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Frontiers in Microbiology 2023species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, spp. can be...
INTRODUCTION
species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, spp. can be opportunistic pathogens in both veterinary and human clinical settings. This study aimed to provide insight into the evolution, population structure, and functional potential of the genus, with an emphasis on antimicrobial resistance (AMR) and virulence potential.
METHODS
All high-quality, publicly available genomes ( = 104, accessed 27 August 2022), plus six South African genomes sequenced here (two strains from bovine clinical mastitis cases and four strains from beef products), underwent taxonomic assignment (using four different approaches), AMR determinant detection (via AMRFinderPlus), and virulence factor detection (using DIAMOND and the core Virulence Factor Database).
RESULTS
Overall, the 110 genomes were of animal commensal, veterinary clinical, food-associated (including food spoilage), and environmental origins; five genomes (4.5%) originated from human clinical cases. Notably, none of the taxonomic assignment methods produced identical results, highlighting the potential for species misidentifications. The most common predicted antimicrobial classes associated with AMR determinants identified across included macrolides, beta-lactams, and aminoglycosides ( = 81, 61, and 44 of 110 genomes; 73.6, 55.5, and 40.0%, respectively). Genes showing homology to exoenzyme aureolysin were detected across multiple species (using 90% coverage, = 40 and 77 genomes harboring aureolysin-like genes at 60 and 40% amino acid [AA] identity, respectively). Panton-Valentine leucocidin toxin-associated and homologs were identified in eight genomes (≥40% AA identity, >85% coverage). Using a method that delineates populations using recent gene flow (PopCOGenT), two species ( and ) were composed of multiple within-species populations. Notably, was partitioned into two populations, which differed in functional potential (e.g., one harbored beta-lactamase family, type II toxin-antitoxin system, and stress response proteins, while the other possessed a Type VII secretion system; PopCOGenT < 0.05).
DISCUSSION
Overall, this study leverages all publicly available genomes in addition to newly sequenced genomes from South Africa to identify genomic elements associated with AMR or virulence potential, which can be queried in future experiments.
PubMed: 37547688
DOI: 10.3389/fmicb.2023.1181376 -
Journal of Dairy Science Dec 2023The possible contribution of brine-derived microflora to the sensory attributes of cheese is still a rather unexplored field. In this study, 365 bacteria and 105 yeast...
The possible contribution of brine-derived microflora to the sensory attributes of cheese is still a rather unexplored field. In this study, 365 bacteria and 105 yeast strains isolated from 11 cheese brines were qualitatively tested for proteolytic and lipolytic activities, and positive strains were identified by sequencing. Among bacteria, Staphylococcus equorum was the most frequent, followed by Macrococcus caseolyticus and Corynebacterium flavescens. As for yeasts, Debaryomyces hansenii, Clavispora lusitaniae, and Torulaspora delbrueckii were most frequently identified. A total of 38% of bacteria and 59% of yeasts showed at least 1 of the metabolic activities tested, with lipolytic activity being the most widespread (81% of bacteria and 95% of yeasts). Subsequently 15 strains of bacteria and 10 yeasts were inoculated in a curd-based medium and assessed via headspace-solid phase microextraction coupled with gas chromatography-mass spectrometry to determine their volatilome. After a 30-d incubation at 12°C, most strains showed a viability increase of about 2 log cfu/mL, suggesting good adaptability to the cheese environment. A total of 26 compounds were detected in the headspace, carbonyl compounds and alcohols being the major contributors to the volatile profile of the curd-based medium. Multivariate analysis was carried out to elucidate the overall differences in volatiles produced by selected strains. Principal component analysis and hierarchical clustering analysis demonstrated that the brine-related microorganisms were separated into 3 different groups, suggesting their different abilities to produce volatile compounds. Some of the selected strains have been shown to have interesting aromatic potential and to possibly contribute to the sensory properties of cheese.
Topics: Animals; Salts; Yeasts; Bacteria; Gas Chromatography-Mass Spectrometry; Cheese
PubMed: 37641243
DOI: 10.3168/jds.2022-23051 -
Foods (Basel, Switzerland) Oct 2023Aquaculture is becoming a strategic sector for many national economies to supply the increasing demand for fish from consumers. Fish culture conditions and processing...
Aquaculture is becoming a strategic sector for many national economies to supply the increasing demand for fish from consumers. Fish culture conditions and processing operations can lead to an increase in microbial contamination of farmed fish that may shorten the shelf-life of fish products and byproducts, and ready-to-eat fishery products. The objective of this study was to evaluate the hygienic-sanitary status of water, environment, and processing of fresh-farmed rainbow trout () fillets produced in a local fish farm in Andalusia, Spain. To achieve this, a longitudinal study was carried out by collecting environmental (air and food-contact surfaces), water from fish ponds, and rainbow trout samples. Thereby, seven sampling visits were performed between February 2021 and July 2022, where foodborne pathogens and spoilage microorganisms, together with physicochemical parameters, were analysed in the collected samples. Further, microbial identification of microbiota was achieved through a culture-dependent technique using blast analysis of 16S RNA gene sequencing. The results showed that and were not detected in the analysed samples. Regarding the hygienic-sanitary status of the fish farm, the slaughtering bath, the eviscerating machine and the outlet water from fish ponds presented the highest counts of coliforms, , and Aerobic Mesophilic Bacteria. and sulphite-reducing were identified in the conveyor belts, fish flesh, and viscera. The 16S RNA identification confirmed the presence of viable spoilage bacteria such as , , , , , , , , and . Three of these genera (, , and ) were present in all types of samples analysed. The results evidenced potential transmission of microbial contamination from contaminated packaging belts and boxes, evisceration and filleting machines to flesh and viscera samples, thus the establishment of control measures should be implemented in fish farm facilities to extend the shelf-life of farmed fishery products.
PubMed: 37893611
DOI: 10.3390/foods12203718 -
Applied Microbiology and Biotechnology Mar 2024Host and tissue-specificity of endophytes are important attributes that limit the endophyte application on multiple crops. Therefore, understanding the endophytic...
Host and tissue-specificity of endophytes are important attributes that limit the endophyte application on multiple crops. Therefore, understanding the endophytic composition of the targeted crop is essential, especially for the dioecious plants where the male and female plants are different. Here, efforts were made to understand the endophytic bacterial composition of the dioecious Siraitia grosvenorii plant using 16S rRNA amplicon sequencing. The present study revealed the association of distinct endophytic bacterial communities with different parts of male and female plants. Roots of male and female plants had a higher bacterial diversity than other parts of plants, and the roots of male plants had more bacterial diversity than the roots of female plants. Endophytes belonging to the phylum Proteobacteria were abundant in all parts of male and female plants except male stems and fruit pulp, where the Firmicutes were most abundant. Class Gammaproteobacteria predominated in both male and female plants, with the genus Acinetobacter as the most dominant and part of the core microbiome of the plant (present in all parts of both, male and female plants). The presence of distinct taxa specific to male and female plants was also identified. Macrococcus, Facklamia, and Propionibacterium were the distinct genera found only in fruit pulp, the edible part of S. grosvenorii. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite (especially mogroside) biosynthesis in the associated endophytic community with predominance in roots. The present study revealed bacterial endophytic communities of male and female S. grosvenorii plants that can be further explored for monk fruit cultivation, mogroside production, and early-stage identification of male and female plants. KEY POINTS: • Male and female Siraitia grosvenorii plants had distinct endophytic communities • The diversity of endophytic communities was specific to different parts of plants • S. grosvenorii-associated endophytes may be valuable for mogroside biosynthesis and monk fruit cultivation.
Topics: RNA, Ribosomal, 16S; Microbiota; Bacteria; Firmicutes; Endophytes; Crops, Agricultural
PubMed: 38427084
DOI: 10.1007/s00253-024-13076-8 -
Frontiers in Physiology 2024To investigate the impact of the effect of high temperature stimulation on larvae after a certain period of time, five experimental groups were established at different...
To investigate the impact of the effect of high temperature stimulation on larvae after a certain period of time, five experimental groups were established at different temperatures. Then, the under high temperature stress was fed at 30°C for 70 days. After that, the growth index of the was counted and analyzed. In terms of growth index, high temperature stress had significant effects on FCR, FBW, WGR, and SGR of ( 0.05). The SR increased after being stimulated by temperature ( 0.1). The study revealed that liver cells of were harmed by elevated temperatures of 36°C and 38°C. In the experimental group, the activities of digestive enzymes changed in the same trend, reaching the highest point in the 32°C group and then decreasing, and the AMS activity in the 38°C group was significantly different from that in the 30°C group ( < 0.05). The activities of antioxidase in liver reached the highest at 34°C, which was significantly different from those at 30°C ( < 0.05). In addition, the expression levels of , , , and other genes increased in the experimental group, reaching the highest point at 34°C, and the expression level of the gene reached the highest point at 32°C, which was significantly different from that at 30°C ( < 0.05). However, the expression level of the gene decreased in the experimental group and reached its lowest point at 34°C ( < 0.05). The expression level of the gene increased with the highest temperature stimulus and reached its highest point at 38°C ( < 0.05). In the α diversity index of intestinal microorganisms in the experimental group, the observed species, Shannon, and Chao1 indexes in the 34°C group were the highest ( < 0.05), and β diversity analysis revealed that the intestinal microbial community in the experimental group was separated after high temperature stimulation. At the phylum level, the three dominant flora are , , and . and abundance increased at the genus level, but and abundance decreased. To sum up, appropriate high-temperature stress can enhance the immunity and adaptability of . These results show that the high temperature stimulation of 32°C-34°C is beneficial to the industrial culture of .
PubMed: 38720786
DOI: 10.3389/fphys.2024.1397818 -
Biotechnologia 2024The ever-increasing demand for wildlife-derived raw or processed meat commonly known as bushmeat, has been identified as one of the critical factors driving the...
The ever-increasing demand for wildlife-derived raw or processed meat commonly known as bushmeat, has been identified as one of the critical factors driving the emergence of infectious diseases. This study focused on examining the bacterial community composition of smoked and fermented bushmeats, specifically grasscutter, rat, rabbit, and mona monkey. The analysis involved exploring 16Sr RNA amplicon sequences isolated from bushmeat using QIIME2. Microbiome profiles and their correlation with proximate components (PLS regression) were computed in STAMP and XLSTAT, respectively. Results indicate the predominance of (70.9%), (18.58%), and (9.12%) in bushmeat samples at the phylum level. , , , and constituted the core microbiomes in bushmeat samples, ranked in descending order. Notably, significant differences were observed between the bacterial communities of bushmeat obtained from omnivores and herbivores (rat and mona monkey, and grasscutter and mona monkey), as well as those with similar feeding habits (rat and monkey, and grasscutter and rabbit) at the family and genus levels. Each type of bushmeat possessed unique microbial diversity, with some proximate components such as fat in rat samples correlating with , while proteins in Mona monkey correlated with and , respectively. The study underscores public health concerns and highlights probiotic benefits, as bushmeat samples contained both pathogenic and beneficial bacteria. Therefore, future research efforts could focus on improving bushmeat quality.
PubMed: 38633890
DOI: 10.5114/bta.2024.135637 -
Foods (Basel, Switzerland) May 2024Dry-aged beef has been long favored by people due to its unique flavor and taste. However, the inner relationship between its overall quality formation and microbial...
Dry-aged beef has been long favored by people due to its unique flavor and taste. However, the inner relationship between its overall quality formation and microbial changes during dry aging has not yet received much attention and research. To deeply reveal the forming mechanism of the unique flavor and taste of dry-aged beef, correlations between its three main quality indicators, i.e., texture, free amino acids (FAAs), volatile flavor compounds (VFCs), and microbial succession were analyzed in this study. The results showed that spp. and spp. were key strains that influenced the total quality of dry-aged beef and strongly correlated with chewiness, hardness, and sweet FAAs (Ala), providing beef with unique palatability and taste. Additionally, among VFCs, spp. and spp. showed a strong correlation with octanal and heptanal, and meanwhile, those highly correlated with nonanal, pentanol, and oct-1-en-3-ol were spp., spp., and spp., respectively, providing beef with a unique flavor. spp. was proposed to be the dominant genus for dry-aged beef. This study provides valuable reference for the understanding of the role of microorganisms involved in dry aging.
PubMed: 38790852
DOI: 10.3390/foods13101552 -
Foods (Basel, Switzerland) Oct 2023In this study, we determined and identified the bacterial diversity of different types of artisanal and industrially produced cheese. The antibiotic (erythromycin,...
In this study, we determined and identified the bacterial diversity of different types of artisanal and industrially produced cheese. The antibiotic (erythromycin, chloramphenicol, kanamycin, ampicillin, clindamycin, streptomycin, tetracycline, and gentamicin) and biocide (peracetic acid, sodium hypochlorite, and benzalkonium chloride) resistance of clinically relevant bacteria was determined as follows: , , sp., , , , , , , , sp., , , , , and Also, the effect of the sub-inhibitory concentration of three biocides on antibiotic resistance was determined. The microbiota of evaluated dairy products comprise diverse and heterogeneous groups of bacteria with respect to antibiotic and disinfectant tolerance. The results indicated that resistance was common in the case of ampicillin, chloramphenicol, erythromycin, and streptomycin. sp. SCSSZT2/3, SRGT/1, SAT/1, MTT/5, and SIJ/2 showed resistance to most antibiotics. The tested bacteria showed sensitivity to peracetic acid and a different level of tolerance to benzalkonium chloride and sodium hypochlorite. The inhibition zone diameter of antibiotics against SZT/2, JS11, CSKO2, and GRT/10 was affected only by the sub-inhibitory concentration of peracetic acid.
PubMed: 37959056
DOI: 10.3390/foods12213937 -
Ecotoxicology and Environmental Safety Jan 2024Thiram, a typical fungicide pesticide, is widely used in agricultural production. The presence of thiram residues is not only due to over-utilization, but is also...
Thiram, a typical fungicide pesticide, is widely used in agricultural production. The presence of thiram residues is not only due to over-utilization, but is also primarily attributed to long-term accumulation. However, there is a paucity of information regarding the impact of prolonged utilization of thiram at low doses on the gut microbiota, particularly with respect to gut fungi. Our objective is to explore the effect of thiram on broilers from the perspective of gut microbiota, which includes both bacteria and fungi. We developed a long-term low-dose thiram model to simulate thiram residue and employed 16 S rRNA and ITS gene sequencing to investigate the diversity and profile of gut microbiota between group CC (normal diet) and TC (normal diet supplemented with 5 mg/kg thiram). The results revealed that low doses of thiram had a detrimental effect on broiler's growth performance, resulting in an approximate reduction of 669.33 g in their final body weight at day 45. Our findings indicated that low-dose thiram had a negative impact on the gut bacterial composition, leading to a notable reduction in the abundance of Merdibacter, Paenibacillus, Macrococcus, Fournierella, and Anaeroplasma (p < 0.05) compared to the CC group. Conversely, the relative level of Myroides was significantly increased (p < 0.05) in response to thiram exposure. In gut fungi, thiram significantly enhanced the diversity and richness of gut fungal populations (p < 0.05), as evidenced by the notable increase in alpha indices, i.e. ACE (CC: 346.49 ± 117.27 vs TC: 787.27 ± 379.14, p < 0.05), Chao 1 (CC: 317.63 ± 69.13 vs TC: 504.85 ± 104.50, p < 0.05), Shannon (CC: 1.28 ± 1.19 vs TC: 5.39 ± 2.66, p < 0.05), Simpson (CC: 0.21 ± 0.21 vs TC: 0.78 ± 0.34, p < 0.05). Furthermore, the abundance of Ascomycota, Kickxellomycota, and Glomeromycota were significantly increased (p < 0.05) by exposure to thiram, conversely, the level of Basidiomycota was decreased (p < 0.05) in the TC group compared to the CC group. Overall, this study demonstrated that low doses of thiram induced significant changes in the composition and abundance of gut microbiota in broilers, with more pronounced changes observed in the gut fungal community as compared to the gut bacterial community. Importantly, our findings further emphasize the potential risks associated with low dose thiram exposure and have revealed a novel discovery indicating that significant alterations in gut fungi may serve as the crucial factor contributing to the detrimental effects exerted by thiram residues.
Topics: Animals; Thiram; Chickens; Gastrointestinal Microbiome; RNA, Ribosomal, 16S; Fungicides, Industrial; Bacteria
PubMed: 38157796
DOI: 10.1016/j.ecoenv.2023.115879 -
Frontiers in Microbiology 2023Spontaneous fermentation of raw cow milk without backslopping is in practice worldwide as part of the traditional food culture, including "" preparation in earthen pots...
INTRODUCTION
Spontaneous fermentation of raw cow milk without backslopping is in practice worldwide as part of the traditional food culture, including "" preparation in earthen pots in Northeast India, "" of Niger and "" of Benin prepared in calabash vessels in West Africa. Very few reports are available about the differences in bacterial communities that evolved during the spontaneous mesophilic fermentation of cow milk in diverse geographical regions.
METHODS
In this study, we used high throughput amplicon sequencing of bacterial 16S rRNA gene to investigate 44 samples of naturally fermented homemade milk products and compared the bacterial community structure of these foods, which are widely consumed in Northeast India and Western Africa.
RESULTS AND DISCUSSION
The spontaneous milk fermentation shared the lactic acid bacteria, mainly belonging to and in these two geographically isolated regions. Indian samples showed a high bacterial diversity with the predominance of and , whereas was abundant in the West African samples. However, the cheese of Benin, prepared by curdling the milk with proteolytic leaf extract of followed by natural fermentation, contained spp.) as the dominant bacteria. Our analysis also detected several potential pathogens, like an emerging infectious foodborne pathogen in samples, an uncultured bacterium of in and samples, and spp. in the samples of Northeast India. These findings will allow us to develop strategies to address the safety issues related to spontaneous milk fermentation and implement technological interventions for controlled milk fermentation by designing starter culture consortiums for the sustainable production of uniform quality products with desirable functional and organoleptic properties.
PubMed: 37886068
DOI: 10.3389/fmicb.2023.1166518