-
Saudi Journal of Biological Sciences Apr 2023Diseases are quite common in fish farms because of changes in physico-chemical characteristics in the aquatic environment, and operational concerns, i.e., overstocking...
Diseases are quite common in fish farms because of changes in physico-chemical characteristics in the aquatic environment, and operational concerns, i.e., overstocking and feeding issues. In the present study, potential factors (water physico-chemical characteristics and heavy metal load) on the disease-causing state of the pathogenic bacteria and sp. were examined with machine learning techniques in a trout farm. Recording of physico-chemical characteristics of the water, fish sampling and bacteria identification were carried out at bimonthly intervals. A dataset was generated from the physico-chemical characteristics of the water and the occurrence of bacteria in the trout samples. The eXtreme Gradient Boosting (XGBoost) algorithm was used to determine the most important independent variables within the generated dataset. The most important seven features affecting bacteria occurrence were determined. The model creation process continued with these seven features. Three well-known machine learning techniques (Support Vector Machine, Logistic Regression and Naïve Bayes) were used to model the dataset. Consequently, all the three models have produced comparable results, and Support Vector Machine (93.3% accuracy) had the highest accuracy. Monitoring changes in the aquaculture environment and detecting situations causing significant losses through machine learning techniques have a great potential to support sustainable production.
PubMed: 37008282
DOI: 10.1016/j.sjbs.2023.103625 -
International Journal of Systematic and... Mar 2023The genus belongs to the family (order Lactobacillales) and is closely related to the genus . Currently, 19 species of the genus have been validly named. In this...
The genus belongs to the family (order Lactobacillales) and is closely related to the genus . Currently, 19 species of the genus have been validly named. In this study, we isolated strain G314F from the common green bottle fly collected in Germany. Sequencing of its almost-complete 16S rRNA gene revealed that the isolate belongs to the genus , being closely related to SS1994 with high sequence identity (99.50 %), followed by D7T301 (98.86 %), SS1995 (98.71 %), DSM 21459 (98.64 %), 2B-2 (98.64 %) and CD276 (98.64 %). Genome sequencing of strain G314F was performed by a combination of Illumina and Oxford Nanopore technology, yielding a circular genome with a size of 2 139 468 bp and an 11 kb plasmid. Average nucleotide identity and digital DNA-DNA hybridization values were calculated between G314F and its closest-related taxa, and found to be <91 % and <40 %, respectively, thus strongly supporting that strain G314F represents a novel species of the genus . Phylogenetic and core protein-based phylogenomic trees revealed that G314F was closely related to a group of three species, SS1994, D7T301 and DSM 21459. Comparatively, the genome of G314F is the smallest in the group of the four related species, and the biochemical pathway comparison using BlastKOALA revealed that G314F has lost some amino acid biosynthetic proteins; however, it has gained enzymes for carbohydrate metabolism. Phenotypically, G314F was consistent with other species of the genus including a negative catalase reaction and non-motility. Using the polyphasic approach, our data supports that the isolate represents a new species, for which we propose the name G314F (=DSM 112651= CCM 9164).
Topics: Fatty Acids; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Sequence Analysis, DNA; Bacterial Typing Techniques; Base Composition; Enterococcaceae; Gram-Positive Cocci; Nucleic Acid Hybridization
PubMed: 37000169
DOI: 10.1099/ijsem.0.005787 -
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 -
Fish & Shellfish Immunology May 2023In this study, the growth performance, health status and intestinal microbiota of juvenile Asian seabass, Lates calcarifer, were assessed after dietary administration of...
In this study, the growth performance, health status and intestinal microbiota of juvenile Asian seabass, Lates calcarifer, were assessed after dietary administration of a prebiotic product obtained from fermented Aspergillus orizae, Fermacto®. Asian seabass were fed three diets; control (without Aspergillus-meal prebiotic), 0.2% and 0.3% Aspergillus-meal prebiotic for 56 days. Fish were raised in freshwater with acceptable water quality. No significant differences were found in the growth performance and composition of dorsal fish muscle among all groups. Fish fed diets supplemented with 0.3% of Aspergillus-meal prebiotic had a significantly higher survival rate after being challenged with V. alginolyticus than fish fed with the control diet. Supplementation of the Aspergillus-meal prebiotic significantly improved immune responses by inducing higher respiratory burst, superoxide dismutase, phagocytic and lysozyme activity compared to the control group. In addition, prebiotic doses significantly induced an up-regulation of heat shock cognate 70 kDa protein (hsp70) in the liver compared to the control group. Signaling pathways were also affected with significantly higher gene expression of complement c-3 (c3), mechanistic target of rapamycin (mtor), and mammalian lethal with SEC13 protein 8 (mlst-8) in the liver of fish fed 0.3% Aspergillus prebiotic. The pro-inflammatory gene, tumor necrosis factor (tnf) and anti-inflammatory gene, transforming growth factor beta-1 (tfg-β1) were significantly higher in the head kidney of fish offered prebiotic diets. Fish receiving Aspergillus-meal prebiotic revealed significantly higher expression of Mx gene 24 h post nervous necrosis virus injection compared to the control. Additionally, the α-diversity of gut microbiota, including genus, Pielou's evenness, Shannon diversity index, and Margalef's species richness were significantly higher in fish fed 0.3% Aspergillus-meal prebiotic than the control group. The principal component analysis eigenvector plots showed that a high abundance of beneficial bacteria, such as Entercoccus faecium, Lactococcus lactis, Macrococcus caseolyticus and Vagococcus fluvialis, along with potentially pathogenic bacteria, such as Staphylococcus sciuri and L. garvieae subsp. garvieae were present in fish treated with Aspergillus-meal prebiotic. Although dietary Aspergillus-meal prebiotic did not improve the growth performance of Asian seabass, 0.3% of Aspergillus-meal prebiotic is recommended to elevate the immunological status of fish.
Topics: Animals; Prebiotics; Gastrointestinal Microbiome; Multilocus Sequence Typing; Diet; Perciformes; Fishes; Health Status; Animal Feed; Mammals
PubMed: 36935042
DOI: 10.1016/j.fsi.2023.108696 -
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 -
Insect Science Aug 2023The black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), is an insect commonly used for the bioconversion of various organic wastes. Not only can the BSF...
Improvement in bioconversion efficiency and reduction of ammonia emission by introduction of fruit fermentation broth in a black soldier fly larvae and kitchen waste conversion system.
The black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), is an insect commonly used for the bioconversion of various organic wastes. Not only can the BSF convert organic waste into macromolecular organic substances, such as insect proteins, but it can also lessen the pollution associated with these waste products by reducing ammonia emissions, for example. In this study, we measured the effects of adding fruit fermentation broth (Fer) and commercial lactic acid bacteria fermentation broth (Em) to kitchen waste (KW), as deodorizing auxiliary substances, on the growth performance of black soldier fly larvae (BSFL), the intestinal flora structure of BSFL, the ammonia emission from the KW substrate, and the microbial community structure of the KW substrate. We found that the addition of Fer or Em increased the body weight of BSFL after 6 d of culture, increasing the growth rate by 9.96% and 7.96%, respectively. The addition of Fer not only reduced the pH of the KW substrate but also increased the relative abundance of probiotics, such as Lactobacillus, Lysinibacillus, and Vagococcus, which inhibited the growth of ammonifiers such as Bacillus, Oligella, Paenalcaligenes, Paenibacillus, Pseudogracilibacillus, and Pseudomonas, resulting in the reduction of ammonia emission in the KW substrate. Moreover, the addition of Fer or Em significantly increased the relative abundances of Bacteroides, Campylobacter, Dysgonomonas, Enterococcus, and Ignatzschineria in the gut of BSFL and increased the species diversity and richness in the KW substrate. Our findings provide a novel way to improve the conversion rate of organic waste and reduce the environmental pollution caused by BSF.
Topics: Animals; Larva; Ammonia; Fruit; Fermentation; Diptera
PubMed: 36773298
DOI: 10.1111/1744-7917.13185 -
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 -
Journal of Applied Microbiology Feb 2023This study aims to assess the use of marine lactic acid bacteria (LAB) to reduce Vibrio parahaemolyticus levels during oyster depuration process.
AIMS
This study aims to assess the use of marine lactic acid bacteria (LAB) to reduce Vibrio parahaemolyticus levels during oyster depuration process.
METHODS AND RESULTS
The inhibitory effect of 30 marine LAB strains against V. parahaemolyticus strains was evaluated by in vitro assays. A total of three positive strains (Latilactobacillus sakei SF1583, Lactococcus lactis SF1945, and Vagococcus fluvialis CD264) were selected for V. parahaemolyticus levels reduction during oyster depuration. Pacific oysters Crassostrea gigas were artificially and independently contaminated by four GFP-labelled V. parahaemolyticus strains (IFVp201, IFVp69, IFVp195, and LMG2850T) at 105 CFU ml-1 and then exposed by balneation to 106 CFU ml-1 of each LAB strains during 24 h, at 19°C. Quantification of V. parahaemolyticus in haemolymph by flow cytometry revealed variations in natural depuration of the different V. parahaemolyticus strains alone. Furthermore, the addition of LABs improved up to 1-log bacteria ml-1 the reduction of IFVp201 concentration in comparison to the control condition.
CONCLUSIONS
Although further optimizations of procedure are needed, addition of marine LABs during oyster depuration may be an interesting strategy to reduce V. parahaemolyticus levels in Crassostrea gigas.
Topics: Animals; Crassostrea; Vibrio parahaemolyticus; Lactobacillales; Food Contamination; Colony Count, Microbial; Temperature; Ostreidae
PubMed: 36626775
DOI: 10.1093/jambio/lxac081 -
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