bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ehrlichia
effector TRP120 manipulates bacteremia to facilitate tick acquisition
Authors: Zhang Tsian , Chien Rory C. , Budachetri Khemraj , Lin Mingqun , Boyaka Prosper , Huang Weiyan , Rikihisa Yasuko 
Published: March 2024

ABSTRACT

Ehrlichia
species are obligatory intracellular bacteria that cause a potentially fatal disease, human ehrlichiosis. The biomolecular mechanisms of tick acquisition of
Ehrlichia
and transmission between ticks and mammals are poorly understood.
Ehrlichia japonica
infection of mice recapitulates the full spectrum of human ehrlichiosis. We compared the pathogenicity and host acquisition of wild-type
E. japonica
with an isogenic transposon mutant of
E. japonica
that lacks tandem repeat protein 120 (TRP120) (ΔTRP120). Both wild-type and ΔTRP120
E. japonica
proliferated similarly in cultures of mammalian and tick cells. Upon inoculation into mice, both wild-type and ΔTRP120
E. japonica
multiplied to high levels in various tissues, with similar clinical chemistry and hematologic changes, proinflammatory cytokine induction, and fatal disease. However, the blood levels of ΔTRP120
E. japonica
were almost undetectable within 24 h, whereas the levels of the wild type increased exponentially. Greater than 90% of TRP120 was released from infected cells into the culture medium. Mouse blood monocytes exposed to native TRP120 from culture supernatants showed significantly reduced cell surface expression of the transmigration-related markers Ly6C and CD11b. Larval ticks attached to mice infected with either wild-type or ΔTRP120
E. japonica
imbibed similar amounts of blood and subsequently molted to nymphs at similar rates. However, unlike wild-type
E. japonica
, the ΔTRP120 mutant was minimally acquired by larval ticks and subsequent molted nymphs and, thus, failed to transmit to naïve mice. Thus, TRP120 is required for bacteremia but not disease. These findings suggest a novel mechanism whereby an obligatory intracellular bacterium manipulates infected blood monocytes to sustain the tick–mammal transmission cycle.

IMPORTANCE

Effective prevention of tick-borne diseases such as human ehrlichiosis requires an understanding of how disease-causing organisms are acquired.
Ehrlichia
species are intracellular bacteria that require infection of both mammals and ticks, involving cycles of transmission between them. Mouse models of ehrlichiosis and tick–mouse transmission can advance our fundamental understanding of the pathogenesis and prevention of ehrlichiosis. Herein, a mutant of
Ehrlichia japonica
was used to investigate the role of a single
Ehrlichia
factor, named tandem repeat protein 120 (TRP120), in infection of mammalian and tick cells in culture, infection and disease progression in mice, and tick acquisition of
E. japonica
from infected mice. Our results suggest that TRP120 is necessary only for
Ehrlichia
proliferation in circulating mouse blood and ongoing bacteremia to permit
Ehrlichia
acquisition by ticks. This study provides new insights into the importance of bacterial factors in regulating bacteremia, which may facilitate tick acquisition of pathogens.
Draft genome of
Kazachstania heterogenica var. weizmannii
, a commensal fungus of the mouse digestive tract
Authors: Kralova Jarmila Sekeresova , Fidel Lena , Donic Catalina , Ben-Dor Shifra , Jung Steffen 
Published: March 2024

ABSTRACT

Kazachstania heterogenica
is a member of the
K. telluris
complex, where all members to date are reported to be pathogenic fungi. We have isolated a strain,
K. heterogenica var. weizmannii,
from the gut of mice that seems to be a commensal strain and sequenced its genome.
Genome sequence and annotation of
Pyramidobacter
sp. strain YE332, isolated from a cattle rumen fermentation of Leucaena leaf
Authors: Gilbert Rosalind , Davis Carl , Gravel Jenny , Ouwerkerk Diane 
Published: March 2024

ABSTRACT

We report the 2.78-Mb circular genome sequence of
Pyramidobacter
sp. strain YE332, isolated from a fermentation of bovine rumen fluid, supplied with leaf material from
Leucaena leucocephala
cv. Cunningham. This genome sequence consists of 2,795,328 bp with 60% G + C content, 2,573 predicted coding DNA sequences, and 70 RNAs.
Draft genome sequence of
Acinetobacter baumannii
Ab10, a clinical isolate from Hospital University Sains Malaysia (HUSM), Malaysia
Authors: Nik Mohd Nazri Nik Zakuan Hakim , Banga Singh Kirnpal Kaur , Ismail Mohamad Izwan 
Published: March 2024

ABSTRACT

Acinetobacter baumannii
strain Ab10 retrieved in Malaysia in 2017 represents a pathogen carrying multiple antibiotic-resistant genes (
blaOXA-23
,
ant(3”)-Ila
,
blaADC-32
, and
blaOXA-699
). We introduce the 3.89 Mbp genome sequence from short-read sequencing (Illumina’s NovaSeq6000).
Draft genome sequence of thermotolerant
Saccharomyces cerevisiae
AH465, isolated from Mt. Tatsuda, Kumamoto, Japan
Authors: Sasano Yu , Hamaguchi Ayuki , Taguchi Hisataka 
Published: March 2024

ABSTRACT

Thermotolerance is a required characteristic for biofuel production by yeast. Here, we report the draft genome sequence of thermotolerant
Saccharomyces cerevisiae
AH465, which was originally isolated by the authors. A hybrid assembly approach using MinION Mk1b and MiSeq sequencers was conducted. The assembled sequence comprises 13.4 Mb in 26 contigs.
Complete genome sequences of
Lactobacillus acidophilus
strain P42 and
Limosilactobacillus reuteri
strain P43 isolated from chicken cecum
Authors: Hassan Hosni M. , Mendoza Mary , Dickey Allison N. 
Published: March 2024

ABSTRACT

The gut microflora contains a diverse microbial population that is influenced by the host and the environment. We report the complete circular genome sequences of
Lactobacillus acidophilus
strain P42 and
Limosilactobacillus reuteri
strain P43 isolated from chicken cecal samples. P42 and P43 could potentially serve as poultry probiotic strains.
Genome sequence of white spot syndrome virus (WSSV) infecting cultured black tiger shrimp (
Penaeus monodon
) in Bangladesh
Authors: Islam S. M. Rafiqul , Ahmed Robel , Sharmen Farjana , Hossain Md. Mobarok , Chakma Kallyan , Tanni Afroza Akter , Akash Md. Ashikur Alim , Hossain Mohammad Enayet , Chowdhury M. Shah Nawaz , Siddiki AMAM Zonaed , Hossain Anwar , Mandal Shankar C. , Crandall Keith A. , Rahnavard Ali , Sharifuzzaman SM , Mannan Adnan 
Published: March 2024

ABSTRACT

The white spot syndrome virus (WSSV) is a causative agent of white spot disease (WSD) in crustaceans, especially in cultivated black tiger shrimp (
Penaeus monodon
), leading to significant economic losses in the aquaculture sector. The present study describes four whole genome sequences of WSSV obtained from coastal regions of Bangladesh.
Temporal dynamics of
Candida albicans
morphogenesis and gene expression reveals distinctions between
in vitro
and
in vivo
filamentation
Authors: Wakade Rohan S. , Wellington Melanie , Krysan Damian J. 
Published: March 2024

ABSTRACT

Candida albicans
is a common human fungal pathogen that is also a commensal of the oral cavity and gastrointestinal tract.
C. albicans
pathogenesis is linked to its transition from budding yeast to filamentous morphologies including hyphae and pseudohyphae. The centrality of this virulence trait to
C. albicans
pathobiology has resulted in extensive characterization of a wide range of factors associated with filamentation with a strong focus on transcriptional regulation. The vast majority of these experiments have used
in vitro
conditions to induce the yeast-to-filament transition. Taking advantage of
in vivo
approaches to quantitatively characterize both morphology and gene expression during filamentation during mammalian infection, we have investigated the dynamics of these two aspects of filamentation
in vivo
and compared them to
in vitro
filament induction with “host-like” tissue culture media supplemented with serum at mammalian body temperature. Although filamentation shares many common features in the two conditions, we have found two significant differences. First, alternative carbon metabolism genes are expressed early during
in vitro
filamentation and late
in vivo
, suggesting significant differences in glucose availability. Second,
C. albicans
begins a hyphae-to-yeast transition after 4-h incubation while we find little evidence of hyphae-to-yeast transition
in vivo
up to 24 h post-infection. We show that the low rate of
in vivo
hyphae-to-yeast transition is likely due to the very low expression of
PES1
, a key driver of lateral yeast
in vitro
and that heterologous expression of
PES1
is sufficient to trigger lateral yeast formation
in vivo
.

IMPORTANCE

Candida albicans
filamentation is correlated with virulence and is an intensively studied aspect of
C. albicans
biology. The vast majority of studies on
C. albicans
filamentation are based on
in vitro
induction of hyphae and pseudohyphae. Here we used an
in vivo
filamentation assay and
in vivo
expression profiling to compare the tempo of morphogenesis and gene expression between
in vitro
and
in vivo
filamentation. Although the hyphal gene expression profile is induced rapidly in both conditions, it remains stably expressed over a 12-h time course
in vivo
while it peaks after 4 h
in vitro
and is reduced. This reduced hyphal gene expression
in vitro
correlates with reduced hyphae and increased hyphae-to-yeast transition. By contrast, there is little evidence of hyphae-to-yeast transition
in vivo
.
Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development
Authors: Xiong Chao , K. Singh Brajesh , Zhu Yong-Guan , Hu Hang-Wei , Li Pei-Pei , Han Yan-Lai , Han Li-Li , Zhang Qin-Bing , Wang Jun-Tao , Liu Si-Yi , Wu Chuan-Fa , Ge An-Hui , Zhang Li-Mei , He Ji-Zheng 
Published: March 2024

ABSTRACT

Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil–plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with
Methylobacterium
,
Azospirillum
,
Bradyrhizobium
, and
Rhizobium
. Furthermore, eight dominant taxa belonging to
Azospirillum
and
Methylobacterium
were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to
Pseudomonas mendocina
. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.

IMPORTANCE
Plants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.
The European livestock resistome
Authors: Munk Patrick , Yang Dongsheng , Röder Timo , Maier Leonie , Petersen Thomas Nordahl , Duarte Ana Sofia Ribeiro , Clausen Philip T. L. C. , Brinch Christian , Van Gompel Liese , Luiken Roosmarijn , Wagenaar Jaap A. , Schmitt Heike , Heederik Dick J. J. , Mevius Dik J. , Smit Lidwien A. M. ,   EFFORT Consortium, Bossers Alex , Aarestrup Frank M. , Graveland Haitske , Gonzalez-Zorn Bruno , Moyano Gabriel , Sanders Pascal , Chauvin Claire , Battisti Antonio , Dewulf Jeroen , Wadepohl Katharina , Wasyl Dariusz , Skarzyńska Magdalena , Zajac Magdalena , Pękala-Safińska Agnieszka , Daskalov Hristo , Stärk Katharina D. C. 
Published: March 2024

ABSTRACT

Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter. The resistomes of veal calves and pigs clustered together, as did those of avian origin, while the rainbow trout resistome was different. Moreover, we identified clear core resistomes for each specific food-producing animal species. We identified positive associations between bacterial alpha diversity and both resistome alpha diversity and abundance. Network analyses revealed very few taxa–ARG associations in pigs but a large number for the avian species. Using updated reference databases and optimized bioinformatics, previously reported significant associations between AMU, biosecurity, and AMR in pig and poultry farms were validated. AMU is an important driver for AMR; however, our integrated analyses suggest that factors contributing to increased bacterial diversity might also be associated with higher AMR load. We also found that dispersal limitations of ARGs are shaping livestock resistomes, and future efforts to fight AMR should continue to emphasize biosecurity measures.

IMPORTANCE
Understanding the occurrence, diversity, and drivers for antimicrobial resistance (AMR) is important to focus future control efforts. So far, almost all attempts to limit AMR in livestock have addressed antimicrobial consumption. We here performed an integrated analysis of the resistomes of five important farmed animal populations across Europe finding that the resistome and AMR levels are also shaped by factors related to bacterial diversity, as well as dispersal limitations. Thus, future studies and interventions aimed at reducing AMR should not only address antimicrobial usage but also consider other epidemiological and ecological factors.
A quorum-sensing regulatory cascade for siderophore-mediated iron homeostasis in
Chromobacterium violaceum
Authors: Batista Bianca B. , de Lima Vinicius M. , Picinato Beatriz A. , Koide Tie , da Silva Neto José F. 
Published: March 2024

ABSTRACT

Iron is a transition metal used as a cofactor in many biochemical reactions. In bacteria, iron homeostasis involves Fur-mediated de-repression of iron uptake systems, such as the iron-chelating compounds siderophores. In this work, we identified and characterized novel regulatory systems that control siderophores in the environmental opportunistic pathogen
Chromobacterium violaceum
. Screening of a 10,000-transposon mutant library for siderophore halos identified seven possible regulatory systems involved in siderophore-mediated iron homeostasis in
C. violaceum
. Further characterization revealed a regulatory cascade that controls siderophores involving the transcription factor VitR acting upstream of the quorum-sensing (QS) system CviIR. Mutation of the regulator VitR led to an increase in siderophore halos, and a decrease in biofilm, violacein, and protease production. We determined that these effects occurred due to VitR-dependent de-repression of
vioS
. Increased VioS leads to direct inhibition of the CviR regulator by protein-protein interaction. Indeed, insertion mutations in
cviR
and null mutations of
cviI
and
cviR
led to an increase of siderophore halos. RNA-seq of the
cviI
and
cviR
mutants revealed that CviR regulates CviI-dependent and CviI-independent regulons. Classical QS-dependent processes (violacein, proteases, and antibiotics) were activated at high cell density by both CviI and CviR. However, genes related to iron homeostasis and many other processes were regulated by CviR but not CviI, suggesting that CviR acts without its canonical CviI autoinducer. Our data revealed a complex regulatory cascade involving QS that controls siderophore-mediated iron homeostasis in
C. violaceum
.

IMPORTANCE

The iron-chelating compounds siderophores play a major role in bacterial iron acquisition. Here, we employed a genetic screen to identify novel siderophore regulatory systems in
Chromobacterium violaceum
, an opportunistic human pathogen. Many mutants with increased siderophore halos had transposon insertions in genes encoding transcription factors, including a novel regulator called VitR, and CviR, the regulator of the quorum-sensing (QS) system CviIR. We found that VitR is upstream in the pathway and acts as a dedicated repressor of
vioS
, which encodes a direct CviR-inhibitory protein. Indeed, all QS-related phenotypes of a
vitR
mutant were rescued in a
vitRvioS
mutant. At high cell density, CviIR activated classical QS-dependent processes (violacein, proteases, and antibiotics production). However, genes related to iron homeostasis and type-III and type-VI secretion systems were regulated by CviR in a CviI- or cell density-independent manner. Our data unveil a complex regulatory cascade integrating QS and siderophores in
C. violaceum
.
Involvement of a putative acyltransferase gene in sporangium formation in
Actinoplanes missouriensis
Authors: Hu Shixuan , Maeda Satoshi , Tezuka Takeaki , Ohnishi Yasuo 
Published: March 2024

ABSTRACT

The actinomycete
Actinoplanes missouriensis
forms branched substrate mycelia during vegetative growth and produces terminal sporangia, each of which contains a few hundred spherical flagellated spores, from the substrate mycelia through short sporangiophores. Based on the observation that remodeling of membrane lipid composition is involved in the morphological development of
Streptomyces coelicolor
A3(2), we hypothesized that remodeling of membrane lipid composition is also involved in sporangium formation in
A. missouriensis
. Because some acyltransferases are presumably involved in the remodeling of membrane lipid composition, we disrupted each of the 22 genes annotated as encoding putative acyltransferases in the
A. missouriensis
genome and evaluated their effects on sporangium formation. The
atsA
(
AMIS_52390
) null mutant (Δ
atsA
) strain formed irregular sporangia of various sizes. Transmission electron microscopy revealed that some Δ
atsA
sporangiospores did not mature properly. Phase-contrast microscopy revealed that sporangium dehiscence did not proceed properly in the abnormally small sporangia of the Δ
atsA
strain, whereas apparently normal sporangia opened to release the spores. Consistently, the number of spores released from Δ
atsA
sporangia was lower than that released from wild-type sporangia. These phenotypic changes were recovered by introducing
atsA
with its own promoter into the Δ
atsA
strain. These results demonstrate that AtsA is required for normal sporangium formation in
A. missouriensis
, although the involvement of AtsA in the remodeling of membrane lipid composition is unlikely because AtsA is an acyltransferase_3 (AT3) protein, which is an integral membrane protein that usually catalyzes the acetylation of cell surface structures.

IMPORTANCE

Actinoplanes missouriensis
goes through a life cycle involving complex morphological development, including mycelial growth, sporangium formation and dehiscence, swimming as zoospores, and germination to mycelial growth. In this study, we carried out a comprehensive gene disruption experiment of putative acyltransferase genes to search for acyltransferases involved in the morphological differentiation of
A. missouriensis
. We revealed that a stand-alone acyltransferase_3 domain-containing protein, named AtsA, is required for normal sporangium formation. Although the molecular mechanism of AtsA in sporangium formation, as well as the enzymatic activity of AtsA, remains to be elucidated, the identification of a putative acyltransferase involved in sporangium formation is significant in the study of morphological development of
A. missouriensis
. This finding will contribute to our understanding of a complex system for producing sporangia, a rare multicellular organism in bacteria.
Progress towards health equity in Vietnam: evidence from nationwide official health statistics, 2010-2020
Authors: Feng Yikai , Tuan Tran Diep , Shi Junyi , Li Zhuo , Maimaitiming Mailikezhati , Jin Yinzi , Zheng Zhijie 
Published: March 2024

IntroductionOne of the ultimate goals of strengthening the health system is to achieve health equity. Vietnam is considered one of the ‘fast-track countries’ to achieve the health-related Millennium Development Goals, but research on its equity strategies remains inadequate.MethodsUsing Vietnamese official health statistics, we investigated inequity in four dimensions including health resources, service delivery, service utilisation and residents’ health status from the perspectives of income levels, poverty rates and subnational regions. The Slope Index of Inequality, concentration curve/Concentration Index, absolute difference and Theil Index were used.ResultsFour indicators showed ‘pro-poor’ inequality in health resources, including the per capita health budget, per capita health personnel, per capita health personnel at the community level and per capita hospital beds at the community level, while provincial hospital beds showed ‘pro-rich’ inequality. Two health service delivery indicators (delivery of antenatal care ≥3 times and proportion of community health service centres with medical doctors) show ‘pro-rich’ inequality, although two health status indicators, mortality and malnutrition rates for children under five, showed ‘pro-poor’ inequality. The Northern Midlands and Mountain Areas, and the Central Highlands were disadvantaged regarding service delivery and health status. Intraregional differences were the main factors contributing to the inequalities in delivery of antenatal care ≥3 times, provincial hospital beds and percentage of community health centres with medical doctors, with the Red River Delta and the South East region experiencing the greatest inequalities.ConclusionThe overall level of health equity in Vietnam has increased over the past decade, although inequality in health service delivery has hindered progress towards health equity based on income, poverty and subnational regions. Targeted policies need to be introduced to reduce inequities relating to the health workforce and service delivery capacity.