The emerging drug resistance and lack of safer and more potent antifungal agents make Candida infections another hot topic in the healthcare system. At the same time, the potential of plant products in developing novel antifungal drugs is also in the limelight. Considering these facts, we have investigated the different extracts of the flowers of Hibiscus rosa-sinensis of the Malvaceae family for their antifungal efficacy against five different pathogenic Candida strains. Among the various extracts, the chloroform extract showed the maximum zone of inhibition (26.6 ± 0.5 mm) against the Candida albicans strain.
Furthermore, the chloroform fraction was isolated, and a sterol compound was identified as β-sitosterol. Mechanistic studies were conducted to understand the mechanism of action, and the results showed that β-sitosterol has significant antifungal activity and is capable of interrupting biofilm formation and acts by inhibiting ergosterol biosynthesis in Candida albicans cells. Microscopic and molecular docking studies confirmed these findings. Overall, the study validates the antifungal efficacy of Candida albicans due to the presence of β-sitosterol which can act as an effective constituent for antifungal drug development individually or in combination.
Infection with SARS-CoV2, which is responsible for COVID-19, can lead to differences in disease development, severity and mortality rates depending on gender, age or the presence of certain diseases. Considering that existing studies ignore these differences, this study aims to uncover potential differences attributable to gender, age and source of sampling as well as viral load using bioinformatics and multi-omics approaches. Differential gene expression analyses were used to analyse the phenotypic differences between SARS-CoV-2 patients and controls at the mRNA level. Pathway enrichment analyses were performed at the gene set level to identify the activated pathways corresponding to the differences in the samples. Drug repurposing analysis was performed at the protein level, focusing on host-mediated drug candidates to uncover potential therapeutic differences. Significant differences (i.e. the number of differentially expressed genes and their characteristics) were observed for COVID-19 at the mRNA level depending on the sample source, gender and age of the samples. The results of the pathway enrichment show that SARS-CoV-2 can be combated more effectively in the respiratory tract than in the blood samples.
Taking into account the different sample sources and their characteristics, different drug candidates were identified. Evaluating disease prediction, prevention and/or treatment strategies from a personalised perspective is crucial. In this study, we not only evaluated the differences in COVID-19 from a personalised perspective, but also provided valuable data for further experimental and clinical efforts. Our findings could shed light on potential pandemics.
Fleagrass, a herb known for its pleasant aroma, is widely used as a mosquito repellent, antibacterial agent, and for treating colds, reducing swelling, and alleviating pain. The antifungal effects of the essential oils of fleagrass and carvacrol against Candida albicans were investigated by evaluating the growth and the mycelial and biofilm development of C. albicans. Transmission electron microscopy was used to evaluate the integrity of the cell membrane and cell wall of C. albicans. Fleagrass exhibited high fungicidal activity against C. albicans at concentrations of 0.5% v/v (via the Ras1/cAMP/PKA pathway). Furthermore, transmission electron microscopy revealed damage to the cell wall and membrane after treatment with the essential oil, which was further confirmed by the increased levels of β-1,3-glucan and chitin in the cell wall. This study showed that fleagrass exerts good fungicidal and hyphal growth inhibition activity against C. albicans by disrupting its cell wall, and thus, fleagrass may be a potential antifungal drug.
Vulvovaginal candidiasis (VVC) is a prevalent condition affecting a significant portion of women worldwide. Licochalcone A (LA), a natural compound with diverse biological activities, holds promise as a protective agent against Candida albicans (C. albicans) infection. This study aims to investigate the potential of LA to safeguard vaginal epithelial cells (VECs) from C. albicans infection and elucidate the underlying molecular mechanisms. To simulate VVC in vitro, VK2-E6E7 cells were infected with C. albicans. Candida albicans biofilm formation, C.
albicans adhesion to VK2-E6E7 cells, and C. albicans-induced cell damage and inflammatory responses were assessed by XTT reduction assay, fluorescence assay, LDH assay, and ELISA. CCK-8 assay was performed to evaluate the cytotoxic effects of LA on VK2-E6E7 cells. Western blotting assay was performed to detect protein expression. LA dose-dependently hindered C. albicans biofilm formation and adhesion to VK2-E6E7 cells. Furthermore, LA mitigated cell damage, inhibited the Bax/Bcl-2 ratio, and attenuated the secretion of pro-inflammatory cytokines in C.
albicans-induced VK2-E6E7 cells. The investigation into LA's impact on the Toll-like receptor 4 (TLR4)/nuclear factor-kappa B (NF-κB) pathway revealed that LA downregulated TLR4 expression and inhibited NF-κB activation in C.
albicans-infected VK2-E6E7 cells. Furthermore, TLR4 overexpression partially abated LA-mediated protection, further highlighting the role of the TLR4/NF-κB pathway. LA holds the potential to safeguard VECs against C. albicans infection, potentially offering therapeutic avenues for VVC management.
To elucidate the function of proteorhodopsin in Candidatus Puniceispirillum marinum strain IMCC1322, a cultivated representative of SAR116, we produced RNA-seq data under laboratory conditions. We examined the transcriptomes of six different cultures, including sets of expression changes under constant dark (DD), constant light (LL), and diel-cycled (LD; 14 h light: 10 h dark) conditions at the exponential and stationary/death phases. Prepared mRNA extracted from the six samples was analyzed on the Solexa Genome Analyzer with 36 cycles.
Differentially expressed genes on the IMCC1322 genome were distinguished as four clusters by K-mean clustering and each CDS (n = 2546) was annotated based on the KEGG BRITE hierarchy. Cluster 0 (n = 1573) covered most constitutive genes including proteorhodopsin, retinoids, and glycolysis/TCA cycle. Cluster 1 genes (n = 754) were upregulated in stationary/death phase under constant dark conditions and included genes associated with bacterial defense, membrane transporters, nitrogen metabolism, and senescence signaling. Cluster 2 genes (n = 197) demonstrated upregulation in exponential phase cultures and included genes involved in genes for oxidative phosphorylation, translation factors, and transcription machinery. Cluster 3 (n = 22) contained light-stimulated upregulated genes expressed under stationary/phases. Stringent response genes belonged to cluster 2, but affected genes spanned various cellular processes such as amino acids, nucleotides, translation, transcription, glycolysis, fatty acids, and cell wall components. The coordinated expression of antagonistic stringent genes, including mazG, ppx/gppA, and spoT/relA may provide insight into the controlled cultural response observed between constant light and constant dark conditions in IMCC1322 cultures, regardless of cell numbers and biomass.
Vaccines are one of the most powerful tools for preventing infectious diseases. To effectively fight pathogens, vaccines should
induce potent and long-lasting immune responses that are specific to the pathogens. However, not all vaccines can induce
effective immune responses, and the responses vary greatly among individuals and populations. Although several factors, such
as age, host genetics, nutritional status, and region, affect the effectiveness of vaccines, increasing data have suggested that
the gut microbiota is critically associated with vaccine-induced immune responses. In this review, I discuss how gut microbiota
affects vaccine effectiveness based on the clinical and preclinical data, and summarize possible underlying mechanisms
related to the adjuvant effects of microbiota. A better understanding of the link between vaccine-induced immune responses
and the gut microbiota using high-throughput technology and sophisticated system vaccinology approaches could provide
crucial insights for designing effective personalized preventive and therapeutic vaccination strategies.
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The existence of biogeography for microorganisms is a raising topic in ecology and researchers are employing better distinctions
between single species, including the most rare ones, to reveal potential hidden patterns. An important volume
of evidence supporting heterogeneous distributions for bacteria, archaea and protists is accumulating, and more recently
a few efforts have targeted microscopic fungi. We propose an insight into this latter kingdom by looking at a group of soil
nematode-trapping fungi whose species are well-known and easily recognizable. We chose a pure culture approach because
of its reliable isolation procedures for this specific group. After morphologically and molecularly identifying all species
collected from 2250 samples distributed in 228 locations across Yunnan province of China, we analyzed occurrence frequencies
and mapped species, genera, and richness. Results showed an apparent cosmopolitan tendency for this group of
fungi, including species richness among sites. However, only four species were widespread across the region, while nonrandom
heterogeneous distributions were observed for the remaining 40 species, both in terms of statistical distribution of
species richness reflected by a significant variance-to-mean ratio, as well as in terms of visually discernible spatial clusters
of rare species and genera on the map. Moreover, several species were restricted to only one location, raising the question
of whether endemicity exists for this microbial group. Finally, environmental heterogeneity showed a marginal contribution
in explaining restricted distributions, suggesting that other factors such as geographical isolation and dispersal capabilities
should be explored. These findings contribute to our understanding of the cryptic geographic distribution of microorganisms
and encourage further research in this direction.
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Microbial communities in the rhizosphere play a crucial role
in determining plant growth and crop yield. A few studies
have been performed to evaluate the diversity and co-occurrence
patterns of rhizosphere microbiomes in soybean (Glycine
max) at a regional scale. Here, we used a culture-independent method to compare the bacterial communities of the
soybean rhizosphere between Nebraska (NE), a high-yield
state, and Oklahoma (OK), a low-yield state. It is well known
that the rhizosphere microbiome is a subset of microbes that
ultimately get colonized by microbial communities from the
surrounding bulk soil. Therefore, we hypothesized that differences
in the soybean yield are attributed to the variations in
the rhizosphere microbes at taxonomic, functional, and community
levels. In addition, soil physicochemical properties
were also evaluated from each sampling site for comparative
study. Our result showed that distinct clusters were formed
between NE and OK in terms of their soil physicochemical
property. Among 3 primary nutrients (i.e., nitrogen, phosphorus,
and potassium), potassium is more positively correlated
with the high-yield state NE samples. We also attempted
to identify keystone communities that significantly affected the
soybean yield using co-occurrence network patterns. Network
analysis revealed that communities formed distinct clusters
in which members of modules having significantly positive
correlations with the soybean yield were more abundant in
NE than OK. In addition, we identified the most influential
bacteria for the soybean yield in the identified modules. For
instance, included are class Anaerolineae, family Micromonosporaceae,
genus Plantomyces, and genus Nitrospira in the
most complex module (ME9) and genus Rhizobium in ME23.
This research would help to further identify a way to increase
soybean yield in low-yield states in the U.S. as well as worldwide
by reconstructing the microbial communities in the
rhizosphere.
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Siboglinid tubeworms thrive in hydrothermal vent and seep
habitats via a symbiotic relationship with chemosynthetic bacteria.
Difficulties in culturing tubeworms and their symbionts
in a laboratory setting have hindered the study of host-microbe
interactions. Therefore, released symbiont genomes are
fragmented, thereby limiting the data available on the genome
that affect subsequent analyses. Here, we present a complete
genome of gammaproteobacterial endosymbiont from the
tubeworm Lamellibrachia satsuma collected from a seep in
Kagoshima Bay, assembled using a hybrid approach that combines
sequences generated from the Illumina and Oxford Nanopore
platforms. The genome consists of a single circular chromosome
with an assembly size of 4,323,754 bp and a GC content
of 53.9% with 3,624 protein-coding genes. The genome
is of high quality and contains no assembly gaps, while the
completeness and contamination are 99.33% and 2.73%,
respectively. Comparative genome analysis revealed a total
of 1,724 gene clusters shared in the vent and seep tubeworm
symbionts, while 294 genes were found exclusively in L. satsuma
symbionts such as transposons, genes for defense mechanisms,
and inorganic ion transportations. The addition of
this complete endosymbiont genome assembly would be valuable
for comparative studies particularly with tubeworm symbiont
genomes as well as with other chemosynthetic microbial
communities.
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Genomic and transcriptomic analyses illuminate the molecular basis of the unique lifestyle of a tubeworm, Lamellibrachia satsuma
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Low electric current can inhibit certain microbial biofilms and
enhance the efficacy of antimicrobials against them. This study
investigated the electricidal and bioelectric effects of direct
current (DC) against Porphyromonas gingivalis biofilms as
well as the underlying mechanisms. Here, we firstly showed
that DC significantly suppressed biofilm formation of P. gingivalis
in time- and intensity-dependent manners, and markedly
inhibited preformed P. gingivalis biofilms. Moreover,
DC enhanced the killing efficacy of metronidazole (MTZ) and
amoxicillin with clavulanate potassium (AMC) against the
biofilms. Notably, DC-treated biofilms displayed upregulated
intracellular ROS and expression of ROS related genes (sod,
feoB, and oxyR) as well as porin gene. Interestingly, DC-induced
killing of biofilms was partially reversed by ROS scavenger
N-dimethylthiourea (DMTU), and the synergistic effect
of DC with MTZ/AMC was weakened by small interfering
RNA of porin gene (si-Porin). In conclusion, DC can
exert electricidal and bioelectric effects against P. gingivalis
biofilms partially via promotion of oxidative stress and antibiotic
transport, which offers a promising approach for effective
management of periodontitis.
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Soil contamination with diesel oil is quite common during
processes of transport and storage. Bioremediation is considered
a safe, economical, and environmentally friendly approach
for contaminated soil treatment. In this context, studies
using hydrocarbon bioremediation have focused on total
petroleum hydrocarbon (TPH) analysis to assess process effectiveness,
while ecotoxicity has been neglected. Thus, this
study aimed to select a microbial consortium capable of detoxifying
diesel oil and apply this consortium to the bioremediation
of soil contaminated with this environmental pollutant
through different bioremediation approaches. Gas chromatography
(GC-FID) was used to analyze diesel oil degradation,
while ecotoxicological bioassays with the bioindicators
Artemia sp., Aliivibrio fischeri (Microtox), and Cucumis
sativus were used to assess detoxification. After 90 days of
bioremediation, we found that the biostimulation and biostimulation/
bioaugmentation approaches showed higher rates
of diesel oil degradation in relation to natural attenuation
(41.9 and 26.7%, respectively). Phytotoxicity increased in the
biostimulation and biostimulation/bioaugmentation treatments
during the degradation process, whereas in the Microtox
test, the toxicity was the same in these treatments as that
in the natural attenuation treatment. In both the phytotoxicity
and Microtox tests, bioaugmentation treatment showed lower
toxicity. However, compared with natural attenuation, this
approach did not show satisfactory hydrocarbon degradation.
Based on the microcosm experiments results, we conclude
that a broader analysis of the success of bioremediation requires
the performance of toxicity bioassays.
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sources. Fecal pollution is especially harmful as it disperses
pathogenic bacteria into waterways. Unraveling origins of
mixed sources of fecal bacteria is difficult and microbial
source tracking (MST) in complex environments is still a
daunting task. Despite the challenges, the need for answers
far outweighs the difficulties experienced. Advancements in
qPCR and next generation sequencing (NGS) technologies
have shifted the traditional culture-based MST approaches
towards culture independent technologies, where communitybased
MST is becoming a method of choice. Metagenomic
tools may be useful to overcome some of the limitations of
community-based MST methods as they can give deep insight
into identifying host specific fecal markers and their association
with different environments. Adoption of machine
learning (ML) algorithms, along with the metagenomic based
MST approaches, will also provide a statistically robust and
automated platform. To compliment that, ML-based approaches
provide accurate optimization of resources. With the
successful application of ML based models in disease prediction,
outbreak investigation and medicine prescription,
it would be possible that these methods would serve as a
better surrogate of traditional MST approaches in future.
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Gloeostereum incarnatum is an edible medicinal mushroom
widely grown in China. Using the whole genome of G. incarnatum,
simple sequence repeat (SSR) markers were developed
and synthetic primers were designed to construct its
first genetic linkage map. The 1,048.6 cm map is composed of
10 linkage groups and contains 183 SSR markers. In total,
112 genome assembly sequences were anchored, representing
16.43 Mb and covering 46.41% of the genome. Selfing
populations were used for quantitative trait loci (QTL) targeting,
and the composite interval mapping method was used
to co-localize the mycelium growth rate (potato dextrose agar
and sawdust), growth period, yield and fruiting body length,
and width and thickness. The 14 QTLs of agronomic traits
had LOD values of 3.20–6.51 and contribution rates of 2.22–
13.18%. No linkage relationship was found between the mycelium
growth rate and the growth period, but a linkage relationship
was observed among the length, width and thickness
of the fruiting bodies. Using NCBI’s BLAST alignment,
the genomic sequences corresponding to the QTL regions
were compared, and a TPR-like protein candidate gene was
selected. Using whole-genome data, 138 candidate genes were
found in four sequence fragments of two SSR markers located
in the same scaffold. The genetic map and QTLs established
in this study will aid in developing selective markers
for agronomic traits and identifying corresponding genes,
thereby providing a scientific basis for the further gene mapping
of quantitative traits and the marker-assisted selection
of functional genes in G. incarnatum breeding programs.
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The growing threat of emergent multidrug-resistant enteric
bacterial pathogens, and their adopted virulence properties
are directing to find alternative antimicrobials and/or development
of dietaries that can improve host gut health and/or
defense. Recently, we found that modified Lactobacillus casei
(Lc + CLA) with increased production of conjugated linoleic
acid has antimicrobial and other beneficial properties.
Further, prebiotic alike products such as berry pomace extracts
(BPEs), increase the growth of probiotics and inhibit
the growth of certain bacterial pathogens. In this study, we
evaluated the antibacterial effect of genetically modified Lc +
CLA along with BPEs against major enteric pathogen Salmonella
enterica serovar Typhimurium (ST). In mixed culture
condition, the growth of ST was significantly reduced in the
presence of Lc + CLA and/or BPEs. Bacterial cell-free cultural
supernatant (CFCS) collected from wild-type Lc or modified
Lc + CLA strains also inhibited the growth and survival of ST,
and those inhibitory effects were enhanced in the presence of
BPEs. We also found that the interaction of the pathogen with
cultured host (HD-11 and INT-407) cells were also altered in
the presence of either Lc or Lc + CLA strain or their CFCSs
significantly. Furthermore, the relative expression of genes
related to ST virulence and physicochemical properties of ST
was altered by the effect of CFCSs of either Lc or Lc + CLA.
These findings indicate that a diet containing synbiotic, specifically
linoleic acid, over-produced Lc + CLA and prebiotic
product BPEs, might have the potential to be effective in controlling
ST growth and pathogenesis.
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Natural anti-adhesive components against pathogenic bacterial adhesion and infection in gastrointestinal tract: case studies of
Helicobacter pylori
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Salmonella enterica
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A chromatin immunoprecipitation (ChIP) assay is a method
to identify how much a protein of interest binds to the DNA
region. This method is indispensable to study the mechanisms
of how the transcription factors or chromatin modifications
regulate the gene expression. Candida albicans is a dimorphic
pathogenic fungus, which can change its morphology very rapidly
from yeast to hypha in response to the environmental
signal. The morphological change of C. albicans is one of the
critical factors for its virulence. Therefore, it is necessary to
understand how to regulate the expression of genes for C.
albicans to change its morphology. One of the essential methods
for us to understand this regulation is a ChIP assay.
There have been many efforts to optimize the protocol to lower
the background signal and to analyze the results accurately
because a ChIP assay can provide very different results even
with slight differences in the experimental procedure. We
have optimized the rapid and efficient ChIP protocol so that
it could be applied equally for both yeast and hyphal forms of
C. albicans. Our method in this protocol is also comparatively
rapid to the method widely used. In this protocol, we described
our rapid method for the ChIP assay in C. albicans in
detail.
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