bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic interplay between
Proteus mirabilis
and
Enterococcus faecalis
facilitates polymicrobial biofilm formation and invasive disease
Authors: Hunt Benjamin C. , Brix Vitus , Vath Joseph , Guterman Lauren Beryl , Taddei Steven M. , Deka Namrata , Learman Brian S. , Brauer Aimee L. , Shen Shichen , Qu Jun , Armbruster Chelsie E. 
Published: October 2024

ABSTRACT

Biofilms play an important role in the development and pathogenesis of catheter-associated urinary tract infection (CAUTI).
Proteus mirabilis
and
Enterococcus faecalis
are common CAUTI pathogens that persistently co-colonize the catheterized urinary tract and form biofilms with increased biomass and antibiotic resistance. In this study, we uncover the metabolic interplay that drives biofilm enhancement and examine the contribution to CAUTI severity. Through compositional and proteomic biofilm analyses, we determined that the increase in biofilm biomass stems from an increase in the protein fraction of the polymicrobial biofilm. We further observed an enrichment in proteins associated with ornithine and arginine metabolism in polymicrobial biofilms compared with single-species biofilms. We show that arginine/ornithine antiport by
E. faecalis
promotes arginine biosynthesis and metabolism in
P. mirabilis
, ultimately driving the increase in polymicrobial biofilm protein content without affecting viability of either species. We further show that disrupting
E. faecalis
ornithine antiport alters the metabolic profile of polymicrobial biofilms and prevents enhancement, and this defect was complemented by supplementation with exogenous ornithine. In a murine model of CAUTI, ornithine antiport did not contribute to
E. faecalis
colonization but was required for the increased incidence of urinary stone formation and bacteremia that occurs during polymicrobial CAUTI with
P. mirabilis
. Thus, disrupting metabolic interplay between common co-colonizing species may represent a viable strategy for reducing risk of bacteremia.

IMPORTANCE

Chronic infections often involve the formation of antibiotic-resistant biofilm communities that include multiple different microbes, which pose a challenge for effective treatment. In the catheterized urinary tract, potential pathogens persistently co-colonize for long periods of time and the interactions between them can lead to more severe disease outcomes. In this study, we identified the metabolite L-ornithine as a key mediator of disease-enhancing interactions between two common and challenging pathogens,
Enterococcus faecalis
and
Proteus mirabilis
. Disrupting ornithine-mediated interactions may therefore represent a strategy to prevent polymicrobial biofilm formation and decrease risk of severe disease.
Epidermal growth factor receptor signaling governs the host inflammatory response to invasive aspergillosis
Authors: Liu Hong , Lin Jianfeng , Phan Quynh T. , Bruno Vincent M. , Filler Scott G. 
Published: October 2024

ABSTRACT

The epidermal growth factor receptor (EGFR) has been identified as an epithelial cell receptor for Mucorales fungi and
Candida albicans
. Blocking EGFR with small molecule inhibitors reduces disease severity in mouse models of mucormycosis and oropharyngeal candidiasis. In contrast, cases of invasive aspergillosis have been reported in cancer patients who were treated with EGFR inhibitors, suggesting that EGFR signaling may play a protective role in the host defense against this infection. Here, we analyzed transcriptomic data from the lungs of mice with invasive aspergillosis and found evidence that
Aspergillus fumigatus
infection activates multiple genes that are predicted to function in the EGFR signaling pathway. We also found that
A. fumigatus
infection activates EGFR in both a human small-airway epithelial (HSAE) cell line and in the lungs of immunosuppressed mice. EGFR signaling in HSAE cells is required for maximal endocytosis of
A. fumigatus
and for fungal-induced proinflammatory cytokine and chemokine production. In a corticosteroid immunosuppressed mouse model of invasive pulmonary aspergillosis, inhibition of EGFR with gefitinib decreased whole-lung cytokine and chemokine levels and reduced accumulation of phagocytes in the lung, leading to a decrease in fungal killing, an increase in pulmonary fungal burden, and accelerated mortality. Thus, EGFR signaling is required for pulmonary epithelial cells to orchestrate the host innate immune defense against invasive aspergillosis in immunosuppressed hosts.

IMPORTANCE

When
A. fumigatus
infects the lungs, it invades epithelial cells that line the airways. During this process, the fungus interacts with epithelial cell receptors. This interaction stimulates epithelial cells to endocytose the fungus. It also induces these cells to secrete proinflammatory cytokines and chemokines that recruit phagocytes to the site of infection where they can kill the fungus. Here, we show that in small-airway epithelial cells, the EGFR acts as a sensor for
A. fumigatus
that triggers the production of chemokines in response to fungal infection. In corticosteroid-immunosuppressed mice, blocking EGFR with the kinase inhibitor gefitinib reduces chemokine production in the lungs. This leads to decreased accumulation of neutrophils and dendritic cells in the lungs, reduced
A. fumigatus
killing, and increased mortality. These results provide a potential explanation as to why some cancer patients who are treated with EGFR inhibitors develop invasive aspergillosis.
PlsX and PlsY: Additional roles beyond glycerophospholipid synthesis in Gram-negative bacteria
Authors: Rex Audrey N. , Simpson Brent W. , Bokinsky Gregory , Trent M. Stephen 
Published: October 2024

ABSTRACT

The unique asymmetry of the Gram-negative outer membrane, with glycerophospholipids (GPLs) in the inner leaflet and lipopolysaccharide (LPS) in the outer leaflet, works to resist external stressors and prevent the entry of toxic compounds. Thus, GPL and LPS synthesis must be tightly controlled to maintain the integrity of this essential structure. We sought to decipher why organisms like
Escherichia coli
possess two redundant pathways—PlsB and PlsX/Y—for synthesis of the GPL precursor lysophosphatidic acid (LPA). LPA is then converted by PlsC to the universal precursor for GPL synthesis, phosphatidic acid (PA). PlsB and PlsC are essential in
E. coli
, indicating they serve as the major pathway for PA synthesis. While loss of PlsX or PlsY individually has little consequence on the cell, the absence of both was lethal. To understand the synthetic lethality of this seemingly redundant PlsX/Y pathway, we performed a suppressor screen. Suppressor analysis indicated that ∆
plsXY
requires increased levels of glycerol-3-phosphate (G3P), a GPL precursor. In agreement, ∆
plsXY
required supplementation with G3P for survival. Furthermore, loss of PlsX dysregulated fatty acid synthesis, resulting in increased long-chain fatty acids. We show that although PlsX/Y together contribute to PA synthesis, they also contribute to the regulation of overall membrane biogenesis. Thus, synthetic lethality of ∆
plsXY
is multifactorial, suggesting that PlsX/Y has been maintained as a redundant system to fine-tune the synthesis of major lipids and promote cell envelope homeostasis.

IMPORTANCE

Gram-negative bacteria must maintain optimal ratios of glycerophospholipids and lipopolysaccharide within the cell envelope for viability. Maintenance of proper outer membrane asymmetry allows for resistance to toxins and antibiotics. Here, we describe additional roles of PlsX and PlsY in
Escherichia coli
beyond lysophosphatidic acid synthesis, a key precursor of all glycerophospholipids. These findings suggest that PlsX and PlsY also play a larger role in impacting homeostasis of lipid synthesis.
Trehalose polyphleates participate in
Mycobacterium abscessus
fitness and pathogenesis
Authors: Malmsheimer Silke , Daher Wassim , Tasrini Yara , Hamela Claire , Aguilera-Correa John Jairo , Chalut Christian , Hatfull Graham F. , Kremer Laurent 
Published: October 2024

ABSTRACT

Mycobacteria produce a large repertoire of surface-exposed lipids with major biological functions. Among these lipids, trehalose polyphleates (TPPs) are instrumental in the infection of
Mycobacterium abscessus
by the therapeutic phage BPs. However, while the biosynthesis and transport of TPPs across the membrane by MmpL10 have been reported, the role of TPPs in host infection remains enigmatic. Here, we addressed whether the loss of TPPs influences interactions with macrophages and the virulence of
M. abscessus
. As anticipated, the deletion of
mmpL10
in smooth (S) and rough (R) variants of
M. abscessus
abrogated TPP production, which was rescued upon gene complementation. Importantly, infection of human THP-1 cells with the
mmpL10
mutants was associated with decreased intramacrophage survival and a reduced proportion of infected cells. The rough
mmpL10
mutant showed an impaired capacity to block phagosomal acidification and was unable to co-localize with Galectin-3, a marker of phagosomal membrane damage. This suggests that TPPs participate, directly or indirectly, in phagolysosomal fusion and in phagosomal membrane damage to establish cytosolic communication. The TPP defect that affects the fitness and virulence of
M. abscessus
was further demonstrated in zebrafish embryos using a rough clinical strain resistant to phage BPs and harboring a frameshift mutation in
mmpL10
. Infection with this strain was correlated with a slight decrease in embryo survival and a reduced bacterial burden as compared to the corresponding parental and complemented derivatives. Together, these results indicate that TPPs are important surface lipids contributing to the pathogenicity of
M. abscessus
.

IMPORTANCE

Trehalose polyphleates (TPPs) are complex lipids associated with the mycobacterial cell surface and were identified 50 years ago. While the TPP biosynthetic pathway has been described recently, the role of these lipids in the biology of mycobacteria remains yet to be established. The wide distribution of TPPs across mycobacterial species suggests that they may exhibit important functions in these actinobacteria. Here, we demonstrate that
Mycobacterium abscessus,
an emerging multidrug-resistant pathogen that causes severe lung diseases in cystic fibrosis patients, requires TPPs for survival in macrophages and virulence in a zebrafish model of infection. These findings support the importance of this underexplored family of lipids in mycobacterial pathogenesis.
Maternal consumption of yoghurt activating the aryl hydrocarbon receptor increases group 3 innate lymphoid cells in murine offspring
Authors: Pimentel Grégory , Roder Thomas , Bär Cornelia , Christensen Sandro , Sattari Zahra , Kalbermatter Cristina , von Ah Ueli , Robert Christelle A. M. , Mateo Pierre , Bruggmann Rémy , Ganal-Vonarburg Stephanie C. , Vergères Guy 
Published: October 2024

ABSTRACT

Indole derivatives are microbial metabolites of the tryptophan pathway involved in gut immune homeostasis. They bind to the aryl hydrocarbon receptor (AhR), thereby modulating development of intestinal group 3 innate lymphoid cells (ILC3) and subsequent interleukin-22 production. In mice, indole derivatives of the maternal microbiota can reach the milk and drive early postnatal ILC3 development. Apart from the gut microbiota, lactic acid bacteria (LAB) also produce indole compounds during milk fermentation. Using germ-free mice, the aim of our study was to test if maternal intake of a dairy product enriched in AhR-activating indoles produced by fermentation could boost maturation of the intestinal innate immune system in the offspring. A set of 631 LAB strains were genetically screened for their potential to produce indole compounds. Among these, 125 strains were tested in combination with standard strains to produce yoghurts that were screened for their ability to activate AhR
in vitro
using the HepG2–AhR–Luc cell line. The most active yoghurt and a control yoghurt were formulated as pellets and fed to germ-free dams during pregnancy and lactation. Analysis of the offspring on postnatal day 14 using flow cytometry revealed an increase in the frequency of small intestinal lamina propria NKp46 +ILC3 s in the pups born to dams that had consumed the purified diet containing an AhR-active yoghurt (AhrY-diet) compared to control yoghurt (ConY-diet). Selection of LABs based on their ability to produce a fermented dairy able to activate AhR appears to be an effective approach to produce a yoghurt with immunomodulatory properties.

IMPORTANCE
Key progresses in the sequencing and functional annotation of microbial organisms have revolutionized research in the fields of human metabolism and food biotechnology. In particular, the gut microbiome is now recognized as an important mediator of the impact of nutrition on human metabolism. Annotated genomes of a large number of bacteria are now available worldwide, which selectively transform food through fermentation to produce specific bioactive compounds with the potential to modulate human health. A previous research has demonstrated that the maternal microbiota shapes the neonatal immune system. Similarly, this report shows that lactic acid bacteria can be selected to produce fermented food that can also modulate postnatal intestinal immunity.
Transcriptional response of
Methanosarcina acetivorans
to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED
Authors: Buan Nicole R. , Metcalf William W. 
Published: October 2024

ABSTRACT

Methane-producing archaea are key organisms in the anaerobic carbon cycle. These organisms, also called methanogens, grow by converting substrate to methane gas in a process called methanogenesis. Previous research showed that the reduction of the terminal electron acceptor is the rate-limiting step in methanogenesis by
Methanosarcina acetivorans
. In order to gain insight into how the cells sense and respond to the availability of the terminal electron acceptor, we designed an experiment to deplete cells of the essential terminal oxidase enzyme, HdrED. We found that the depletion of HdrED
in vivo
results in a higher abundance of transcripts for methyltransferases (
mtaC2, mtaB3, mtaC3
), coenzyme B biosynthesis, C1 metabolism, and pyrimidine compounds. In most cases, these changes were distinct from transcript abundance changes observed during the transition from exponential growth to stationary phase cultures. These data implicate the methylotrophic methanogenesis regulator MsrC (MA4383) in CoM-S-S-CoB heterodisulfide sensing and indicate cells have a specific mechanism to sense intracellular ratio of CoM-S-S-CoB, coenzyme M, and coenzyme B thiols and further suggest transcripts encoding translation and methanogenesis functions are controlled by feed-forward regulation depending on substrate availability.

IMPORTANCE

Methanosarcina
is an emerging model archaeon and synthetic biology platform for the production of renewable energy and sustainable chemicals to reduce dependence on petroleum. Research into metabolic networks and gene regulation in this organism and other methanogens will inform genome-scale metabolic modeling and microbial function prediction in uncultured or non-model anaerobes and archaea. This study suggests methanogens use unknown mechanisms to efficiently couple methanogenesis to gene regulation via CoM-S-S-CoB and ATP availability.
Highlight signatures of vaginal microbiota and metabolome contributed to the occurrence and recurrence of vulvovaginal candidiasis
Authors: Liang Yiheng , Huang Zhuoqi , Fan Shangrong , Li Changzhong , Huang Liting , Huang Chunhua , Hutchins Andrew P. , Fang Chao , Zhang Xiaowei 
Published: October 2024

ABSTRACT

Vulvovaginal candidiasis (VVC) is a common vaginal infectious disease caused by
Candida
. The high recurrence rate of VVC is a great clinical challenge, with recurrent VVC (RVVC) defined as four or more episodes within a year. In this study, we recruited 31 RVVC patients, 28 VVC patients, and 29 healthy women. Vaginal samples were collected for metagenomic and metabolic analysis. RVVC and VVC groups presented similar clinical symptoms, with only a significantly increased incidence of swelling in the VVC group. Vaginal microbiota in VVC/RVVC exhibited a decreased abundance of
Lactobacillus
and increased bacterial vaginosis-associated bacteria, such as
Gardnerella
,
Prevotella
, and
Atopobium
. Notably,
Lactobacillus iners
was higher in RVVC, suggesting not all
Lactobacillus
species are protective. Healthy women showed lower overall microbiota diversity, emphasizing single-species dominance for stability. Glycogen metabolism pathways were enriched in RVVC/VVC, and were correlated with
Atopobium vaginae
,
Prevotella bivia
, and
Lactobacillus jensenii
. Peptidoglycan synthesis pathways, associated with
P. bivia
, were enriched, with the substrate L-glutamate elevated in RVVC, possibly promoted by
L. iners
. These findings shed light on potential therapeutic targets for recurrent VVC, contributing to the understanding of the intricate interplay between the metabolism of vaginal microbiome and disease.

IMPORTANCE

This study enhances our knowledge of the vaginal microbiota dynamics and the role of associated metabolites in individuals with vulvovaginal candidiasis (VVC) and recurrent vulvovaginal candidiasis through shotgun sequencing and multi-omics analysis. The relationship between metabolites and vaginal microbiota and disease state was revealed. The accumulation of L-glutamate generated in glycogen metabolism, which is governed by
Lactobacillus iners
or bacterial vaginosis-associated bacteria, may contribute to the incidence and recurrence of VVC. Such insights have the potential to impact the treatment and prevention strategies for these common yet distressing conditions, potentially leading to targeted therapies and improved patient outcomes.
Cariogenic potential of the
Streptococcus mutans
Cid/Lrg system: an
in vivo
animal case study
Authors: Ahn Sang-Joon , Rice Kelly C. , Culp David J. 
Published: October 2024

ABSTRACT

In our prior study using a dual-species (
Streptococcus mutans/Streptococcus gordonii
) competitive mouse caries model to investigate the contribution of
S. mutans
LrgAB to
in vivo
fitness,
S. mutans
wild-type and Δ
lrgAB
mutants consistently outnumbered
S. gordonii
and had high caries scores, even though the Δ
lrgAB
mutant is highly sensitive to oxidative stress. To determine whether the highly cariogenic sucrose diet used in the previous study masked the contribution of LrgAB to competitive fitness of
S. mutans
against
S. gordonii
, we recapitulated our previous mouse caries experiment with a modification in which 4% sucrose drinking water was replaced with sterile water, hypothesized to decrease the frequency of exposure of mice to sucrose, a determinant in the cariogenicity of
S. mutans
. Given that both
S. mutans
Δ
lrgAB
and Δ
cidB
mutants are sensitive to oxidative stress and share similar transcriptional profiles, these strains, as well as wild-type UA159, were tested in this modified dual-species mouse caries model. When comparing between groups the colonization within molar dental biofilms of
S. mutans
strains, Δ
lrgAB
mutant was at a level similar to the wild type, whereas
S. mutans
Δ
cidB
was modestly lower than both wild-type and
S. mutans
Δ
lrgAB
. The severity of total sulcal caries in both the
∆cidB
and
∆lrgAB
mutant infections was significantly lower than that of wild type. These results demonstrate that the Cid/Lrg system aids in
S. mutans
fitness against
S. gordonii
and caries potential
in vivo
, a phenotype likely masked in our previous study by more frequent exposure to sucrose.

IMPORTANCE

The development of a mature biofilm on the tooth surface is the central event in the pathogenesis of dental caries, which primarily requires that cariogenic organisms withstand the limited resources or environmental fluctuations experienced in the oral cavity. The sensitive and heterogeneous response of the
cid
and
lrg
operons to complex external signals has been hypothesized to trigger differentiation of the
Streptococcus mutans
biofilm community into distinct functional subpopulations to promote survival and persistence of the
S. mutans
community when challenged by an unfavorable environment. The study described herein enlightens our understanding of how Cid/Lrg contributes to
S. mutans
pathogenic potential
in vivo
(caries development), warranting further research regarding the adaptive role of Cid/Lrg system in human oral biofilms toward the development of anti-caries strategies directed at the Cid/Lrg system.
Unraveling antibiotic resistance in
Achromobacter mucicolens
IA strain: genomic insights, structural analysis, and prospects for targeted therapeutics
Authors: Al-Asadi Sura Ali , Abdul Wahhab Batool Hazim , Bootwala Jamila , Alwatar Wifaq M. Ali , Al-Kahachi Rusul Emaduldeen S. 
Published: October 2024

ABSTRACT

The mortality rate of infectious diseases caused by
Achromobacter mucicolens
is increasing. The enhanced antibiotic resistance among bacterial species through genetic transfer and mutations in the efflux mediating genes has made the treatment quite challenging.
A. mucicolens
is an aerobic, gram-negative, and non-fermenting opportunistic pathogen found in immunocompromised patients.
A. mucicolens
shows resistance against beta-lactams and other antibiotics through intrinsic resistance mechanisms, including multi-drug efflux pumps and beta-lactamases. In this study, the clinical isolate whole genome sequencing of
A. mucicolens
data was analyzed to identify the genes and mutations responsible for antimicrobial resistance. The identified genes and their mutants were then subjected to structural analysis to better understand the impact of mutations on the protein structure, and domain analysis was performed to investigate the role of domains in antibiotic resistance. A total of 4 genes,
acrR, macB, msbA,
and
tolC
, were identified with significant mutations, whereas
macB
was shortlisted for further analysis based on the conserved regions, sequence alignment, and the maximum number of mutations. All the mutants of the
macB
gene contain the two common domains, the ABC transporter-like ATP-binding domain and the AAA + ATPase domain. These domains are crucial in efflux mediating drug transport and can be targeted to design novel drugs for treating infections caused by
A. mucicolens
.

IMPORTANCE

Achromobacter
species represent a significant threat as opportunistic pathogens, particularly in healthcare settings. Their resilience to antibiotics, demonstrated by strains like A.
mucicolens
, poses a serious challenge in treating infections, especially in immunocompromised patients. This study emphasizes the critical need for heightened vigilance among healthcare professionals regarding
Achromobacter
infections. By analyzing the whole genome sequencing data of
A. mucicolens
, the study sheds light on the genetic basis of antimicrobial resistance, aiding in more targeted treatment strategies. Furthermore, structural and domain analyses offer insights into how mutations impact protein structure and function, crucial for developing effective interventions. Ultimately, implementing rigorous sanitation measures and antibiotic stewardship protocols is needed to mitigate the spread of
Achromobacter
and safeguard vulnerable patient populations.