bluuebunny/crossref_metadata_2025 huggingface dataset:
Time spent on active learning activities does not necessarily correlate with student exam performance: a controlled case study
Authors: Cen Xinjian , Lee Rachel J. , Contreras Christopher , Owens Melinda T. , Maloy Jeffrey
Published: August 2024

Active learning, including student thinking and discussion in class, has been shown to increase student learning gains. However, it is less clear how instructor-level variation in the implementation and timing of active learning activities affects student gains. Our study aims to investigate the extent to which the time spent on individual episodes of active learning activities influences student performance. We hypothesized that instructors who let students spend more time on peer discussion and individual thinking on practice problems associated with particular learning objectives would have better student exam scores on exam questions addressing those objectives. To test this hypothesis, we obtained a large data set of classroom recordings and student exam scores from an introductory biology course at a large 4-year university, where three instructors shared identical teaching materials and exams for different course offerings. Contrary to our hypothesis, although the three instructors spent significantly different amounts of time on episodes of thinking and peer discussion, there was no correlation between the total time spent on active learning activities and student performance on exam questions. Linear mixed-effects modeling of the effect of the length of episodes of student thinking and discussion on exam score found that in the context of shared instructional materials, the amount of course time spent on active learning activities did not reliably predict student performance on associated exam questions. This result held true even when only considering learning objectives with high variations in performance between offerings, difficult exam questions, or exam questions requiring higher-order thinking skills. Although our study was only conducted in one course, our results imply that time spent per individual episode of student thinking or peer discussion may not be the primary factor explaining the positive effects of active learning and that it may be worthwhile to explore other factors.
Enhancing student engagement with introductory microbiology and immunology topics using a novel board game
Authors: Rivard Rebecca S.
Published: August 2024

In introductory microbiology courses for non-biology majors, it can be difficult to ensure that students gain a functional understanding of the interplay between the host immune system and an invading infectious agent. Immune Battle is a board game that allows students to explore pathogen evolution and the immune system’s response to incursions in a captivating way, leveraging battleship and worker placement styles of gameplay. Students play in teams as either a pathogenic microbe attempting to reproduce and transmit itself to new hosts or as the immune system trying to defend the host from infection. Immune Battle seeks to mimic real-world interactions between immune cells and microbes using board game mechanics. For example, students will quickly find that adaptive immune system actions are better at fighting off microbial incursions than innate immune actions but require more time to activate. In this way, Immune Battle reinforces student’s understanding of the immune system and pathogenic virulence in an exciting and interactive way that keeps them thinking about host defenses long after the end of the class period or exam. This board game is well suited for advanced high school courses and introductory college-level courses that have only limited time to cover the immune system and microbiology. Documents containing the necessary components of the board game (not including a six-sided die) are included in the supplemental materials, so educators can print out their own copies and use this board game in their classes with no cost to themselves or their students.
How students taking introductory biology experience the chemistry content
Authors: Mendez Lilyan , Rivera Angelita T. , Vasquez Izabella , Godínez Aguilar Alfonso , Owens Melinda T. , Meaders Clara L.
Published: August 2024

Student experiences learning chemistry have been well studied in chemistry courses but less so in biology courses. Chemistry concepts are foundational to introductory biology courses, and student experiences learning chemistry concepts may impact their overall course experiences and subsequent student outcomes. In this study, we asked undergraduate students enrolled in introductory biology courses at a public R1 institution an open-response question asking how their experiences learning chemistry topics affected their identities as biologists. We used thematic analysis to identify common ideas in their responses. We found that while almost half of student respondents cited learning chemistry as having positive impacts on their experiences learning biology, students who struggled with chemistry topics were significantly more likely to have negative experiences learning biology. We also found significant relationships between prior chemistry preparation, student background, and the likelihood of students struggling with chemistry and negative experiences learning biology. These findings emphasize the impact of learning specific content on student psychosocial metrics and suggest areas for biology educators to focus on to support learning and alleviate student stress in introductory biology.
Afucosylated anti-EBOV antibody MIL77-3 engages sGP to elicit NK cytotoxicity
Authors: Zhang Yuting , Zhang Min , Wu Haiyan , Wu Xiaonan , Zheng Hang , Feng Junjuan , Wang Mianjing , Wang Jing , Luo Longlong , Xiao He , Qiao Chunxia , Li Xinying , Zheng Yuanqiang , Huang Weijin , Wang Youchun , Wang Yi , Feng Jiannan , Chen Guojiang
Published: August 2024

MIL77-3 is one component of antibody cocktail that is produced in our lab and represents an effective regimen for animals suffering from Zaire Ebolavirus (EBOV) infection. MIL77-3 is engineered to increase its affinity for the FcγRIIIa (CD16a) by deleting the fucose in the framework region. The potential effects of this modification on host immune responses, however, remain largely unknown. Herein, we demonstrated that MIL77-3 recognized secreted glycoproptein (sGP), produced by EBOV, and formed the immunocomplex to potently augment antibody-dependent cytotoxicity of human peripheral blood-derived natural killer cells (pNKs), including CD56
dim
and CD56
bright
subpopulations, in contrast to the counterparts (Mab114, rEBOV548, fucosylated MIL77-3). Intriguingly, this effect was not observed when NK92-CD16a cell line was utilized and restored by the addition of beads-coupled or membrane-anchored sGP in combination with MIL77-3. Furthermore, sGP bound to unrecognized receptors on T cells contaminated in pNKs rather than NK92-CD16a cells. Administration of beads-coupled sGP/MIL77-3 complex in mice elicited NK activation. Overall, this work reveals an immune-stimulating function of sGP/MIL77-3 complex by triggering cytotoxic activity of NK cells, highlighting the necessity to evaluate the potential impact of MIL77-3 on host immune reaction in clinical trials.

IMPORTANCE

Zaire Ebolavirus (EBOV) is highly lethal and causes sporadic outbreaks. The passive administration of monoclonal antibodies (mAbs) represents a promising treatment regimen against EBOV. Mounting evidence has shown that the efficacy of a subset of therapeutic mAbs
in vivo
is intimately associated with its capacity to trigger NK activity, supporting glycomodification of Fc region of anti-EBOV mAbs as a putative strategy to enhance Fc-mediated immune effector function as well as protection
in vivo
. Our work here uncovers the potential harmful influence of this modification on host immune responses, especially for mAbs with cross-reactivity to secreted glycoproptein (sGP) (e.g., MIL77-3), and highlights it is necessary to evaluate the NK-stimulating activity of a fucosylated mAb engaged with sGP when a new candidate is developed.
Whole-genome sequencing of three ciprofloxacin-resistant
Salmonella
Reading (ST93) strains, an emerging
Salmonella
serovar in the poultry sector of Pakistan
Authors: Siddique Abubakar , Tauqeer Azka , Ali Amjad , Ahsan Aitezaz , Iqbal Sajid , Patel Ami , Moore Terence , Ganda Erika , Rahman Abdur
Published: August 2024

In this study, we performed whole-genome sequencing of three ciprofloxacin-resistant
Salmonella
Reading strains isolated from poultry meat. Genomes of
S
. Reading strains contained an average of 4.81 Mbp size with 52.1% GC. The isolates exhibited

bla
OXA-10

,
aac
[
6′
]
-Iaa
,
aadA1
,
cmlA1
,
qnrS1
, and
tetA
resistance genes and
IncX1
and
IncX2
plasmids.
Complete genome sequence of
Streptococcus intermedius
strain XH2169
Authors: Zhang Yisha , Yao Yue , Zhao Feng , Yu Yunsong , Hua Xiaoting
Published: August 2024

Here, we report the complete genome sequence of
Streptococcus intermedius
strain XH2169 isolated from a blood sample in China. The genome comprises a single circular chromosome with a length of 1,944,282 bp. It harbored 1,891 coding gene sequences, 16 rRNA genes, 60 tRNA genes, and 3 noncoding RNA genes.
Draft genome sequences of
Klebsiella
spp. isolated from produce and agricultural water in South Korea
Authors: Oh Kwang-Kyo , Cho Gyu-Sung , Franz Charles M. A. P.
Published: August 2024

This report outlines the draft genome sequences of six
Klebsiella
spp. strains from South Korea’s agricultural produce and environments. Genome sizes ranged from 5.25 to 6.21 Mbp with 55.64% to 57.55% GC content. Each strain contained multiple plasmid sequences identified by PlasmidFinder, indicating significant antimicrobial resistance.
Complete genome sequence of
Pigmentibacter ruber
isolated from a human patient in Japan
Authors: Hayashi Masahiro , Niwa Ayumi , Yonetamari Jun , Muto Yoshinori , Yokoyama Sodai , Nakamura Motohiro , Yokobori Yuta , Ogawa Mizuki , Ichioka Rina , Kikuchi Ryosuke , Okura Hiroyuki , Ogura Shinji , Tetsuka Nobuyuki , Baba Hisashi , Tanaka Kaori
Published: August 2024

Pigmentibacter ruber
is a newly described bacterium belonging to the Silvanigrellaceae family that was isolated from human blood in 2021. We report the complete genome sequence of a clinical isolate of
P. ruber
(GTC16762) obtained from a human patient in Japan. Its genome contains a 3.6-Mb chromosome and three circular plasmids.
Draft genome sequence of two
Fusobacterium varium
strains isolated from patients in Kazakhstan with colorectal cancer
Authors: Kurentay Botakoz , Gusmaulemova Alua , Utupov Talgat , Auganova Dana , Tarlykov Pavel , Daniyarov Asset , Khamzina Saule , Mamlin Meiram , Kozhakhmetov Arman , Shalekenov Sanzhar , Kulmambetova Gulmira
Published: August 2024

Fusobacterium varium
is a Gram-negative, invasive, obligate anaerobe in the gastrointestinal tract microbiota, associated with various clinical conditions, including colorectal cancer (CRC). Here, we announce the draft genome sequence of two
F. varium
strains Fv36kaz and Fv63kaz from patients with CRC in Kazakhstan.
Draft genome sequence of
Amyloporia xantha
strain YAFMF0618, isolated from Gaoligong Mountain
Authors: Zhao Xiaolei , Yuan Xiaolong , Yin Yihang , Yu Jiaojun , Zheng Yuan , Wang Yi
Published: August 2024

The
Amyloporia
genus is an important Chinese medicinal fungus. Here, we present a draft genome sequence of
Amyloporia xantha
strain YAFMF0618. The genome resource will support subsequent research into the potential secondary metabolite diversity of
A. xantha
.
Genome sequences of
Clostridium perfringens
isolated from diseased dogs
Authors: Sekse Camilla , Solsvik Helene K. , Haverkamp Thomas H. A. , Kaspersen Håkon , Gulliksen Wenche S. , Campos Sabrina R. , Nørstebø Simen F. , Bøe Cathrine A.
Published: August 2024

Two
Clostridium perfringens
isolates originating from two Norwegian dogs with acute hemorrhagic diarrhea were sequenced. Based on Illumina and Oxford Nanopore Technology sequencing, hybrid assemblies were generated, and one of the genomes was completed and closed. For both isolates, virulence genes and their genomic location have been identified.
Detection of mobile colistin resistance genes
mcr-9.1
and
mcr-10.1
in
Enterobacter asburiae
from Ecuadorian children
Authors: Cifuentes Sara G. , Graham Jay , Trueba Gabriel , Cádenas Paúl A.
Published: August 2024

Colistin is one of the last-line treatments for multi-drug resistant Gram-negative bacterial infections. The emergence of mobile colistin resistance genes has driven global concern and triggered the need for surveillance. Our report reveals the identification of
mcr-9.1
and
mcr-10.1
in Ecuador by employing a proximity ligation technique.
Complete genome sequence of the OXA-48-producing
Klebsiella pneumoniae
strain 11978
Authors: Raro Otávio Hallal Ferreira , Nordmann Patrice , Poirel Laurent
Published: August 2024

We announce the complete genome sequence of
Klebsiella pneumoniae
strain 11978 isolated from a patient hospitalized in Turkey in 2001. The genome belongs to sequence type 14 and includes three plasmids. Notably, it presents an IncL plasmid carrying
bla
OXA-48
, which demonstrated global success in terms of dissemination.
Complete genome sequence of a
Salimicrobium
sp. PL1-032A isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia
Authors: Young Crystal E. , Alattas Hussain , Scott Colin , Murphy Daniel V. , Tiwari Ravi , Reeve Wayne G.
Published: August 2024

Salimicrobium
sp. PL1-032A was isolated from Pearse Lakes, Western Australia. The sequenced genome consists of a single chromosome (2,705,688  bp) with a GC content of 47.2%. The isolation of
Salimicrobium
sp. PL1-032A contributes to the collection of culturable extremophiles and offers potential insight into the Pearse Lakes biome.
Whole-genome sequencing of
Enterococcus faecalis
probiotic strains isolated from raw milk of healthy cows
Authors: Rahman Md. Morshedur , Siddique Naim , Rahman ANM Aminoor , Das Ziban Chandra , Islam Tofazzal , Hoque M. Nazmul
Published: August 2024

We report the draft genomes of two
Enterococcus faecalis
strains MBBL1 and MBBL2, isolated from raw milk of healthy cows. The genome of MBBL1 is 2,681,695 bp with 57.41× coverage, and MBBL2 is 2,681,119 bp with 99.81× coverage, spanned across 14 and 13 contigs, respectively.
Draft genome for
Flavobacterium psychrophilum
isolates from diseased coho salmon (
Oncorhynchus kisutch
) in Chile
Authors: Avendaño-Herrera Ruben , Saldarriaga-Córdoba Mónica , Ilardi Pedro
Published: August 2024

We present the draft genome sequences of six
Flavobacterium psychrophilum
isolates recovered from diseased coho salmon (
Oncorhynchus kisutch
) cultured by two farms in Chile. This study provides the first detailed insights into the genomic characteristics of this fish pathogen recovered from a host with limited information and cultured in Chile.
Report of SARS-CoV-2 JN.1 variant in Morocco
Authors: Bouddahab Oumaima , El Hamouchi Adil , Aqillouch Safaa , Charoute Hicham , Noureddine Rachid , Aainouss Achraf , Baba Hanâ , Ouladlahsen Ahd , Nourlil Jalal , Sarih M'hammed , Maaroufi Abderrahmane , Lkhider Mustapha , Barakat Abdelhamid , Ezzikouri Sayeh
Published: August 2024

In this study, we report the identification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) JN.1 variant and the quasi-complete genomic sequencing of four clinical samples in Morocco. Nasopharyngeal swabs were obtained from four patients (one female, three males). The Illumina COVIDSeq Test was used for comprehensive genomic analysis.
Complete genomic sequence of a
Marinobacter
species, a potential polyethylene degrader isolated from surface seawater
Authors: Iizuka Ryo , Uemura Sotaro
Published: August 2024

The bacterium
Marinobacter
sp. RI1 was isolated from surface seawater through an enrichment culture using low-density polyethylene as the sole carbon source. Herein, we report its complete genomic sequence. Genomic annotation revealed that the strain harbors the genes encoding enzymes involved in alkane degradation, thus supporting polyethylene degradation.
Mapping disparities in viral infection rates using highly multiplexed serology
Authors: Piña Alejandra , Elko Evan A. , Caballero Rachel , Metrailer Morgan , Mulrow Mary , Quan Dan , Nordstrom Lora , Altin John A. , Ladner Jason T.
Published: August 2024

Despite advancements in medical interventions, the disease burden caused by viral pathogens remains large and highly diverse. This burden includes the wide range of signs and symptoms associated with active viral replication as well as a variety of clinical sequelae of infection. Moreover, there is growing evidence supporting the existence of sex- and ethnicity-based health disparities linked to viral infections and their associated diseases. Despite several well-documented disparities in viral infection rates, our current understanding of virus-associated health disparities remains incomplete. This knowledge gap can be attributed, in part, to limitations of the most commonly used viral detection methodologies, which lack the breadth needed to characterize exposures across the entire virome. Additionally, virus-related health disparities are dynamic and often differ considerably through space and time. In this study, we utilize PepSeq, an approach for highly multiplexed serology, to broadly assess an individual’s history of viral exposures, and we demonstrate the effectiveness of this approach for detecting infection disparities through a pilot study of 400 adults aged 30–60 in Phoenix, AZ. Using a human virome PepSeq library, we observed expected seroprevalence rates for several common viruses and detected both expected and previously undocumented differences in inferred rates of infection between our male/female and Hispanic/non-Hispanic White individuals.

IMPORTANCE

Our understanding of population-level virus infection rates and associated health disparities is incomplete. In part, this is because of the high diversity of human-infecting viruses and the limited breadth and sensitivity of traditional approaches for detecting infection events. Here, we demonstrate the potential for modern, highly multiplexed antibody detection methods to greatly increase our understanding of disparities in rates of infection across subpopulations (e.g., different sexes or ethnic groups). The use of antibodies as biomarkers allows us to detect evidence of past infections over an extended period, and our approach for highly multiplexed serology (PepSeq) allows us to measure antibody responses against hundreds of viruses in an efficient and cost-effective manner.
Cultivation in long-term simulated microgravity is detrimental to pyocyanin production and subsequent biofilm formation ability of
Pseudomonas aeruginosa
Authors: Chen Kenny Zhi Ming , Vu Linda My , Vollmer Amy Cheng
Published: August 2024

Pseudomonas aeruginosa
forms aggregates known as biofilms. Previous studies have shown that when
P. aeruginosa
is cultivated in space, thicker and structurally different biofilms are formed than from those grown on Earth. We investigated how microgravity, simulated in a laboratory setting, influenced the growth, colonization, and virulence potentials of a
P. aeruginosa
PA14 wild-type strain, as well as two surface attachment-defective (
sad
) mutants altered at crucial biofilm-forming steps:
flgK
and
pelA
. Using high-aspect ratio rotating-wall vessel (HARV) bioreactors,
P. aeruginosa
bacteria were grown to stationary phase under prolonged (6 days) exposure to simulated microgravity or normal gravity conditions. After the exposure, the capacity of the culture to form biofilms was measured. Additionally, pigment (pyocyanin) formed by each culture during the incubation was extracted and quantified. We demonstrate that the first prolonged exposure to low-shear modeled microgravity (LSMMG) and without nutrient replenishment significantly diminishes wild-type
P. aeruginosa
PA14 biofilm formation abilities after exposure and pyocyanin production during exposure, while the mutant strains exhibit differing outcomes for both properties.

IMPORTANCE

Given plans for humans to engage in prolonged space travel, we investigated biofilm and pigment/virulence factor formation in
Pseudomonas aeruginosa
when cultivated in microgravity. These bacteria are opportunistic pathogens in immunocompromised individuals. Previous studies of space travelers have shown some immune system diminutions. Hence, our studies shed some light on how prolonged cultivation of bacteria in simulated microgravity conditions affect their growth characteristics.
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

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

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

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

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

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

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

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

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

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.
Nosocomial transmission of fluconazole-resistant
Candida glabrata
bloodstream isolates revealed by whole-genome sequencing
Authors: Hwang In Ji , Kwon Yong Jun , Lim Ha Jin , Hong Ki Ho , Lee Hyukmin , Yong Dongeun , Won Eun Jeong , Byun Seung A. , Lee Ga Yeong , Kim Soo Hyun , Song Eun Song , Shin Jong Hee
Published: August 2024

The clonal transmission of fluconazole-resistant
Candida glabrata
isolates within hospitals has seldom been analyzed by whole-genome sequencing (WGS). We performed WGS on 79
C
.
glabrata
isolates, comprising 31 isolates from three premature infants with persistent
C. glabrata
bloodstream infection despite antifungal treatment in the same neonatal intensive care unit (NICU) in 2022 and 48 (27 fluconazole-resistant and 21 fluconazole-susceptible dose-dependent) bloodstream isolates from 48 patients in 15 South Korean hospitals from 2010 to 2022. Phylogenetic analysis based on WGS single-nucleotide polymorphisms (SNPs) distinguished the 79 isolates according to multilocus sequence typing (MLST) (17 sequence type [ST]3, 13 ST7, two ST22, 41 ST26, four ST55, and two ST59 isolates) and unveiled two possible clusters of nosocomial transmission among ST26 isolates. One cluster from two premature infants with overlapping NICU hospitalizations in 2022 encompassed 15 fluconazole-resistant isolates harboring pleiotropic drug-resistance transcription factor (Pdr1p) P258L (13 isolates) or N1086I (two isolates), together with 10 fluconazole-susceptible dose-dependent isolates lacking Pdr1p SNPs. The other cluster indicated unforeseen clonal transmission of fluconazole-resistant bloodstream isolates among five patients (four post-lung transplantation and one with diffuse interstitial lung disease) in the same hospital over 8 months. Among these five isolates, four obtained after exposure to azole antifungals harbored distinct Pdr1p SNPs (N1091D, E388Q, K365E, and R376Q). The findings reveal the transmission patterns of clonal bloodstream isolates of
C. glabrata
among patients undergoing antifungal treatment, exhibiting different levels of fluconazole susceptibility or distinct Pdr1p SNP profiles.

IMPORTANCE

The prevalence of fluconazole-resistant bloodstream infections caused by
Candida glabrata
is increasing globally, but the transmission of these resistant strains within hospitals has rarely been documented. Through whole-genome sequencing and epidemiological analyses, this study identified two potential clusters of
C. glabrata
bloodstream infections within the same hospital, revealing the transmission of clonal
C. glabrata
strains with different levels of fluconazole susceptibility or distinct transcription factor pleiotropic drug resistance protein 1 (Pdr1p) single-nucleotide polymorphism profiles among patients receiving antifungal therapy.
Hetero-antagonism of avibactam and sulbactam with cefiderocol in carbapenem-resistant
Acinetobacter
spp.
Authors: Wong Olivia , Mezcord Vyanka , Lopez Christina , Traglia German Matias , Pasteran Fernando , Tuttobene Marisel R. , Corso Alejandra , Tolmasky Marcelo E. , Bonomo Robert A. , Ramirez María Soledad
Published: August 2024

Cefiderocol, a siderophore-cephalosporine conjugate antibiotic, shows promise as a therapeutic option for carbapenem-resistant (CR)
Acinetobacter
infections. While resistance has already been reported in
A. baumannii
, combination therapies with avibactam or sulbactam reduce MICs of cefiderocol, extending its efficacy. However, careful consideration is necessary when using these combinations. In our experiments, exposure of
A. baumannii
and
A. lwoffii
to cefiderocol and sulbactam or avibactam led to the selection of cefiderocol-resistant strains. Three of those were subjected to whole genome sequencing and transcriptomic analysis. The strains all possessed synonymous and non-synonymous substitutions and short deletions. The most significant mutations affected efflux pumps, transcriptional regulators, and iron homeostasis genes. Transcriptomics showed significant alterations in expression levels of outer membrane proteins, iron homeostasis, and β-lactamases, suggesting adaptive responses to selective pressure. This study underscores the importance of carefully assessing drug synergies, as they may inadvertently foster the selection of resistant variants and complicate the management of CR
Acinetobacter
infections.

IMPORTANCE

The emergence of carbapenem-resistant
Acinetobacter
strains as a serious global health threat underscores the urgent need for effective treatment options. Although few drugs show promise against CR
Acinetobacter
infections, resistance to both drugs has been reported. In this study, the molecular characterization of spontaneous cefiderocol-resistant variants, a CR
A. baumannii
strain with antagonism to sulbactam, and an
A. lwoffii
strain with antagonism to avibactam, provides valuable insights into the mechanisms of resistance to cefiderocol. Some mechanisms observed are associated with mutations affecting efflux pumps, regulators, and iron homeostasis genes. These findings highlight the importance of understanding resistance mechanisms to optimize treatment options. They also emphasize the importance of early evaluation of drug synergies to address the challenges of antimicrobial resistance in
Acinetobacter
infections.