bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative evaluation of Sensititre YeastOne and CLSI M38-Ed3 reference method for determining echinocandin minimum effective concentrations against
Aspergillus
isolates
Authors: Potruch Assaf , Elinav Hila , Cohen Matan J. , Rouvinski Alexander , Polacheck Itzhack , Korem Maya 
Published: August 2024

ABSTRACT

The minimum inhibitory concentration (MIC) of echinocandins against
Aspergillus
spp. does not represent the actual inhibition threshold of echinocandins. Therefore, the recommended method to evaluate their activity is determining the minimum effective concentration (MEC) in broth microdilution, a method that is less common in clinical settings. This study aimed to assess a user-friendly commercial method, Sensititre YeastOne (SYO), to determine the effectiveness of echinocandins (caspofungin, anidulafungin and micafungin) against
Aspergillus
spp. Echinocandins MEC was determined against 23 isolates of
Aspergillus
spp. using SYO and the reference Clinical and Laboratory Standards Institute (CLSI) method. MECs were read with an inverted microscope and a reading mirror. Essential agreement (EA) between the tested methods was defined as a ±twofold dilution difference. There was a high EA (91%–100%) between the reference method and SYO in determining echinocandins MEC against
Aspergillus
isolates using inverted microscopy. A high EA was also observed between SYO MEC determined by inverted microscopy and a reading mirror, but different incubation times were required. SYO is a reliable, simple method for determining the MEC of echinocandins against
Aspergillus
isolates, preferably with an inverted microscope, and can be easily used in clinical laboratories when echinocandin susceptibility testing is required.

IMPORTANCE

Using a commercial method such as Sensititre YeastOne (SYO) to determine the minimum effective concentration (MEC) of echinocandins against
Aspergillus
spp. has been shown to be a reliable alternative to the Clinical and Laboratory Standards Institute (CLSI) reference method. This makes it more suitable for high-volume clinical laboratories. SYO provides accurate results comparable to the standard method and could potentially improve patient care by guiding more optimal antifungal treatment choices for patients with
Aspergillus
infections.
Genomic and pathogenicity analysis of two novel highly pathogenic recombinant NADC30-like PRRSV strains in China, in 2023
Authors: Chang Hao , Gao Xiaopeng , Wu Yu , Wang Fang , Lai Minting , Zheng Jiaying , Qiu Yingwu , He Yiping , Liang Xiangjie , Yuan Kun , Lin Limiao , Zhao Haishen , Zhang Guihong , Li Qunhui , Sun Yankuo 
Published: August 2024

ABSTRACT

Porcine reproductive and respiratory syndrome viruses (PRRSVs) exhibit high mutability and recombination, posing challenges to their immunization and control. This study isolated two new PRRSV strains, GD-7 and GX-3, from samples collected in Guangdong and Guangxi in 2023. Whole-genome sequencing, along with phylogenetic and recombination analyses, confirmed that GD-7 and GX-3 are natural novel recombinant strains of NADC30 PRRSV. Moreover, we established a pathogenicity model for piglets and sows based on the two isolates. The results of piglet pathogenicity revealed that both GD-7 and GX-3 caused clinical symptoms such as fever, loss of appetite, depression, and slow weight gain. Moreover, we observed that the mortality rate of GD-7-inoculated group piglets was 33.3%, which was similar to that of piglets infected with other highly pathogenic PRRSV strains and exceeded the mortality rate of most NADC30-like PRRSV. In pregnant sow models, the survival rate of sows in the GD-7 group was 75%, in contrast to the GX-3 group, where no sow mortality was observed, and both strains resulted in abortion, mummified fetuses, and stillbirths. These results highlight the elevated pathogenicity of these recombinant strains in sows, with GD-7 mainly causing sows to abort, and GX-3 mainly causing sows to give birth to mummified fetuses. This study introduces two distinct clinical recombinant PRRSV strains that differ from the prevalent strains in China. This research furthers our understanding of the epidemiology of PRRSV and underscores the significance of ongoing monitoring and research in the face of evolving virus strains. Moreover, these discoveries act as early warnings, underscoring the necessity for active control and immunization against PRRSV.

IMPORTANCE
Since the discovery of NADC30-like PRRSV in China in 2013, it has gradually become the dominant strain of PRRSV in China. NADC30-like PRRSV exhibits high recombination characteristics, constantly recombining with different strains, leading to the emergence of numerous novel strains. Of particular importance is the observation that NADC30-like PRRSV with different recombination patterns exhibits varying pathogenicity, which has a significant impact on the pig farming industry. This emphasizes the necessity of monitoring and responding to evolving PRRSV strains to develop effective immunization and control strategies. In this paper, we conducted pathogenicity studies on the isolated NADC30-like PRRSV and analyzed the differences in the genomes and pathogenicity of the different strains by recording clinical symptoms, temperature changes, detoxification tests, and changes in viremia and histopathology in infected pigs. This was done to provide a theoretical basis for the epidemiological situation and epidemic prevention and control of PRRSV.
A novel clinically relevant human fecal microbial transplantation model in humanized mice
Authors: Yang Shuai , Tong Linglin , Li Xin , Zhang Yuchen , Chen Hao , Zhang Wei , Zhang He , Chen Yang , Chen Renjin 
Published: August 2024

ABSTRACT

The intact immune system of mice exhibits resistance to colonization by exogenous microorganisms, but the gut microbiota profiles of the humanized mice and the patterns of human fecal microbiota colonization remain unexplored. Humanized NCG (huNCG) mice were constructed by injected CD34 +stem cells. 16S rRNA sequencing and fecal microbiota transplantation (FMT) technologies were used to detect the differences in microbiota and selective colonization ability for exogenous community colonization among three mice cohorts (C57BL/6J, NCG, and huNCG). Flow cytometry analysis showed that all huNCG mice had over 25% hCD45 +in peripheral blood. 16S rRNA gene sequence analysis showed that compared with NCG mice, the gut microbiota of huNCG mice were significantly altered. After FMT, the principal coordinates analysis (PCoA) showed that the gut microbial composition of huNCG mice (huNCG-D9) was similar to that of donors. The relative abundance of Firmicutes and Bacteroidetes were significantly increased in huNCG mice compared to NCG mice. Further comparison of ASV sequences revealed that
Bacteroides plebeius
,
Bacteroides finegoldii
,
Escherichia fergusonii
,
Escherichia albertii
,
Klebsiella pneumoniae,
and
Klebsiella variicola
exhibited higher abundance and stability in huNCG mice after FMT. Furthermore, PICRUSt2 analysis showed that huNCG mice had significantly enhanced metabolism and immunity. This study demonstrated that humanized mice are more conducive to colonization within the human gut microbiota, which provides a good method for studying the association between human diseases and microbiota.

IMPORTANCE
The gut microbiota and biomarkers of humanized mice are systematically revealed for the first time. The finding that human fecal microbiota colonize humanized mice more stably provides new insights into the study of interactions between immune responses and gut microbiota.
Transgressive phenotypes from outbreeding between the
Trichoderma reesei
hyper producer RutC30 and a natural isolate
Authors: Chan Ho Tong Laetitia , Jourdier Etienne , Naquin Delphine , Ben Chaabane Fadhel , Aouam Thiziri , Chartier Gwladys , Castro González Itzel , Margeot Antoine , Bidard Frederique 
Published: August 2024

ABSTRACT

Trichoderma reesei,
the main filamentous fungus used for industrial cellulase production, was long considered to be asexual. The recent discovery of the mating type locus in the natural isolate QM6a and the possibility to cross this sterile female strain with a fertile natural female strain opened up a new avenue for strain optimization. We crossed the hyperproducer RutC30 with a compatible female ascospore-derived isolate of the wild-type strain CBS999.97 and analyzed about 300 offspring. A continuous distribution of secreted protein levels was observed in the progeny, confirming the involvement of several mutated loci in the hyperproductive phenotype. A bias toward
MAT1-2
strains was identified for higher producers, but not directly linked to the Mating-type locus itself. Transgressive phenotypes were observed in terms of both productivity and secretome quality, with offspring that outperform their parents for three enzymatic activities. Genomic sequences of the 10 best producers highlighted the genetic diversity generated and the involvement of parental alleles in hyperproduction and fertility.

IMPORTANCE

The filamentous fungus
Trichoderma reesei
produces cellulolytic enzymes that are essential for the hydrolysis of lignocellulosic biomass into monomerics sugars. The filamentous fungus
T. reesei
produces cellulolytic enzymes that are essential for the hydrolysis of lignocellulosic biomass into monomerics sugars, which can in turn be fermented to produce second-generation biofuels and bioproducts. Production performance improvement, which is essential to reduce production cost, relies on classical mutagenesis and genetic engineering techniques. Although sexual reproduction is a powerful tool for improving domesticated species, it is often difficult to apply to industrial fungi since most of them are considered asexual. In this study, we demonstrated that outbreeding is an efficient strategy to optimize
T. reesei
. Crossing between a natural isolate and a mutagenized strain generated a biodiverse progeny with some offspring displaying transgressive phenotype for cellulase activities.
Hanensula anomala
isolated from the Berkeley Pit, Butte, MT, is a metal-specific extremophile
Authors: Roessler Kyle , Friedlander Mariah C. , VanSickle Marthe Y. , Rush Christina L. 
Published: August 2024

ABSTRACT

A yeast-like extremophile organism,
Hansenula anomala
, has been isolated from the superfund site the Berkeley Pit Lake in Butte, Montana. Studies demonstrate
H. anomala
growth in some of the known Berkeley Pit Lake solutes. Microbial growth dynamics under controlled conditions were compared of
H. anomala
for multiple metal concentrations. Each solute/metal was tested separately at previously reported concentrations on the geochemistry of the Berkeley Pit lake in the first 0.2 m in spring (pH 2.5).
H. anomala
grew well with sulfur (S), MgSO
4
, CaSO
4
, potassium chloride (KCl), and NaSO
4
and was inhibited with FeSO
4
, MnSO
4
, CuSO
4
, AlSO
4
, or ZnSO
4
. With the addition of elemental S, growth was observed for FeSO
4
indicating minimal growth rescue. PCR amplification of genomic DNA from the organism using known ribosomal primers indicates the strain to be ATCC8168 (CBS 5759). From this data, it can be concluded that
H. anomala
ATCC8168 from the Berkeley Pit is an extremophile that exhibits metal-specific growth.

IMPORTANCE

Laboratory growth studies of a strain of
Hansenula anomala
from the Berkeley Pit have found the organism to be metal specific indicating some unique metabolism possibilities. These studies show that this strain is metal-dependent and provides information about the adaptable tolerance of organisms in superfund sites as well as giving a basis for future bioremediation development utilizing
H. anomala
.
Molecular investigation of
Treponema pallidum
strains associated with ocular syphilis in the United States, 2016–2020
Authors: Pillay Allan , Vilfort Kendra , Debra Alyssa , Katz Samantha S. , Thurlow Charles M. , Joseph Sandeep J. , Lundy Stephanie , Ji Andrew , Jaeyoung Hong , Workowski Kimberly A. , Barrow Roxanne Y. , Danavall Damien , Pettus Kevin , Chi Kai-Hua , Kersh Ellen N. , Cao Weiping , Chen Cheng Y. ,   OS Surveillance Working Group
Published: August 2024

ABSTRACT

Ocular syphilis is a serious complication of
Treponema pallidum
infection that can occur at any stage of syphilis and affect any eye structure. It remains unknown if certain
T. pallidum
strains are associated with ocular infections; therefore, we performed genotyping and whole genome sequencing (WGS) to characterize strains from patients with ocular syphilis. Seventy-five ocular or non-ocular specimens from 55 ocular syphilis patients in 14 states within the United States were collected between February 2016 and November 2020. Sufficient
T. pallidum
DNA was available from nine patients for genotyping and three for WGS. Genotyping was done using the augmented Centers for Disease Control and Prevention typing scheme, and WGS was performed on Illumina platforms. Multilocus sequence typing allelic profiles were predicted from whole genome sequence data.
T. pallidum
DNA was detected in various specimens from 17 (30.9%) of the 55 patients, and typing was done on samples from 9 patients. Four complete strain types (14d10/g, 14b9/g, 14d9/g, and 14e9/f) and five partial types were identified. WGS was successful on samples from three patients and all three strains belonged to the SS14 clade of
T. pallidum
. Our data reveal that multiple strain types are associated with ocular manifestations of syphilis. While genotyping and WGS were challenging due to low amounts of
T. pallidum
DNA in specimens, we successfully performed WGS on cerebrospinal fluid, vitreous fluid, and whole blood.

IMPORTANCE

Syphilis is caused by the spirochete
Treponema pallidum
. Total syphilis rates have increased significantly over the past two decades in the United States, and the disease remains a public health concern. In addition, ocular syphilis cases has also been on the rise, coinciding with the overall increase in syphilis rates. We conducted a molecular investigation utilizing traditional genotyping and whole genome sequencing over a 5-year period to ascertain if specific
T. pallidum
strains are associated with ocular syphilis. Genotyping and phylogenetic analysis show that multiple
T. pallidum
strain types are associated with ocular syphilis in the United States.
Development of an inducer-free, virulence gene promoter-controlled, and fluorescent reporter-labeled CRISPR interference system in
Staphylococcus aureus
Authors: Miah Roni , Johannessen Mona , Kjos Morten , Lentz Christian S. 
Published: August 2024

ABSTRACT

The dCas9-based Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) interference (CRISPRi) gene regulation technique requires two components: a catalytically inactive Cas9 protein (dCas9) and a single-guide RNA that targets the gene of interest. This system is commonly activated by expressing dCas9 through an inducible gene promoter, but these inducers may affect cellular physiology, and accessibility and permeability of the inducer are limited in relevant model systems. Here, we have developed an alternative approach for CRISPRi activation in the clinical isolate
Staphylococcus aureus
USA300 LAC, where dCas9 was expressed through endogenous virulence gene promoters (vgp); coagulase, autolysin, or fibronectin-binding protein A. Additionally, we integrated a fluorescent reporter gene into the vgp-CRISPRi system to monitor the activity of the
dcas9
-controlling promoter. Testing the efficacy of vgp-CRISPRi by inducing growth arrest (when targeting penicillin-binding protein 1), downregulating target gene expression, or blocking coagulase-dependent coagulation of blood plasma, we provide a proof-of-concept demonstration that the virulence gene promoter-driven CRISPRi system is functional in
S. aureus
.

IMPORTANCE
The presented inducer-free, endogenous virulence gene promoter-induced, dCas9-based Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) interference (CRISPRi system addresses several shortcomings related to the use of inducer-dependent systems such as effects on cell physiology or limitations in permeability, and it avoids the high, putatively toxic levels of dCas9 in CRISPRi systems controlled by strong, constitutive promoters.
Identification and genomic analysis of a thermophilic bacterial strain that reduces ammonia loss from composting
Authors: Chen Xuejuan , Feng Rong , Du Qianhui , Mauchline Tim H. , Clark Ian M. , Lu Yingang , Liu Li 
Published: August 2024

ABSTRACT

Ammonia loss is the most severe during the high-temperature stage (>50°C) of aerobic composting. Regulating ammonia volatilization during this period via thermophilic microbes can significantly improve the nitrogen content of compost and reduce air pollution due to ammonia loss. In this study, an ammonia-assimilating bacterial strain named LL-8 was screened out as having the strongest ammonia nitrogen conversion rate (32.7%) at high temperatures (50°C); it is able to significantly reduce 42.9% ammonia volatile loss in chicken manure composting when applied at a high-temperature stage. Phylogenetic analysis revealed that LL-8 was highly similar (>98%) with
Priestia aryabhattai
B8W22
T
and identified as
Priestia aryabhatta
. Genomic analyses indicated that the complete genome of LL-8 comprised 5,060,316 base pairs with a GC content of 32.7% and encoded 5,346 genes. Genes, such as
gudB
,
rocG
,
glnA
,
gltA
, and
gltB
, that enable bacteria to assimilate ammonium nitrogen were annotated in the LL-8 genome based on the comparison to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The results implied that the application of thermophilic ammonia-assimilating strain
P. aryabhatta
LL-8 would be a promising solution to reduce ammonia loss and mitigate air pollution of aerobic composting.

IMPORTANCE
Aerobic composting is one of the essential ways to recycle organic waste, but its ammonia volatilization is severe and results in significant nitrogen loss, especially during the high-temperature period, which is also harmful to the environment. The application of thermophilic bacteria that can use ammonia as a nitrogen source at high temperatures is helpful to reduce the ammonia volatilization loss of composting. In this study, we screened and identified a bacteria strain called LL-8 with high temperature (50°C) resistance and strong ammonia-assimilating ability. It also revealed significant effects on decreasing ammonia volatile loss in composting. The whole-genome analysis revealed that LL-8 could utilize ammonium nitrogen by assimilation to decrease ammonia volatilization. Our work provides a theoretical basis for the application of this functional bacteria in aerobic composting to control nitrogen loss from ammonia volatilization.
Dynamic distribution of gut microbiota-metabolites during post-weaning longissimus dorsi muscle development in Ningxiang pigs
Authors: Su Jiayi , Li Jinxuan , Azad Md. Abul Kalam , Wang Wenliang , Luo Zhili , Wang Jing , Yin Jie , Yin Yulong , Tan Bie , Chen Jiashun 
Published: August 2024

ABSTRACT

Ningxiang pigs (NXPs) have a strong ability to deposit fat and intramuscular fat (IMF). However, microbiota-metabolite development and the role in IMF deposition have been rarely reported. Here, we compared the gut microbiota and metabolite profiles and IMF content at 30, 70, 150, 200, and 250 days of age of NXPs. The results revealed that the IMF content in NXPs increased significantly (
P
< 0.05) as the pigs’ age extended. Additionally, the C14:0 content in the longissimus dorsi muscle at 30 and 70 days of age was significantly lower (
P
< 0.05) than that at 150 and 200 days of age. The Shannon index and ACE index showed a pattern of initially increasing and then decreasing. LEfSe analysis revealed that 41 differential bacteria at the genus level were specific to different growth stages, indicating the dominant bacteria’s dynamic changes in the NXPs during different stages of age. Furthermore, we found that there were significant differences in cecal metabolism, the classification of differential metabolites revealed that 15.61% of compounds were fatty acyls, 13.98% were prenol lipids, and 10.57% were steroids and steroid derivatives. Next, the network analysis showed that
Lachnospiraceae-XPB1014-group
was positively related to 4-2-Aminophenyl-2-4-dioxobutanoic-acid, (Z)-3-Octene, 5-Methyl-furaldehyde, Propyl-2-4-decadienoate, which were also positively correlated with the IMF content. Our findings illustrated the dynamic distribution of cecal microbiota and metabolite composition at different growth stages in NXPs and their correlation with IMF deposition. These results provide a valuable insight into optimizing meat quality and overall health in post-weaning NXPs, providing a foundation for enhancement in pork product.

IMPORTANCE
Understanding the dynamic interplay between gut microbiota, metabolites, and intramuscular fat (IMF) deposition in pigs at various growth stages holds significant importance for the pork industry. This research sheds light on how the composition of gut microbiota and metabolites changes throughout the developmental stages of pigs, impacting IMF content in meat. By identifying specific bacterial genera and metabolites associated with IMF deposition, this study offers valuable insights for optimizing meat quality and health in post-weaning pigs. Such knowledge could lead to targeted interventions or management strategies aimed at enhancing pork product quality and overall profitability for producers. Ultimately, this research contributes to advancing our understanding of the complex relationship between gut microbiota, metabolites, and meat quality, offering practical implications for the swine industry.