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Heliyon May 2024Investigating oat tissue microflora during its different developmental stages is necessary for understanding its growth and anti-disease mechanism. In this study, 16S...
Investigating oat tissue microflora during its different developmental stages is necessary for understanding its growth and anti-disease mechanism. In this study, 16S rDNA and ITS (Internally Transcribed Spacer) high-throughput sequencing technology were used to explore the microflora diversity of oat tissue. Twenty-seven samples of leaves, stems, and roots from three developmental stages, namely the seedling stage (SS), jointing stage (JS), and maturity stage (MS), underwent sequencing analysis. The analysis showed that 6480 operational taxonomic units (OTUs) were identified in the examined samples, of which 1698 were fungal and 4782 were bacterial. Furthermore, 126 OTUs were shared by fungi, mainly , , and at the phylum level, and 39 OTUs were shared by bacteria, mainly and at the phylum level. The microbial diversity of oat tissue in the three developmental stages showed differences, and the α-diversity of the bacteria and β-diversity of the bacteria and fungi in the roots were higher than those of the stems and leaves. Among the bacteria species, , and were predominant in the leaves, MND1 was predominant in the roots, and was predominant in the stems. Moreover, maintained a stable state at all growth stages. In the fungal species, was dominant in the leaves, was dominant in the roots, and was dominant in the stems. All species with a high abundance were related to the growth process of oats and antagonistic bacteria. Furthermore, connection modules were denser in bacterial than in fungal populations. The samples were treated with superoxide dismutase and peroxidase. There were 42 strains associated with SOD (Superoxide dismutase), 60 strains associated with POD (Peroxidase), and 38 strains in total, which much higher than fungi. The network analysis showed that bacteria might have more dense connection modules than fungi, The number of bacterial connections to enzymes were much higher than that of fungi. Furthermore, these results provide a basis for further mechanistic research.
PubMed: 38711667
DOI: 10.1016/j.heliyon.2024.e30276 -
Microbiome Apr 2024Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal...
The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits.
BACKGROUND
Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.
RESULTS
Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.
CONCLUSION
Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.
Topics: Cheese; Food Microbiology; Microbiota; Gene Transfer, Horizontal; Metagenome; Drug Resistance, Microbial
PubMed: 38678226
DOI: 10.1186/s40168-024-01790-4 -
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 -
The Journal of Antimicrobial... May 2024Corynebacterium (C.) sp. 22KM0430 related to C. oculi and isolated from a dog exhibited resistance to tetracycline, and its WGS analysis revealed a putative resistance...
BACKGROUND
Corynebacterium (C.) sp. 22KM0430 related to C. oculi and isolated from a dog exhibited resistance to tetracycline, and its WGS analysis revealed a putative resistance gene on a 35 562-bp plasmid also harbouring the MLSB resistance gene erm(X).
OBJECTIVES
To characterize the novel tetracycline resistance gene tet(65) and demonstrate its functionality by expression in C. glutamicum and Escherichia coli and plasmid curing of the host strain.
METHODS
tet(65) was cloned with and without its repressor tetR(65) and expressed in C. glutamicum DSM20300 and E. coli DH5α. Plasmid was cured by non-selective passages. Minimal inhibitory concentrations (MICs) of tetracyclines were determined according to CLSI guidelines. Association of tet(65) with efflux was shown by the addition of reserpine to MIC assays. Phylogenetic position and transmembrane structure of Tet(65) were analysed using MEGA11 and DeepTMHMM.
RESULTS
Tet(65) shows 73% amino acid identity with the closest related Tet(Z), contains 12 transmembrane domains and is structurally related to the Major Facilitator Superfamily. The tetracycline MICs decreased in the plasmid-cured strain and increased when tet(65) was expressed in C. glutamicum and in E. coli. The MICs of tetracycline decreased in the presence of reserpine indicating that tet(65) functions as an efflux pump. A GenBank search also identified tet(65) in C. diphtheriae and Brevibacterium (B.) casei and B. luteolum.
CONCLUSIONS
A novel tetracycline efflux gene tet(65) was identified in a C. oculi related species and was also present in the human pathogen C. diphtheriae and in Brevibacterium species indicating broader potential for dissemination.
Topics: Plasmids; Tetracycline Resistance; Microbial Sensitivity Tests; Anti-Bacterial Agents; Escherichia coli; Corynebacterium; Animals; Drug Resistance, Multiple, Bacterial; Phylogeny; Dogs; Tetracycline; Cloning, Molecular; Corynebacterium Infections; Dog Diseases
PubMed: 38497972
DOI: 10.1093/jac/dkae066 -
Journal of Dairy Science Mar 2024To evaluate the sodium chloride content effect on microbiological, biochemical, physicochemical and sensorial characteristics, Munster cheeses were prepared from...
To evaluate the sodium chloride content effect on microbiological, biochemical, physicochemical and sensorial characteristics, Munster cheeses were prepared from pasteurized milk seeded with 3 yeasts (Kluyveromyces marxianus, Debaryomyces hansenii, Geotrichum candidum) and 5 ripening bacteria (Arthrobacter arilaitensis, Brevibacterium aurantiacum, Corynebacterium casei, Hafnia alvei, and Staphylococcus equorum). Experiments were performed under 1.0%, 1.7% and 2.4% NaCl levels in cheese in triplicate. Ripening (d2 - d27) was carried under 12°C and 96% RH. These kinetics were both reproducible and repeatable at 99% confidence level. For each microbial, biochemical and physicochemical parameter, 2 kinetic descriptors (maximal or minimal rate and its occurrence time) were defined. On d2 the physicochemical variables (water activity, dry matter, water content) were strongly dependent on the salting level. From d2 to d27 K. lactis was insensitive to salt while D. hansenii was stimulated. G. candidum growth appeared very sensitive to salt in cheese: at 1.0% NaCl G. candidum exhibited overgrowth, negatively impacting rind appearance, underrind consistency and thickness and off-flavor flaws. Salt concentration of 2.4% induced death of G. candidum. Four bacteria (A. arilaitensis, B. aurantiacum, C. casei, and H. alvei) were moderately sensitive to salt while S. equorum was insensitive to it. Salt level in cheese had a significant effect on carbon substrate consumption rates. Lactate consumption rate in 1.0% salted cheeses was approximately twice higher than under 2.4% NaCl. Data analysis of microorganism, biochemical, and physicochemical kinetics and sensory analysis showed that the best salt level in Munster-type cheeses to achieve an optimum balance between cheese characteristics, sensory qualities and marketability was 1.7% NaCl.
PubMed: 38490552
DOI: 10.3168/jds.2024-24307 -
Scientific Reports Feb 2024Traditional alcoholic beverages have played a significant role in the cultural, social, and culinary fabric of societies worldwide for centuries. Studying the microbial...
Traditional alcoholic beverages have played a significant role in the cultural, social, and culinary fabric of societies worldwide for centuries. Studying the microbial community structure and their metabolic potential in such beverages is necessary to define product quality, safety, and consistency, as well as to explore associated biotechnological applications. In the present investigation, Illumina-based (MiSeq system) whole-genome shotgun sequencing was utilized to characterize the microbial diversity and conduct predictive gene function analysis of keem, a starter culture employed by the Jaunsari tribal community in India for producing various traditional alcoholic beverages. A total of 8,665,213 sequences, with an average base length of 151 bps, were analyzed using MG-RAST. The analysis revealed the dominance of bacteria (95.81%), followed by eukaryotes (4.11%), archaea (0.05%), and viruses (0.03%). At the phylum level, Actinobacteria (81.18%) was the most abundant, followed by Firmicutes (10.56%), Proteobacteria (4.00%), and Ascomycota (3.02%). The most predominant genera were Saccharopolyspora (36.31%), followed by Brevibacterium (15.49%), Streptomyces (9.52%), Staphylococcus (8.75%), Bacillus (4.59%), and Brachybacterium (3.42%). At the species level, the bacterial, fungal, and viral populations of the keem sample could be categorized into 3347, 57, and 106 species, respectively. Various functional attributes to the sequenced data were assigned using Cluster of Orthologous Groups (COG), Non-supervised Orthologous Groups (NOG), subsystem, and KEGG Orthology (KO) annotations. The most prevalent metabolic pathways included carbohydrate, lipid, and amino acid metabolism, as well as the biosynthesis of glycans, secondary metabolites, and xenobiotic biodegradation. Given the rich microbial diversity and its associated metabolic potential, investigating the transition of keem from a traditional starter culture to an industrial one presents a compelling avenue for future research.
Topics: Microbiota; Bacteria; Firmicutes; Archaea; Metabolic Networks and Pathways
PubMed: 38369518
DOI: 10.1038/s41598-024-53350-3 -
Frontiers in Microbiology 2024Proso millet, a high-quality fermentation material used for Chinese yellow wine production, can produce special flavored substances; however, its role in improving the...
INTRODUCTION
Proso millet, a high-quality fermentation material used for Chinese yellow wine production, can produce special flavored substances; however, its role in improving the flavor and altering microbial communities of light-flavored Baijiu during fermentation remain unknown. Thus, we aimed to investigate the effect of proso millet on improving the flavor of light-flavored Baijiu and altering microbial communities during different fermentation stages.
METHODS
The dynamic changes in the microbial communities and flavor of proso millet (50%) + sorghum (50%) mixed fermentation samples were analyzed through intermittent sampling on days 7, 14, 21, and 28 of the fermentation process. Microbial high-throughput sequencing and the analysis of flavor characteristics were conducted through 16S DNA/ ITS amplicon sequencing and gas chromatography (multi-capillary column)-ion mobility spectrometry, respectively.
RESULTS
Proso millet significantly changed the core flavor compound composition of traditional light-flavored Baijiu from ethyl acetate, ethyl hexanoate, ethyl hexanoate dimer, ethyl butanoate, ethyl lactate, and butyl acetate to oct-2-ene, 2-butanol, propyl propanoate, 2-pentenal, and 4-methylpentanal. The amplicon sequencing analysis revealed that the alpha diversity parameters of bacterial and fungal communities, including the Chao1, Pielou_e, Shannon, and Simpson indices, for proso millet-sorghum mixed fermentation samples were significantly higher than those for sorghum fermentation samples ( < 0.05). Of the 40 most significant microbial genera in two treatments, proso millet significantly increased the abundance of 12 bacterial and 18 fungal genera. Among the 40 most significant bacterial and fungal species, 23 bacterial species belonged to the genus, whereas the 30 primary fungal species belonged to 28 different genera. The analysis of the relationship between microbial changes and the main flavor compounds of light-flavored Baijiu showed that bacteria from the , , , , , , , , , , , genera and fungi from the , , , , , , and genera significantly inhibited the synthesis of ethyl hexanoate, ethyl butanoate, ethyl lactate ethyl lactate, and butyl acetate but increased the synthesis of ethyl acetate ( < 0.05). Moreover, these microbes exhibited a significantly greater abundance in proso millet-sorghum mixed fermentation samples than in sorghum samples. The synthesis of special flavored compounds in proso millet Baijiu was significantly positively correlated with the presence of fungi from the , , , , and genera but negative correlated with the presence of bacteria from the , , , , , and genera. Regarding ethanol content, the low alcohol content of Fenjiu may be due to the significantly high abundance of fungi from the genus and bacteria from the , , , and genera during fermentation. In summary, proso millet significantly altered the flavor of light-flavored Baijiu by inducing the formation of a special microbial community; however, it did not increase alcohol concentration.
DISCUSSION
This study lays the foundation for future research on Baijiu fermentation. Additionally, the study findings may help improve the production efficiency and elevate the quality and flavor of the final product.
PubMed: 38318340
DOI: 10.3389/fmicb.2024.1333466 -
Microorganisms Jan 2024Washing machines are one of the tools that bring great convenience to people's daily lives. However, washing machines that have been used for a long time often develop...
Washing machines are one of the tools that bring great convenience to people's daily lives. However, washing machines that have been used for a long time often develop issues such as odor and mold, which can pose health hazards to consumers. There exists a conspicuous gap in our understanding of the microorganisms that inhabit the inner workings of washing machines. In this study, samples were collected from 22 washing machines in Shanghai, China, including both water eluted from different parts of washing machines and biofilms. Quantitative qualitative analysis was performed using fluorescence PCR quantification, and microbial communities were characterized by high-throughput sequencing (HTS). This showed that the microbial communities in all samples were predominantly composed of bacteria. HTS results showed that in the eluted water samples, the bacteria mainly included , , , and . Conversely, in the biofilm samples, and were the predominant bacterial microorganisms. Correlation analysis results revealed that microbial colonies in washing machines were significantly correlated with years of use and the type of detergent used to clean the washing machine. As numerous pathogenic microorganisms can be observed in the results, effective preventive measures and future research are essential to mitigate these health problems and ensure the continued safe use of these household appliances.
PubMed: 38257987
DOI: 10.3390/microorganisms12010160 -
Poultry Science Feb 2024The threat of antimicrobial resistance (AMR) is on the rise globally, especially with the development of animal husbandry and the increased demand for antibiotics....
The threat of antimicrobial resistance (AMR) is on the rise globally, especially with the development of animal husbandry and the increased demand for antibiotics. Livestock and poultry farms, as key sites for prevalence of antibiotic-resistant bacteria (ARB), can spread antimicrobial resistance genes (ARGs) through microbial aerosols and affect public health. In this study, total suspended particulate matter (TSP) and airborne culturable microorganisms were collected from duck houses in Tai'an, Shandong Province, and the bacterial communities and airborne ARGs were analyzed using metagenomics and PCR methods. The results showed that the bacterial communities in the air of duck houses were mainly Actinobacteria, Firmicutes, Proteobactria, Chlamydia, and Bcateroidetes at the phylum level. At the genus level, the air was dominated by Corynebacterium, Jeotgalicoccus, Staphylococcus, Brevibacterium, and Megacoccus, and contained some pathogenic bacteria such as Staphylococcus aureus, Corynebacterium diphtheriae, Klebsiella oxytoca, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were also potential hosts for ARGs. The airborne ARGs were mainly macrolides (10.97%), penicillins (10.73%), cephalosporins (8.91%), streptozotocin (8.91%), and aminoglycosides (8.02%). PCR detected 27 ARGs in airborne culturable microorganisms, and comparative analysis between PCR and the metagenomic data revealed that a total of 9 ARGs were found to the same, including macrolides ErmA, ErmF, tetracyclines tetG, tetX, methicarbamazepines dfrA12, dfrA15, aminoglycosides APH3-VI, ANT2-Ⅰ, and sulfonamides sul2. Moreover, inhalation exposure modeling showed that the workers in duck houses inhaled higher concentrations of ARB, human pathogenic bacteria (HPB) and human pathogenic antibiotic-resistant bacteria (HPARB) than hospital workers. These results provide new insights into airborne microorganisms and ARGs in animal farms and lay the foundation for further study.
Topics: Animals; Aminoglycosides; Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Anti-Bacterial Agents; Bacteria; Chickens; Drug Resistance, Bacterial; Ducks; Genes, Bacterial; Macrolides; Metagenome; Polymerase Chain Reaction
PubMed: 38157791
DOI: 10.1016/j.psj.2023.103365 -
Plant Direct Dec 2023Tobacco wildfire disease caused by pv. is one of the most destructive foliar bacterial diseases occurring worldwide. However, the effect of wildfire disease on cigar...
Tobacco wildfire disease caused by pv. is one of the most destructive foliar bacterial diseases occurring worldwide. However, the effect of wildfire disease on cigar tobacco leaves has not been clarified in detail. In this study, the differences in microbiota and chemical factors between wildfire disease-infected leaves and healthy leaves were characterized using high-throughput Illumina sequencing and a continuous-flow analytical system, respectively. The results demonstrated significant alterations in the structure of the phyllosphere microbial community in response to wildfire disease, and the infection of pv. led to a decrease in bacterial richness and diversity. Furthermore, the content of nicotine, protein, total nitrogen, and Cl in diseased leaves significantly increased by 47.86%, 17.46%, 20.08%, and 72.77% in comparison to healthy leaves, while the levels of total sugar and reducing sugar decreased by 59.59% and 70.0%, respectively. Notably, the wildfire disease had little effect on the content of starch and K. Redundancy analysis revealed that , , , and displayed positive correlations with nicotine, protein, total nitrogen, Cl and K contents, while , , , , , , , and displayed positive correlations with total sugar and reducing sugar contents. , , and were found to be enriched in diseased leaves, suggesting their potential role in disease suppression. Co-occurrence network analysis indicated that positive correlations were prevalent in microbial networks, and the bacterial network of healthy tobacco leaves exhibited greater complexity compared to diseased tobacco leaves. This study revealed the impact of wildfire disease on the microbial community and chemical compositions of tobacco leaves and provides new insights for the biological control of tobacco wildfire disease.
PubMed: 38099080
DOI: 10.1002/pld3.551