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Microorganisms Mar 2023Northern Thailand, the main part of the Lanna region, is home to a diverse range of ethnic groups, each with their own food and cultural heritage. The bacterial...
Northern Thailand, the main part of the Lanna region, is home to a diverse range of ethnic groups, each with their own food and cultural heritage. The bacterial compositions in fermented soybean (FSB) products indigenous to three Lanna ethnolinguistic groups, including Karen, Lawa, and Shan, were investigated in this study. Bacterial DNA was extracted from the FSB samples and subjected to 16S rRNA gene sequencing using the Illumina sequencing platform. Metagenomic data showed that the predominant bacteria in all FSBs were members of the genus (49.5-86.8%), and the Lawa FSB had the greatest bacterial diversity. The presence of genera , , in the Karen and Lawa FSBs and in the Shan FSB might be indicators of food hygiene problems during processing. The network analysis predicted antagonistic effects of against some indicator and pathogenic bacteria. The functional prediction revealed some potential functional properties of these FSBs. The presence of in all FSBs and in the Shan FSB suggests that these FSBs could potentially be good sources of beneficial bacteria, and they should be conserved and promoted for health and food security reasons. However, food processing hygiene measures should be introduced and monitored to warrant their properties as health foods.
PubMed: 36985222
DOI: 10.3390/microorganisms11030649 -
Animals : An Open Access Journal From... Mar 2023Previous studies have demonstrated that the strains L1, L21 and CLFP3 are probiotics against vibriosis or lactococosis in sea bass or rainbow trout. In this study,...
Previous studies have demonstrated that the strains L1, L21 and CLFP3 are probiotics against vibriosis or lactococosis in sea bass or rainbow trout. In this study, the utility of these bacterial strains in the control of saprolegniosis was evaluated. For this purpose, both in vitro inhibition studies and competition for binding sites against and in vivo tests with experimentally infected rainbow trout were carried out. In the in vitro tests, the three isolates showed inhibitory activity upon mycelium growth and cyst germination and reduced the adhesion of cysts to cutaneous mucus; however, this effect depended on the number of bacteria used and the incubation time. In the in vivo test, the bacteria were administered orally at 10 CFU g in the feed or at 10 CFU ml in the tank water for 14 days. None of the three bacteria showed protection against infection either through water or feed, and the cumulative mortality reached 100% within 14 days post infection. The obtained results show that the use of an effective probiotic against a certain disease in a host may not be effective against another pathogen or in another host and that the results obtained in vitro may not always predict the effects when used in vivo.
PubMed: 36899810
DOI: 10.3390/ani13050954 -
Euro Surveillance : Bulletin Europeen... Feb 2023IntroductionEnterococci harbouring genes encoding resistance to florfenicol and the oxazolidinone antimicrobial linezolid have emerged among food-producing animals and...
High occurrence of , , and harbouring oxazolidinone resistance genes in raw meat-based diets for companion animals - a public health issue, Switzerland, September 2018 to May 2020.
IntroductionEnterococci harbouring genes encoding resistance to florfenicol and the oxazolidinone antimicrobial linezolid have emerged among food-producing animals and meat thereof, but few studies have analysed their occurrence in raw meat-based diets (RMBDs) for pets.AimWe aimed to examine how far RMBDs may represent a source of bacteria with oxazolidinone resistance genes.MethodsFifty-nine samples of different types of RMBDs from 10 suppliers (three based in Germany, seven in Switzerland) were screened for florfenicol-resistant Gram-positive bacteria using a selective culture medium. Isolates were phenotypically and genotypically characterised.ResultsA total of 27 , , and isolates were obtained from 24 of the 59 samples. The , , and genes were identified in 24/27, 6/27 and 5/27 isolates, respectively. Chloramphenicol and linezolid minimum inhibitory concentrations (MICs) ranged from 24.0 mg/L-256.0 mg/L, and 1.5 mg/L-8.0 mg/L, respectively. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoints, 26 of 27 isolates were resistant to chloramphenicol (MICs ≥ 32 mg/L), and two were resistant to linezolid (MICs ≥ 8 mg/L). Multilocus sequence typing analysis of the 17 isolates identified 10 different sequence types (ST)s, with ST593 (n = 4 isolates) and ST207 (n = 2 isolates) occurring more than once, and two novel STs (n = 2 isolates). isolates belonged to four different STs (168, 264, 822, and 1846).ConclusionThe high occurrence in our sample of Gram-positive bacteria harbouring genes encoding resistance to the critical antimicrobial linezolid is of concern since such bacteria may spread from companion animals to humans upon close contact between pets and their owners.
Topics: Humans; Animals; Oxazolidinones; Enterococcus faecalis; Enterococcus faecium; Linezolid; Anti-Bacterial Agents; Pets; Public Health; Switzerland; Drug Resistance, Bacterial; Chloramphenicol; Anti-Infective Agents; Meat; Diet; Microbial Sensitivity Tests; Gram-Positive Bacterial Infections
PubMed: 36757316
DOI: 10.2807/1560-7917.ES.2023.28.6.2200496 -
Environmental Research Feb 2023The disposal of healthcare waste without prior elimination of pathogens and hazardous contaminants has negative effects on the environment and public health. This study...
Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams.
The disposal of healthcare waste without prior elimination of pathogens and hazardous contaminants has negative effects on the environment and public health. This study aimed to profile the complete microbial community and correlate it with the antibiotic compounds identified in microwave pre-treated healthcare wastes collected from three different waste operators in Peninsular Malaysia. The bacterial and fungal compositions were determined via amplicon sequencing by targeting the full-length 16S rRNA gene and partial 18S with full-length ITS1-ITS2 regions, respectively. The antibiotic compounds were characterized using high-throughput spectrometry. There was significant variation in bacterial and fungal composition in three groups of samples, with alpha- (p-value = 0.04) and beta-diversity (p-values <0.006 and < 0.002), respectively. FC samples were found to acquire more pathogenic microorganisms than FA and FV samples. Paenibacillus and unclassified Bacilli genera were shared among three groups of samples, meanwhile, antibiotic-resistant bacteria Proteus mirabilis, Enterococcus faecium, and Enterococcus faecalis were found in modest quantities. A total of 19 antibiotic compounds were discovered and linked with the microbial abundance detected in the healthcare waste samples. The principal component analysis demonstrated a positive antibiotic-bacteria correlation for genera Pseudomonas, Aerococcus, Comamonas, and Vagococcus, while the other bacteria were negatively linked with antibiotics. Nevertheless, deep bioinformatic analysis confirmed the presence of bla and penP which are associated with the production of class A beta-lactamase and beta-lactam resistance pathways. Microorganisms and contaminants, which serve as putative indicators in healthcare waste treatment evaluation revealed the ineffectiveness of microbial inactivation using the microwave sterilization method. Our findings suggested that the occurrence of clinically relevant microorganisms, antibiotic contaminants, and associated antibiotic resistance genes (ARGs) represent environmental and human health hazards when released into landfills via ARGs transmission.
Topics: Humans; Anti-Bacterial Agents; beta-Lactams; Genes, Bacterial; RNA, Ribosomal, 16S; Pandemics; COVID-19; Bacteria; Drug Resistance, Microbial; Microbiota
PubMed: 36565841
DOI: 10.1016/j.envres.2022.115139 -
Microbiology Spectrum Dec 2022The linezolid resistance mediated by has exhibited an increasing trend among Gram-positive bacteria, which greatly limits the treatment options for severe bacterial...
The linezolid resistance mediated by has exhibited an increasing trend among Gram-positive bacteria, which greatly limits the treatment options for severe bacterial infections. However, the prevalence of was usually underestimated based on the existing screening methods. In this study, we used a traditional method and an improved method that included a high-salinity condition treatment after enrichment to screen for -carrying bacteria from stool samples from 1,018 healthy donors in Hangzhou, China. The fecal carriage rate of -carrying bacteria was 19.25% when screened by the improved method (196/1,018), which was much higher than that of the traditional method at 5.89% (60/1,018). Enterococci were the majority of the -positive isolates, while five nonenterococcal isolates were also obtained, including two Streptococcus gallolyticus, one Vagococcus lutrae, one Lactococcus garvieae, and one Lactococcus formosensis isolate. Whole-genome sequencing analysis identified four novel OptrA variants, IDKKGPM, IDKKGP, KLDK, and EYDDI, in these isolates, whose flanking regions with a gene downstream were bounded by different insertion sequences. In conclusion, our optimized method displayed high sensitivity in the detection of -positive bacteria in fecal samples and revealed a high carriage rate in a healthy population. Although enterococci are dominant, multiple -carrying Gram-positive bacteria were also found. This study represented an optimized screening approach for the gene, which is an important mechanism of antimicrobial resistance to linezolid as a last resort for the treatment of infections caused by multiresistant Gram-positive bacteria. We revealed a high fecal carriage rate of the gene among adults by this method and reported the first identification of in Lactococcus formosensis as well as the identification of this gene in Vagococcus lutrae and of the gene in Ligilactobacillus salivarius of human origin, suggesting the wide spread of the gene in the Gram-positive bacterial community.
Topics: Adult; Humans; Oxazolidinones; Linezolid; Anti-Bacterial Agents; Enterococcus faecalis; Enterococcus faecium; Drug Resistance, Bacterial; Enterococcus; Gram-Positive Bacterial Infections; Microbial Sensitivity Tests
PubMed: 36377960
DOI: 10.1128/spectrum.02974-22 -
International Journal of Molecular... Sep 2022Lipidic metabolites play essential roles in host physiological health and growth performance, serving as the major structural and signaling components of membranes,...
Lipidomics for Determining Giant Panda Responses in Serum and Feces Following Exposure to Different Amount of Bamboo Shoot Consumption: A First Step towards Lipidomic Atlas of Bamboo, Giant Panda Serum and Feces by Means of GC-MS and UHPLC-HRMS/MS.
Lipidic metabolites play essential roles in host physiological health and growth performance, serving as the major structural and signaling components of membranes, energy storage molecules, and steroid hormones. Bamboo, as wild giant pandas' exclusive diet, is the main determinant of giant pandas' lipidome, both as a direct source and through microbiota activity. Interestingly, the consumption of bamboo has attracted little attention from a lipidomic perspective. In the current study, we outline the lipidomic atlas of different parts of bamboo. By gas chromatography-mass spectrometry (GC-MS), we have been able to obtain the absolute quantification of 35 fatty acids pertaining to short chain fatty acids (8), medium chain fatty acids (6), long chain fatty acids (17), and very long chain fatty acids (4), while liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS/MS) allowed us to obtain the relative quantification of another 1638 lipids. Among the fatty acids quantified in absolute terms, eight showed significantly distinct concentrations among different bamboo parts. Subsequently, we investigated how the giant panda's serum and fecal lipidome adapt to the most important annual change in their diet, represented by the consumption of high amounts of bamboo shoots, typical of spring, the weight-gaining season. Five fatty acids were significantly altered in feces and two in serum, respectively, due to the different levels of bamboo shoot consumption. Furthermore, significant differences of the main bacteria strains were observed in feces between the two groups at the genus level, pertaining to , , and Correlations between giant panda fecal microbiome and lipidome were evaluated by Pearson correlation analysis. These findings suggest that a balanced diet, important for the overall lipidomic function and giant panda health, could be reached even in this remarkable case of a single food-based diet, by administering to the giant panda's combinations of different parts of bamboo, with specific lipidome profiles.
Topics: Animals; Chromatography, High Pressure Liquid; Fatty Acids; Feces; Gas Chromatography-Mass Spectrometry; Hormones; Lipidomics; Lipids; Ursidae; Vegetables
PubMed: 36232846
DOI: 10.3390/ijms231911544 -
Foods (Basel, Switzerland) Sep 2022-fermented red mold rice (RMR) has excellent physiological efficacy on lipid metabolism and liver function. This study investigated the ameliorative effects of...
-fermented red mold rice (RMR) has excellent physiological efficacy on lipid metabolism and liver function. This study investigated the ameliorative effects of monascuspiloin (MP) from RMR on alcoholic liver injury in mice, and further clarified its mechanism of action. Results showed that MP intervention obviously ameliorated lipid metabolism and liver function in mice with over-drinking. In addition, dietary MP intervention reduced liver MDA levels and increased liver CAT, SOD, and GSH levels, thus alleviating liver oxidative stress induced by excessive drinking. 16S rRNA amplicon sequencing showed that MP intervention was beneficial to ameliorate intestinal microbiota dysbiosis by elevating the proportion of norank_f_, , , , , etc., but decreasing the proportion of , norank_f_, _UCG-001, , norank_f_, unclassified_f_, etc. Additionally, correlation network analysis indicated that the key intestinal bacterial taxa intervened by MP were closely related to some biochemical parameters of lipid metabolism, liver function, and oxidative stress. Moreover, liver metabolomics analysis revealed that dietary MP supplementation significantly regulated the levels of 75 metabolites in the liver, which were involved in the synthesis and degradation of ketone bodies, taurine, and hypotaurine metabolism, and other metabolic pathways. Furthermore, dietary MP intervention regulated gene transcription and protein expression associated with hepatic lipid metabolism and oxidative stress. In short, these findings suggest that MP mitigates alcohol-induced liver injury by regulating the intestinal microbiome and liver metabolic pathway, and thus can serve as a functional component to prevent liver disease.
PubMed: 36230124
DOI: 10.3390/foods11193048 -
Microbiology Spectrum Dec 20225-Fluorouracil (5-FU), irinotecan (CPT-11), oxaliplatin (L-OHP), and calcium folinate (CF) are widely used chemotherapeutic drugs to treat colorectal cancer. However,...
Chemotherapeutic Drugs Induce Different Gut Microbiota Disorder Pattern and NOD/RIP2/NF-κB Signaling Pathway Activation That Lead to Different Degrees of Intestinal Injury.
5-Fluorouracil (5-FU), irinotecan (CPT-11), oxaliplatin (L-OHP), and calcium folinate (CF) are widely used chemotherapeutic drugs to treat colorectal cancer. However, chemotherapeutic use is often accompanied by intestinal inflammation and gut microbiota disorder. Changes in gut microbiota may destroy the intestinal barrier, which contributes to the severity of intestinal injury. However, intestinal injury and gut microbiota disorder have yet to be compared among 5-FU, CPT-11, L-OHP, and CF in detail, thereby limiting the development of targeted detoxification therapy after chemotherapy. In this study, a model of chemotherapy-induced intestinal injury in tumor-bearing mice was established by intraperitoneally injecting chemotherapeutic drugs at a clinically equivalent dose. 16S rRNA gene sequencing was used to detect gut microbiota. We found that 5-FU, CPT-11, and l-OHP caused intestinal injury, inflammatory cytokine (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α], interleukin-1β [IL-1β], and IL-6) secretion, and gut microbiota disorder. We established a complex but clear network between the pattern of changes in gut microbiota and degree of intestinal damage induced by different chemotherapeutic drugs. L-OHP caused the most severe damage in the intestine and disorder of the gut microbiota and showed a considerable overlap of the pattern of changes in microbiota with 5-FU and CPT-11. Analysis by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt v.1.0) showed that the microbiota disorder pattern induced by 5-FU, CPT-11, and L-OHP was related to the NOD-like signaling pathway. Therefore, we detected the protein expression of the NOD/RIP2/NF-κB signaling pathway and found that L-OHP most activated this pathway. Redundancy analysis/canonical correlation analysis (RDA/CCA) revealed that , , , , , , , Proteus, Escherichia , , , Streptococcus, and " Saccharimonas" were highly correlated with the NOD/RIP2/NF-κB signaling pathway and influenced by chemotherapeutic drugs. Chemotherapy-induced intestinal injury limits the clinical use of drugs. Intestinal injury involves multiple signaling pathways and gut microbiota disruption. Our results suggested that the degree of intestinal injury caused by different drugs of the first-line colorectal chemotherapy regimen is related to the pattern of changes in microbiota. The activation of the NOD/RIP2/NF-κB signaling pathway was also related to the pattern of changes in microbiota. l-OHP caused the most severe damage to the intestine and showed a considerable overlap of the pattern of changes in microbiota with 5-FU and CPT-11. Thirteen bacterial genera were related to different levels of intestinal injury and correlated with the NOD/RIP2/NF-κB pathway. Here, we established a network of different chemotherapeutic drugs, gut microbiota, and the NOD/RIP2/NF-κB signaling pathway. This study likely provided a new basis for further elucidating the mechanism and clinical treatment of intestinal injury caused by chemotherapy.
Topics: Animals; Mice; Antineoplastic Agents; Fluorouracil; Gastrointestinal Microbiome; Intestinal Diseases; Irinotecan; NF-kappa B; Oxaliplatin; Phylogeny; RNA, Ribosomal, 16S; Signal Transduction
PubMed: 36222691
DOI: 10.1128/spectrum.01677-22 -
Microorganisms Aug 2022Biofilm contamination in food production threatens food quality and safety, and causes bacterial infections. Study of food biofilms (BF) is of great importance. The...
Biofilm contamination in food production threatens food quality and safety, and causes bacterial infections. Study of food biofilms (BF) is of great importance. The taxonomic composition and structural organization of five foods BF taken in different workshops of a meat-processing plant (Moscow, RF) were studied. Samples were taken from the surface of technological equipment and premises. Metagenomic analysis showed both similarities in the presented microorganisms dominating in different samples, and unique families prevailing on certain objects were noted. The bacteria found belonged to 11 phyla (no archaea). The dominant ones were , , , and . The greatest diversity was in BFs taken from the cutting table of raw material. Biofilms' bacteria may be the cause of meat, fish and dairy products spoilage possible representatives include , , , , , , etc.). Opportunistic human and animal pathogens (possible representatives include , , , etc.) were also found. Electron-microscopic studies of BF thin sections revealed the following: (1) the diversity of cell morphotypes specific to multispecies BFs; (2) morphological similarity of cells in BFs from different samples, micro-colonial growth; (3) age heterogeneity of cells within the same microcolony (vegetative and autolyzed cells, resting forms); (4) heterogeneity of the polymer matrix chemical nature according to ruthenium red staining.
PubMed: 36014001
DOI: 10.3390/microorganisms10081583 -
BMC Genomics Aug 2022Vagococcus fluvialis is a species of lactic acid bacteria found both free-living in river and seawater and associated to hosts, such as marine sponges. This species has...
BACKGROUND
Vagococcus fluvialis is a species of lactic acid bacteria found both free-living in river and seawater and associated to hosts, such as marine sponges. This species has been greatly understudied, with no complete genome assembly available to date, which is essential for the characterisation of the mobilome.
RESULTS
We sequenced and assembled de novo the complete genome sequences of five V. fluvialis isolates recovered from marine sponges. Pangenome analysis of the V. fluvialis species (total of 17 genomes) showed a high intraspecific diversity, with 45.5% of orthologous genes found to be strain specific. Despite this diversity, analyses of gene functions clustered all V. fluvialis species together and separated them from other sequenced Vagococcus species. V. fluvialis strains from different habitats were highly similar in terms of functional diversity but the sponge-isolated strains were enriched in several functions related to the marine environment. Furthermore, sponge-isolated strains carried a significantly higher number of mobile genetic elements (MGEs) compared to previously sequenced V. fluvialis strains from other environments. Sponge-isolated strains carried up to 4 circular plasmids each, including a 48-kb conjugative plasmid. Three of the five strains carried an additional circular extrachromosomal sequence, assumed to be an excised prophage as it contained mainly viral genes and lacked plasmid replication genes. Insertion sequences (ISs) were up to five times more abundant in the genomes of sponge-isolated strains compared to the others, including several IS families found exclusively in these genomes.
CONCLUSIONS
Our findings highlight the dynamics and plasticity of the V. fluvialis genome. The abundance of mobile genetic elements in the genomes of sponge-isolated V. fluvialis strains suggests that the mobilome might be key to understanding the genomic signatures of symbiosis in bacteria.
Topics: Animals; Enterococcaceae; Interspersed Repetitive Sequences; Phylogeny; Porifera; Sequence Analysis, DNA
PubMed: 36008774
DOI: 10.1186/s12864-022-08842-9