bluuebunny/crossref_metadata_2025_split huggingface dataset:
A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals
Authors: Sato Yoshiaki , Takebe Hiroaki , Tominaga Kento , Yasuda Jumpei , Kumagai Hajime , Hirooka Hiroyuki , Yoshida Takashi 
Published: December 2023

ABSTRACT

Viruses have a potential to modify the ruminal digestion via infection and cell lysis of prokaryotes, suggesting that viruses are related to animal performance and methane production. This study aimed to elucidate the genome-based diversity of rumen viral communities and the differences in virus structure between individuals and cattle breeds and to understand how viruses influence on the rumen. To these ends, a metagenomic sequencing of virus-like particles in the rumen of 22 Japanese cattle, including Japanese Black (JB,
n
= 8), Japanese Shorthorn (
n
= 2), and Japanese Black sires × Holstein dams crossbred steers (F1,
n
= 12) was conducted. Additionally, the rumen viromes of six JB and six F1 that were fed identical diets and kept in a single barn were compared. A total of 8,232 non-redundant viral genomes (≥5-kb length and ≥50% completeness), including 982 complete genomes, were constructed, and rumen virome exhibited lysogenic signatures. Furthermore, putative hosts of 1,223 viral genomes were predicted using tRNA and clustered regularly interspaced short palindromic repeat (CRISPR)-spacer matching. The genomes included 1 and 10 putative novel complete genomes associated with
Fibrobacter
and
Ruminococcus
, respectively
,
which are the main rumen cellulose-degrading bacteria. Additionally, the hosts of 22 viral genomes, including 2 complete genomes, were predicted as methanogens, such as
Methanobrevibacter
and
Methanomethylophilus
. Most rumen viruses were highly rumen and individual specific and related to rumen-specific prokaryotes. Furthermore, the rumen viral community structure was significantly different between JB and F1 steers, indicating that cattle breed is one of the factors influencing the rumen virome composition.

IMPORTANCE
Here, we investigated the individual and breed differences of the rumen viral community in Japanese cattle. In the process, we reconstructed putative novel complete viral genomes related to rumen fiber-degrading bacteria and methanogen. The finding strongly suggests that rumen viruses contribute to cellulose and hemicellulose digestion and methanogenesis. Notably, this study also found that rumen viruses are highly rumen and individual specific, suggesting that rumen viruses may not be transmitted through environmental exposure. More importantly, we revealed differences of viral communities between JB and F1 cattle, indicating that cattle breed is a factor that influences the establishment of rumen virome. These results suggest the possibility of rumen virus transmission from mother to offspring and its potential to influence beef production traits. These rumen viral genomes and findings provide new insights into the characterizations of the rumen viruses.
Selected cachaça yeast strains share a genomic profile related to traits relevant to industrial fermentation processes
Authors: Campos Anna Clara Silva , Araújo Thalita Macedo , Moraes Lauro , Corrêa dos Santos Renato Augusto , Goldman Gustavo Henrique , Riano-Pachon Diego Maurício , Oliveira Juliana Velasco de Castro , Squina Fabio Marcio , Castro Ieso de Miranda , Trópia Maria José Magalhães , da Cunha Aureliano Claret , Rosse Izinara C. , Brandão Rogelio Lopes 
Published: December 2023

ABSTRACT

The isolation and selection of yeast strains to improve the quality of the
cachaça
—Brazilian Spirit—have been studied in our research group. Our strategy considers
Saccharomyces cerevisiae
as the predominant species involved in sugarcane juice fermentation and the presence of different stressors (osmolarity, temperature, ethanol content, and competition with other microorganisms). It also considers producing balanced concentrations of volatile compounds (higher alcohols and acetate and/or ethyl esters), flocculation capacity, and ethanol production. Since the genetic bases behind these traits of interest are not fully established, the whole genome sequencing of 11 different
Saccharomyces cerevisiae
strains isolated and selected from different places was analyzed to identify the presence of a specific genetic variation common to cachaça yeast strains. We have identified 20,128 single-nucleotide variants shared by all genomes. Of these shared variants, 37 were new variants (being six missenses), and 4,451 were identified as missenses. We performed a detailed functional annotation (using enrichment analysis, protein–protein interaction network analysis, and database and in-depth literature searches) of these new and missense variants. Many genes carrying these variations were involved in the phenotypes of flocculation, tolerance to fermentative stresses, and production of volatile compounds and ethanol. These results demonstrate the existence of a genetic profile shared by the 11 strains under study that could be associated with the applied selective strategy. Thus, this study points out genes and variants that may be used as molecular markers for selecting strains well suited to the fermentation process, including genetic improvement by genome editing, ultimately producing high-quality beverages and adding value.

IMPORTANCE
This work demonstrates the existence of new genetic markers related to different phenotypes used to select yeast strains and mutations in genes directly involved in producing flavoring compounds and ethanol, and others related to flocculation and stress resistance.
First Canadian report of transmission of fluconazole-resistant
Candida parapsilosis
within two hospital networks confirmed by genomic analysis
Authors: McTaggart Lisa R. , Eshaghi AliReza , Hota Susy , Poutanen Susan M. , Johnstone Jennie , De Luca Domenica G. , Bharat Amrita , Patel Samir N. , Kus Julianne V. 
Published: December 2023

ABSTRACT

Candida parapsilosis
is a common cause of non
-
albicans candidemia. It can be transmitted in healthcare settings resulting in serious healthcare-associated infections and can develop drug resistance to commonly used antifungal agents. Following a significant increase in the percentage of fluconazole (FLU)-nonsusceptible isolates from sterile site specimens of patients in two Ontario acute care hospital networks, we used whole genome sequence (WGS) analysis to retrospectively investigate the genetic relatedness of isolates and to assess potential in-hospital spread. Phylogenomic analysis was conducted on all 19 FLU-resistant and seven susceptible-dose dependent (SDD) isolates from the two hospital networks, as well as 13 FLU susceptible
C. parapsilosis
isolates from the same facilities and 20 isolates from patients not related to the investigation. Twenty-five of 26 FLU-nonsusceptible isolates (resistant or SDD) and two susceptible isolates from the two hospital networks formed a phylogenomic cluster that was highly similar genetically and distinct from other isolates. The results suggest the presence of a persistent strain of FLU-nonsusceptible
C. parapsilosis
causing infections over a 5.5-year period. Results from WGS were largely comparable to microsatellite typing. Twenty-seven of 28 cluster isolates had a K143R substitution in lanosterol 14-α-demethylase (ERG11) associated with azole resistance. As the first report of a healthcare-associated outbreak of FLU-nonsusceptible
C. parapsilosis
in Canada, this study underscores the importance of monitoring local antimicrobial resistance trends and demonstrates the value of WGS analysis to detect and characterize clusters and outbreaks. Timely access to genomic epidemiological information can inform targeted infection control measures.
Single-tube protocol for culture-independent spoligotyping of
Mycobacterium tuberculosis
based on MeltArray
Authors: Xia Zihan , Su Biyi , Tu Chunxia , Sun Siyang , Tan Yaoju , Xu Ye , Li Qingge 
Published: December 2023

ABSTRACT

Spacer oligonucleotide typing (spoligotyping), the first-line genotyping assay for
Mycobacterium tuberculosis
(MTB), plays a fundamental role in the investigation of its epidemiology and evolution. However, the traditional spoligotyping protocol was established by using the reverse dot blot hybridization technique, which is characterized by a complex procedure, long turnaround time, and subjectivity in result interpretation, thus hindering its widespread use in low- and middle-income countries (LMICs) with a high tuberculosis burden. In this study, we established a single-tube spoligotyping assay using MeltArray, a highly multiplex polymerase chain reaction (PCR) approach that runs on a real-time PCR thermocycler. The MeltArray protocol included an internal positive control,
gyrB
, to indicate the abundance of MTB via the quantification cycle (Cq) and 43 spacers to identify the spoligotype via melting curve analysis. The entire protocol was completed in a single step within 2.5 hours. The lowest detectable copy number for the tested strains was 20 copies/reaction. In a blind evaluation of 318 MTB isolates, the MeltArray assay yielded 98.1% (312/318) concordance with the traditional approach and 100.0% with Sanger sequencing. Further evaluation of 151 liquid culture-matched sputum samples showed that all qualified (Cq <35) sputum samples (80.8%, 122/151) yielded results consistent with those of the liquid culture samples, including 97.5% (119/122) single spoligotypes and 2.5% (3/122) mixed spoligotypes. We conclude that MeltArray-based spoligotyping could be used immediately in LMICs, given its easy access, improved throughput, and potential applicability to clinical samples.

IMPORTANCE

Spacer oligonucleotide typing (spoligotyping), the first-line genotyping assay for
Mycobacterium tuberculosis
(MTB), plays a fundamental role in the investigation of its epidemiology and evolution. In this study, we established a single-tube spoligotyping assay using MeltArray, a highly multiplex polymerase chain reaction (PCR) approach that runs on a real-time PCR thermocycler. The MeltArray protocol included an internal positive control,
gyrB
, to indicate the abundance of MTB via the quantification cycle and 43 spacers to identify the spoligotype via melting curve analysis. The entire protocol was completed in a single step within 2.5 hours. The lowest detectable copy number for the tested strains was 20 copies/reaction and thus sufficient for analyzing both culture and sputum samples. We conclude that MeltArray-based spoligotyping could be used immediately in low- and middle-income countries with a high tuberculosis burden, given its easy access, improved throughput, and potential applicability to clinical samples.
The complete genome of two
Lactiplantibacillus plantarum
isolates from the traditional Mexican fermented pulque beverage assembled with a combination of PacBio and Illumina platforms
Authors: Gutiérrez Rodríguez Elisa Karen , Astudillo-Melgar Fernando , Larios Violeta , Bolívar Francisco , Escalante Adelfo , Giles-Gómez Martha 
Published: December 2023

ABSTRACT

We report the sequence of the complete genome and associated plasmids of two
Lactiplantibacillus plantarum
isolates from the traditional Mexican pulque beverage assembled with a combination of PacBio and Illumina data. The resulting complete genome for strain LB1_P46 is 3,287,706 bp; for strain LB2_P47, the complete genome is 3,289,072 bp.
The complete genome sequence of
Kineothrix
sp. MB12-C1, isolated from the feces of black soldier fly larvae
Authors: Guo Wenjie , Qiu Wanling , Zhu Junyu , Shih Chao-Jen , Wu Yen-Chi , Lai Shu-Jung , Zhou Jiahui , Zhu Zetao , You Yi-Ting , Li Yin , Chen Sheng-Chung 
Published: December 2023

ABSTRACT

Here, we present the complete genome sequence of
Kineothrix
sp. MB12-C1 (= BCRC 81406), isolated from the feces of black soldier fly (
Hermetia illucens
) larvae. The genome of strain MB12-C1 was chosen for further species classification and comparative genomic analysis.
Genome sequence of an
Acinetobacter pittii
strain obtained from a red
-
lored parrot with pneumonia
Authors: Bello-López E. , Escobedo-Muñoz A. S. , Hernández-Castro R. , Cevallos M. A. 
Published: December 2023

ABSTRACT

Acinetobacter pittii
978-A_19 was obtained from a parrot with pneumonia. It is resistant to ampicillin, carbenicillin, cephalosporins, clindamycin, and trimethoprim + sulfamethoxazole. The genome encodes a new
bla
ADC allele, a
bla
OXA-502 gene, possesses several virulence genes related to adherence and biofilm formation, and has types I, II, and IV secretion systems.
Distinct epigenetic signatures of classical and hypervirulent
Klebsiella pneumoniae
Authors: Ghosh Dipannita , Pal Arijit , Mohapatra Sarita , Raj Stephen , Vivekanandan Perumal 
Published: December 2023

ABSTRACT

Emergence and spread of the hypervirulent pathotype of
Klebsiella pneumoniae
have significantly increased infection rates in community as well as healthcare settings. There is an increasing interest to identify discriminating features between classical
K. pneumoniae
(cKp) and hypervirulent
K. pneumoniae
(hvKp) to facilitate our understanding of the rapid emergence and dissemination of the hypervirulent pathotype. Here, we sought to identify unique epigenetic signatures of hvKp pathotype that differ from its classical counterpart using single-base resolution methylome analysis of native DNA sequencing on the Oxford Nanopore Technologies platform. The overall global adenine methylation in GATC motifs (i.e., Dam methylation motif) and cytosine methylation in CCWGG motifs (i.e., Dcm methylation motif) were significantly higher in hvKp isolates compared to that in cKp isolates, irrespective of their position in chromosomes or putative extra-chromosomal genetic elements. Notably, we observed significant enrichment of hypermethylated GATC and CCWGG motifs in the virulome of hvKp compared to hvKp genes not directly associated with virulence. We also observed increased methylation of GATC and CCWGG motifs in the capsule synthesis locus of hvKp isolates compared to cKp isolates. Furthermore, we identified several differentially methylated genes (DMGs) between the two pathotypes; interestingly, these DMGs include metal ion transporters, multidrug efflux pumps, transcriptional regulators of stress response, and genes associated with biofilm formation. Our results highlight hypermethylation of GATC and CCWGG motifs as unique epigenetic signatures of hvKp isolates.

IMPORTANCE

Hypervirulent
Klebsiella pneumoniae
(hvKp) is a more virulent and rapidly evolving hypermucoviscous pathotype of classical
K. pneumoniae
(cKp). The hypervirulent pathotype is a major public health concern and is associated with high infection rates in community as well as hospital settings. With the recent emergence of multidrug-resistant hvKp, it has become imperative to investigate non-classical mechanisms such as epigenetics in addition to canonical biochemical and genetic mechanisms that delineate and differentiate the hypervirulent pathotype from its classical counterpart. Here, we identify genome-wide differences in adenine and cytosine methylation marks at well-characterized motifs between the two pathotypes. Overall, significantly higher levels of methylation were observed across chromosomal DNA and extrachromosomal elements in hvKp compared to cKp. Among hvKp isolates, the genes associated with virulence are particularly enriched for methylation marks. Our findings shed light on how epigenetic signatures may help distinguish the pathogenic potential of bacteria.
Synergistic horizontal transfer of antibiotic resistance genes and transposons in the infant gut microbial genome
Authors: Ding Yanwen , Jiang Xin , Wu Jiacheng , Wang Yihui , Zhao Lanlan , Pan Yingmiao , Xi Yaxuan , Zhao Guoping , Li Ziyun , Zhang Lei 
Published: December 2023

ABSTRACT

Transposons, plasmids, bacteriophages, and other mobile genetic elements facilitate horizontal gene transfer in the gut microbiota, allowing some pathogenic bacteria to acquire antibiotic resistance genes (ARGs). Currently, the relationship between specific ARGs and specific transposons in the comprehensive infant gut microbiome has not been elucidated. In this study, ARGs and transposons were annotated from the Unified Human Gastrointestinal Genome (UHGG) and the Early-Life Gut Genomes (ELGG). Association rules mining was used to explore the association between specific ARGs and specific transposons in UHGG, and the robustness of the association rules was validated using the external database in ELGG. Our results suggested that ARGs and transposons were more likely to be relevant in infant gut microbiota compared to adult gut microbiota, and nine robust association rules were identified, among which
Klebsiella pneumoniae
,
Enterobacter hormaechei_A
, and
Escherichia coli_D
played important roles in this association phenomenon. The emphasis of this study is to investigate the synergistic transfer of specific ARGs and specific transposons in the infant gut microbiota, which can contribute to the study of microbial pathogenesis and the ARG dissemination dynamics.

IMPORTANCE

The transfer of transposons carrying antibiotic resistance genes (ARGs) among microorganisms accelerates antibiotic resistance dissemination among infant gut microbiota. Nonetheless, it is unclear what the relationship between specific ARGs and specific transposons within the infant gut microbiota.
K. pneumoniae
,
E. hormaechei_A
, and
E. coli_D
were identified as key players in the nine robust association rules we discovered. Meanwhile, we found that infant gut microorganisms were more susceptible to horizontal gene transfer events about specific ARGs and specific transposons than adult gut microorganisms. These discoveries could enhance the understanding of microbial pathogenesis and the ARG dissemination dynamics within the infant gut microbiota.
Study protocol for Care cOORDInatioN And sympTom managEment (COORDINATE) programme: a feasibility study
Authors: Koirala Binu , Badawi Sarah , Frost Steven , Ferguson Caleb , Hager David N , Street Lara , Perrin Nancy , Dennison Himmelfarb Cheryl , Davidson Patricia 
Published: December 2023

IntroductionSustainable approaches to support care coordination and symptom management needs of critically ill adults living with multimorbidity are needed to combat the challenges and complexity that multimorbidity presents. The study aims to test the feasibility of the Care cOORDInatioN And sympTom managEment (COORDINATE) intervention to improve health outcomes of adults living with multimorbidity.Methods and analysisA multicomponent nurse-driven intervention was developed using experience-based co-design and human-centred design. Inclusion criteria include (1) age 55 years and older, (2) admitted to an intermediate care unit, (3) presence of two or more chronic health conditions and (4) signed informed consent. Data collection will occur at baseline (time of recruitment predischarge) and 6 weeks and 3 months following hospital discharge. Outcome of interest from this feasibility study is to evaluate the financial, technical and logistic feasibility of a full-scale study including data collection and protocol adherence. Additionally, Cohen’s d effect sizes for the change in outcomes over time will be computed to establish power calculations required for a full-scale study. The protocol was prepared in accordance with Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklist.Ethics and disseminationThe study has been reviewed and approved by the Institutional Review Board of Johns Hopkins Medical Institutions. Given the success of this feasibility study, the potential for the COORDINATE intervention to decrease the symptom burden and improve participant quality of life among critically ill people with multimorbidity will be tested in a full-scale study, and findings will be actively disseminated.Trial registration numberNCT05985044.
A novel, multidomain, primary care nurse-led and mHealth-assisted intervention for dementia risk reduction in middle-aged adults (HAPPI MIND): study protocol for a cluster randomised controlled trial
Authors: Cross Amanda J , Geethadevi Gopisankar Mohanannair , Magin Parker , Baker Amanda L , Bonevski Billie , Godbee Kali , Ward Stephanie A , Mahal Ajay , Versace Vincent , Bell J Simon , Mc Namara Kevin , O'Reilly Sharleen L , Thomas Dennis , Manias Elizabeth , Anstey Kaarin J , Varnfield Marlien , Jayasena Rajiv , Elliott Rohan A , Lee Cik Y , Walker Christine , van den Bosch Denise , Tullipan Mary , Ferreira Catherine , George Johnson 
Published: December 2023

IntroductionMiddle-aged multidomain risk reduction interventions targeting modifiable risk factors for dementia may delay or prevent a third of dementia cases in later life. We describe the protocol of a cluster randomised controlled trial (cRCT), HAPPI MIND (Holistic Approach in Primary care for PreventIng Memory Impairment aNd Dementia). HAPPI MIND will evaluate the efficacy of a multidomain, nurse-led, mHealth supported intervention for assessing dementia risk and reducing associated risk factors in middle-aged adults in the Australian primary care setting.Methods and analysisGeneral practice clinics (n≥26) across Victoria and New South Wales, Australia, will be recruited and randomised. Practice nurses will be trained to implement the HAPPI MIND intervention or a brief intervention. Patients of participating practices aged 45–65 years with ≥2 potential dementia risk factors will be identified and recruited (approximately 15 patients/clinic). Brief intervention participants receive a personalised report outlining their risk factors for dementia based on Australian National University Alzheimer’s Disease Risk Index (ANU-ADRI) scores, education booklet and referral to their general practitioner as appropriate. HAPPI MIND participants receive the brief intervention as well as six individualised dementia risk reduction sessions with a nurse trained in motivational interviewing and principles of behaviour change, a personalised risk reduction action plan and access to the purpose-built HAPPI MIND smartphone app for risk factor self-management. Follow-up data collection will occur at 12, 24 and 36 months. Primary outcome is ANU-ADRI score change at 12 months from baseline. Secondary outcomes include change in cognition, quality of life and individual risk factors of dementia.Ethics and disseminationProject approved by Monash University Human Research Ethics Committee (ID: 28273). Results will be disseminated in peer-reviewed journals and at healthcare conferences. If effective in reducing dementia risk, the HAPPI MIND intervention could be integrated into primary care, scaled up nationally and sustained over time.Trial registration numberACTRN12621001168842.