin-17; Oryzias
PubMed: 32256492
DOI: 10.3389/fimmu.2020.00425 -
Frontiers in Cellular and Infection... 2022The influence of dietary probiotic on the growth performance, digestive enzyme activity, immune parameters and disease resistance of yellow catfish () was evaluated....
The influence of dietary probiotic on the growth performance, digestive enzyme activity, immune parameters and disease resistance of yellow catfish () was evaluated. Commercial diet (C) or diet containing 10 cfu/g (T) was fed for 4 weeks, and final weight (FW), specific growth rate (SGR) and feed conversion ratio (FCR) were improved (0.05) in the T group. Dietary increased protease and amylase activities in the digestive tract after 2 and 4 weeks, respectively. Respiratory burst (RB), plasma lysozyme (LZM) activity, total antioxidant capacity (T-AOC) and superoxide dismutase (SOD) activity were also elevated (0.05). Immune-related genes signal transducer and activator of transcription 1 (STATA-1), immunoglobulin M (IgM) and C-type lectin (CTL) were upregulated (0.05), but interleukin-1 β (IL-1β) was not (0.05). Intestinal microbiota analysis showed that the community structure was significantly different between the two groups; the relative abundance of was increased but was decreased in T. Moreover, challenge tests showed that the resistance of fish fed against and was significantly enhanced (0.05). In conclusion, dietary supplementation of can effectively improve the growth performance, digestive enzyme activity, immune responses, intestinal microbiota composition and disease resistance of yellow catfish.
Topics: Animals; Catfishes; Bacillus amyloliquefaciens; Gastrointestinal Microbiome; Disease Resistance; Diet; Gastrointestinal Agents
PubMed: 36452300
DOI: 10.3389/fcimb.2022.1047351 -
International Journal of Molecular... Sep 2020is a Gram-negative, rod-shaped bacterium which causes foodborne intestinal infections, including gastroenteritis. It is one of the most frequent causes of travellers'...
is a Gram-negative, rod-shaped bacterium which causes foodborne intestinal infections, including gastroenteritis. It is one of the most frequent causes of travellers' diarrhoea. Lipopolysaccharide (LPS, endotoxin), an important virulence factor of the species, is in most cases characterised by a smooth character, demonstrated by the presence of all regions, such as lipid A, core oligosaccharide, and O-specific polysaccharide, where the latter part determines O-serotype. LPS is still a poorly characterised virulence factor considering a "translation" of the particular O-serotype into chemical structure. To date, LPS structure has only been elucidated for 15 strains out of 102 O-serotypes. Structures of the new O-specific polysaccharide and core oligosaccharide of from the Czechoslovak National Collection of Type Cultures CNCTC 90/89 LPS (O22), investigated by chemical analysis, mass spectrometry, and H,C nuclear magnetic resonance (NMR) spectroscopy, have now been reported. The pentasaccharide repeating unit of the O-specific polysaccharide is built of one d-QuiNAc and is rich in four d-GalNAcAN residues. Moreover, the new core oligosaccharide shares common features of other endotoxins, i.e., the lack of phosphate groups and the presence of uronic acids.
Topics: Carbohydrate Sequence; Lipopolysaccharides; Nuclear Magnetic Resonance, Biomolecular; O Antigens; Oligosaccharides; Plesiomonas; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 32947917
DOI: 10.3390/ijms21186788 -
Frontiers in Bioengineering and... 2023Polyhydroxyalkanoate (PHA) synthases (PhaCs) are key enzymes in PHA polymerization. PhaCs with broad substrate specificity are attractive for synthesizing structurally...
Polyhydroxyalkanoate (PHA) synthases (PhaCs) are key enzymes in PHA polymerization. PhaCs with broad substrate specificity are attractive for synthesizing structurally diverse PHAs. In the PHA family, 3-hydroxybutyrate (3HB)-based copolymers are industrially produced using Class I PhaCs and can be used as practical biodegradable thermoplastics. However, Class I PhaCs with broad substrate specificities are scarce, prompting our search for novel PhaCs. In this study, four new PhaCs from the bacteria , , , and were selected a homology search against the GenBank database, using the amino acid sequence of PHA synthase (PhaC), a Class I enzyme with a wide range of substrate specificities, as a template. The four PhaCs were characterized in terms of their polymerization ability and substrate specificity, using as a host for PHA production. All the new PhaCs were able to synthesize P(3HB) in with a high molecular weight, surpassing PhaC. The substrate specificity of PhaCs was evaluated by synthesizing 3HB-based copolymers with 3-hydroxyhexanoate, 3-hydroxy-4-methylvalerate, 3-hydroxy-2-methylbutyrate, and 3-hydroxypivalate monomers. Interestingly, PhaC from (PhaC) exhibited relatively broad substrate specificity. PhaC was further engineered through site-directed mutagenesis, and the variant resulted in an enzyme with improved polymerization ability and substrate specificity.
PubMed: 36896015
DOI: 10.3389/fbioe.2023.1114946 -
Life (Basel, Switzerland) Jun 2021An increasing number of fishmeal supplements are becoming the focus of aquaculture research, with a special emphasis on microalgae/cyanobacteria such as spirulina being...
An increasing number of fishmeal supplements are becoming the focus of aquaculture research, with a special emphasis on microalgae/cyanobacteria such as spirulina being considered as sustainable alternatives. New feed ingredients can have a far-reaching impact on the intestinal microbiome and therefore play an important role in the development and the health of fish. However, the influence of these alternatives on the microbiome is largely unknown. We undertook a 10 weeks feeding experiment on 120 African catfish with an initial body weight of 50.1 ± 2.95 g. To understand the effect of the spirulina supplementation, two isoenergetic experimental diets were formulated, containing either fishmeal or spirulina as a protein source. The 16S rRNA sequencing was used to analyze the intestinal bacteria microbiota. Results show that the observed richness indicated no significant statistical difference, but Chao1, ACE, Shannon, and Simpson indices indicate a possible increase in bacterial richness for the spirulina diet. The most abundant bacteria in both experimental groups were with the only taxa from the genus . The bacterium from genus was more likely to be found in the microbiome of fish fed the fishmeal diet. In spirulina-fed fish, the genera and were the most dominant microbes observed. Even though some genera were more abundant in the spirulina group, the overall microbial community structure was not affected by diets.
PubMed: 34198518
DOI: 10.3390/life11060558 -
Microbiological Research Aug 2024The α-Gal syndrome (AGS) is an IgE-mediated tick borne-allergy that results in delayed anaphylaxis to the consumption of mammalian meat and products containing α-Gal....
The α-Gal syndrome (AGS) is an IgE-mediated tick borne-allergy that results in delayed anaphylaxis to the consumption of mammalian meat and products containing α-Gal. Considering that α-Gal-containing microbiota modulates natural antibody production to this glycan, this study aimed to evaluate the influence on tick salivary compounds on the gut microbiota composition in the zebrafish (Danio rerio) animal model. Sequencing of 16 S rDNA was performed in a total of 75 zebrafish intestine samples, representing different treatment groups: PBS control, Ixodes ricinus tick saliva, tick saliva non-protein fraction (NPF), tick saliva protein fraction (PF), and tick saliva protein fractions 1-5 with NPF (F1-5). The results revealed that treatment with tick saliva and different tick salivary fractions, combined with α-Gal-positive dog food feeding, resulted in specific variations in zebrafish gut microbiota composition at various taxonomic levels and affected commensal microbial alpha and beta diversities. Metagenomics results were corroborated by qPCR, supporting the overrepresentation of phylum Firmicutes in the tick saliva group, phylum Fusobacteriota in group F1, and phylum Cyanobacteria in F2 and F5 compared to the PBS-control. qPCRs results at genus level sustained significant enrichment of Plesiomonas spp. in groups F3 and F5, Rhizobium spp. in NPF and F4, and Cloacibacterium spp. dominance in the PBS control group. This study provides new results on the role of gut microbiota in allergic reactions to tick saliva components using a zebrafish model of AGS. Overall, gut microbiota composition in response to tick saliva biomolecules may be associated with allergic reactions to mammalian meat consumption in AGS.
Topics: Animals; Saliva; Gastrointestinal Microbiome; Zebrafish; Food Hypersensitivity; RNA, Ribosomal, 16S; Meat; Bacteria; Metagenomics; Salivary Proteins and Peptides; Ixodes; Disease Models, Animal
PubMed: 38820703
DOI: 10.1016/j.micres.2024.127786 -
Antioxidants (Basel, Switzerland) Jun 2023This study aimed to investigate the potential adverse effects of the practical application of copper sulfate on yellow catfish () and to provide insights into the gill...
This study aimed to investigate the potential adverse effects of the practical application of copper sulfate on yellow catfish () and to provide insights into the gill toxicity induced by copper sulphate. Yellow catfish were exposed to a conventional anthelmintic concentration of copper sulphate (0.7 mg/L) for seven days. Oxidative stress biomarkers, transcriptome, and external microbiota of gills were examined using enzymatic assays, RNA-sequencing, and 16S rDNA analysis, respectively. Copper sulphate exposure led to oxidative stress and immunosuppression in the gills, with increased levels of oxidative stress biomarkers and altered expression of immune-related differentially expressed genes (DEGs), such as IL-1β, IL4Rα, and CCL24. Key pathways involved in the response included cytokine-cytokine receptor interaction, NOD-like receptor signaling pathway, and Toll-like receptor signaling pathway. The 16S rDNA analysis revealed copper sulphate altered the diversity and composition of gill microbiota, as evidenced by a significant decrease in the abundance of Bacteroidotas and Bdellovibrionota and a significant increase in the abundance of Proteobacteria. Notably, a substantial 8.5-fold increase in the abundance of was also observed at the genus level. Our findings demonstrated that copper sulphate induced oxidative stress, immunosuppression, and gill microflora dysbiosis in yellow catfish. These findings highlight the need for sustainable management practices and alternative therapeutic strategies in the aquaculture industry to mitigate the adverse effects of copper sulphate on fish and other aquatic organisms.
PubMed: 37372018
DOI: 10.3390/antiox12061288 -
PeerJ 2023The Andean condor () is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the...
BACKGROUND
The Andean condor () is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome.
METHODS
This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways.
RESULTS
Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with , a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for and , respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.
Topics: Animals; Gastrointestinal Microbiome; Metagenomics; Falconiformes; Acclimatization; Chile; Clostridium perfringens
PubMed: 37434868
DOI: 10.7717/peerj.15235 -
Drug Design, Development and Therapy 2024Willd. (PT), a traditional Chinese medicinal plant extensively employed in managing Alzheimer's disease, exhibits notable gastrointestinal side effects as highlighted...
Magnolia Officinalis Alcohol Extract Alleviates the Intestinal Injury Induced by Polygala Tenuifolia Through Regulating the PI3K/AKT/NF-κB Signaling Pathway and Intestinal Flora.
PURPOSE
Willd. (PT), a traditional Chinese medicinal plant extensively employed in managing Alzheimer's disease, exhibits notable gastrointestinal side effects as highlighted by prior investigations. In contrast, Rehd. et Wils (MO), a traditional remedy for gastrointestinal ailments, shows promising potential for ameliorating this adverse effect of PT. The objective of this study is to examine the underlying mechanism of MO in alleviating the side effects of PT.
METHODS
Hematoxylin-eosin (H&E) staining was used to observe the structural damage of zebrafish intestine, and enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of inflammatory factors and oxidative stress. The integrity of the intestinal tight junctions was examined using transmission electron microscope (TEM). Moreover, the expression of intestinal barrier genes and PI3K/AKT/NF-κB signaling pathway-related genes was determined through quantitative real-time PCR. The changes in intestinal microbial composition were analyzed using 16S rRNA and metagenomic techniques.
RESULTS
MO effectively ameliorated intestinal pathological damage and barrier gene expression, and significantly alleviated intestinal injury by reducing the expression of inflammatory cytokines IL-1β, IL-6, TNF-α, and inhibiting the activation of PI3K/AKT/NF-κB pathway. Furthermore, MO could significantly increase the relative abundance of beneficial microorganisms ( and ), and reduce the relative abundance of pathogenic bacteria ( and ).
CONCLUSION
MO alleviated PT-induced intestinal injury, and its mechanism may be related to the inhibition of PI3K/AKT/NF-κB pathway activation and regulation of intestinal flora.
Topics: Magnolia; Polygala; Animals; Gastrointestinal Microbiome; NF-kappa B; Signal Transduction; Proto-Oncogene Proteins c-akt; Phosphatidylinositol 3-Kinases; Zebrafish; Plant Extracts; Intestines
PubMed: 38799799
DOI: 10.2147/DDDT.S461152