bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering transcript architectural complexity in bacteria and archaea
Authors: Mattick John S. A. , Bromley Robin E. , Watson Kaylee J. , Adkins Ricky S. , Holt Christopher I. , Lebov Jarrett F. , Sparklin Benjamin C. , Tyson Tyonna S. , Rasko David A. , Dunning Hotopp Julie C. 
Published: September 2024

ABSTRACT

RNA transcripts are potential therapeutic targets, yet bacterial transcripts have uncharacterized biodiversity. We developed an algorithm for transcript prediction called tp.py using it to predict transcripts (mRNA and other RNAs) in
Escherichia coli
K12 and E2348/69 strains (Bacteria:gamma-Proteobacteria),
Listeria monocytogenes
strains Scott A and RO15 (Bacteria:Firmicute),
Pseudomonas aeruginosa
strains SG17M and NN2 strains (Bacteria:gamma-Proteobacteria), and
Haloferax volcanii
(Archaea:Halobacteria). From >5 million
E. coli
K12 and >3 million
E. coli
E2348/69 newly generated Oxford Nanopore Technologies direct RNA sequencing reads, 2,487 K12 mRNAs and 1,844 E2348/69 mRNAs were predicted, with the K12 mRNAs containing more than half of the predicted
E. coli
K12 proteins. While the number of predicted transcripts varied by strain based on the amount of sequence data used, across all strains examined, the predicted average size of the mRNAs was 1.6–1.7 kbp, while the median size of the 5′- and 3′-untranslated regions (UTRs) were 30–90 bp. Given the lack of bacterial and archaeal transcript annotation, most predictions were of novel transcripts, but we also predicted many previously characterized mRNAs and ncRNAs, including post-transcriptionally generated transcripts and small RNAs associated with pathogenesis in the
E. coli
E2348/69
LEE
pathogenicity islands. We predicted small transcripts in the 100–200 bp range as well as >10 kbp transcripts for all strains, with the longest transcript for two of the seven strains being the
nuo
operon transcript, and for another two strains it was a phage/prophage transcript. This quick, easy, and reproducible method will facilitate the presentation of transcripts, and UTR predictions alongside coding sequences and protein predictions in bacterial genome annotation as important resources for the research community.

IMPORTANCE
Our understanding of bacterial and archaeal genes and genomes is largely focused on proteins since there have only been limited efforts to describe bacterial/archaeal RNA diversity. This contrasts with studies on the human genome, where transcripts were sequenced prior to the release of the human genome over two decades ago. We developed software for the quick, easy, and reproducible prediction of bacterial and archaeal transcripts from Oxford Nanopore Technologies direct RNA sequencing data. These predictions are urgently needed for more accurate studies examining bacterial/archaeal gene regulation, including regulation of virulence factors, and for the development of novel RNA-based therapeutics and diagnostics to combat bacterial pathogens, like those with extreme antimicrobial resistance.
The interplay between mobilome and resistome in
Staphylococcus aureus
Authors: Contarin Rachel , Drapeau Antoine , François Pauline , Madec Jean-Yves , Haenni Marisa , Dordet-Frisoni Emilie 
Published: September 2024

ABSTRACT

Antibiotic resistance genes (ARGs) in
Staphylococcus aureus
can disseminate vertically through successful clones, but also horizontally through the transfer of genes conveyed by mobile genetic elements (MGEs). Even though underexplored, MGE/ARG associations in
S. aureus
favor the emergence of multidrug-resistant clones, which are challenging therapeutic success in both human and animal health. This study investigated the interplay between the mobilome and the resistome of more than 10,000
S
.
aureus
genomes from human and animal origin. The analysis revealed a remarkable diversity of MGEs and ARGs, with plasmids and transposons being the main carriers of ARGs. Numerous MGE/ARG associations were identified, suggesting that MGEs play a critical role in the dissemination of resistance. A high degree of similarity was observed in MGE/ARG associations between human and animal isolates, highlighting the potential for unrestricted spread of ARGs between hosts. Our results showed that in parallel to clonal expansion, MGEs and their associated ARGs can spread across different strain types sequence types (STs), favoring the evolution of these clones and their adaptation in selective environments. The high variability of MGE/ARG associations within individual STs and their spread across several STs highlight the crucial role of MGEs in shaping the
S. aureus
resistome. Overall, this study provides valuable insights into the complex interplay between MGEs and ARGs in
S. aureus
, emphasizing the need to elucidate the mechanisms governing the epidemic success of MGEs, particularly those implicated in ARG transfer.

IMPORTANCE

The research presented in this article highlights the importance of understanding the interactions between mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) carried by
Staphylococcus aureus
, a versatile bacterium that can be both a harmless commensal and a dangerous pathogen for humans and animals.
S. aureus
has a great capacity to acquire and disseminate ARGs, enabling efficient adaption to various environmental or clinical conditions. By analyzing a large data set of
S. aureus
genomes, we highlighted the substantial role of MGEs, particularly plasmids and transposons, in disseminating ARGs within and between
S. aureus
populations, bypassing host barriers. Given that multidrug-resistant
S. aureus
strains are classified as a high-priority pathogen by global health organizations, this knowledge is crucial for understanding the complex dynamics of transmission of antibiotic resistance in this species.
Draft genomes of multidrug-resistant
Campylobacter jejuni
and
Campylobacter coli
strains from Brazil representing novel sequence types
Authors: Portes Ana Beatriz , Panzenhagen Pedro , dos Santos Anamaria Mota Pereira , de Jesus Ana Carolina Silva , Ochioni Alan Clavelland , Duque Sheila da Silva , Aburjaile Flávia Figueira , Brenig Bertram , Azevedo Vasco , Conte Junior Carlos Adam 
Published: September 2024

ABSTRACT

Whole-genome sequencing identified three previously unidentified multilocus sequence types of
Campylobacter jejuni
(ST-12332) and
Campylobacter coli
(ST-12333 and ST-12663), harboring resistance genes for multiple antimicrobial classes. The sources of isolation highlight the circulation of resistance strains within animals and humans, emphasizing the need for preventive measures.
Biosynthetic gene clusters from uncultivated soil bacteria of the Atacama Desert
Authors: Andreani-Gerard Constanza M. , Cambiazo Verónica , González Mauricio 
Published: September 2024

ABSTRACT

Soil microorganisms mediate several biological processes through the secretion of natural products synthesized in specialized metabolic pathways, yet functional characterization in ecological contexts remains challenging. Using culture-independent metagenomic analyses of microbial DNA derived directly from soil samples, we examined the potential of biosynthetic gene clusters (BGCs) from six bacterial communities distributed along an altitudinal gradient of the Andes Mountains in the Atacama Desert. We mined 38 metagenome-assembled genomes (MAGs) and identified 168 BGCs. Results indicated that most predicted BGCs were classified as non-ribosomal-peptides (NRP), post-translational modified peptides (RiPP), and terpenes, which were mainly identified in genomes of species from
Acidobacteriota
and
Proteobacteria
phyla. Based on BGC composition according to types of core biosynthetic genes, six clusters of MAGs were observed, three of them with predominance for a single phylum, of which two also showed specificity to a single sampling site. Comparative analyses of accessory genes in BGCs showed associations between membrane transporters and other protein domains involved in specialized metabolism with classes of biosynthetic cores, such as resistance-nodulation-cell division (RND) multidrug efflux pumps with RiPPs and the iron-dependent transporter TonB with terpenes. Our findings increase knowledge regarding the biosynthetic potential of uncultured bacteria inhabiting pristine locations from one of the oldest and driest nonpolar deserts on Earth.

IMPORTANCE

Much of what we know about specialized metabolites in the Atacama Desert, including Andean ecosystems, comes from isolated microorganisms intended for drug development and natural product discovery. To complement research on the metabolic potential of microbes in extreme environments, comparative analyses on functional annotations of biosynthetic gene clusters (BGCs) from uncultivated bacterial genomes were carried out. Results indicated that in general, BGCs encode for structurally unique metabolites and that metagenome-assembled genomes did not show an obvious relationship between the composition of their core biosynthetic potential and taxonomy or geographic distribution. Nevertheless, some members of
Acidobacteriota
showed a phylogenetic relationship with specific metabolic traits and a few members of
Proteobacteria
and
Desulfobacterota
exhibited niche adaptations. Our results emphasize that studying specialized metabolism in environmental samples may significantly contribute to the elucidation of structures, activities, and ecological roles of microbial molecules.
Exploring the vitamin biosynthesis landscape of the human gut microbiota
Authors: Tarracchini Chiara , Lugli Gabriele Andrea , Mancabelli Leonardo , van Sinderen Douwe , Turroni Francesca , Ventura Marco , Milani Christian 
Published: September 2024

ABSTRACT

The human gut microbiota possesses the capacity to synthesize vitamins, especially B group vitamins, which are recognized as indispensable for various biological processes both among members of these bacterial communities and host cells. Accordingly, vitamin production by intestinal commensals has attracted significant interest. Nevertheless, our current understanding of bacterial vitamin synthesis is primarily based on individual genomic and monoculture investigations, therefore not providing an overall view of the biosynthetic potential of complex microbial communities. In the current study, we utilized over 100 bacterial genes known to be involved in the biosynthesis of B group and K vitamins to assess the corresponding vitamin biosynthetic potential of approximately 8,000 human gut microbiomes. Our analyses reveal that host-associated factors, such as age and geographical origin, appear to influence the diversity and abundance of vitamin biosynthetic pathways. Furthermore, we identify gut microbiota members that substantially contribute to these biosynthetic functions at each stage of human life. Interestingly, inference of microbial co-associations and network relationships uncovered the apparent key role played by folate and cobalamin in equilibrium establishment of the infant and adult gut microbial communities, respectively.

IMPORTANCE
Overall, this study expands our understanding of microbe-mediated vitamin biosynthesis in the human gut and may provide potential novel targets to improve availability of these essential micronutrients in the host.
Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination and
Eimeria tenella
challenge
Authors: Liu Po-Yu , Liaw Janie , Soutter Francesca , Ortiz José Jaramillo , Tomley Fiona M. , Werling Dirk , Gundogdu Ozan , Blake Damer P. , Xia Dong 
Published: September 2024

ABSTRACT

Coccidiosis, caused by
Eimeria
parasites, significantly impacts poultry farm economics and animal welfare. Beyond its direct impact on health,
Eimeria
infection disrupts enteric microbial populations leading to dysbiosis and increases vulnerability to secondary diseases such as necrotic enteritis, caused by
Clostridium perfringens
. The impact of
Eimeria
infection or anticoccidial vaccination on host gastrointestinal phenotypes and enteric microbiota remains understudied. In this study, the metabolomic profiles and microbiota composition of chicken caecal tissue and contents were evaluated concurrently during a controlled experimental vaccination and challenge trial. Cobb500 broilers were vaccinated with a
Saccharomyces cerevisiae
-vectored anticoccidial vaccine and challenged with 15,000
Eimeria tenella
oocysts. Assessment of caecal pathology and quantification of parasite load revealed correlations with alterations to caecal microbiota and caecal metabolome linked to infection and vaccination status. Infection heightened microbiota richness with increases in potentially pathogenic species, while vaccination elevated beneficial
Bifidobacterium
. Using a multi-omics factor analysis, data on caecal microbiota and metabolome were integrated and distinct profiles for healthy, infected, and recovering chickens were identified. Healthy and recovering chickens exhibited higher vitamin B metabolism linked to short-chain fatty acid-producing bacteria, whereas essential amino acid and cell membrane lipid metabolisms were prominent in infected and vaccinated chickens. Notably, vaccinated chickens showed distinct metabolites related to the enrichment of sphingolipids, important components of nerve cells and cell membranes. Our integrated multi-omics model revealed latent biomarkers indicative of vaccination and infection status, offering potential tools for diagnosing infection, monitoring vaccination efficacy, and guiding the development of novel treatments or controls.

IMPORTANCE
Advances in anticoccidial vaccines have garnered significant attention in poultry health management. However, the intricacies of vaccine-induced alterations in the chicken gut microbiome and its subsequent impact on host metabolism remain inadequately explored. This study delves into the metabolic and microbiotic shifts in chickens post-vaccination, employing a multi-omics integration analysis. Our findings highlight a notable synergy between the microbiome composition and host-microbe interacted metabolic pathways in vaccinated chickens, differentiating them from infected or non-vaccinated cohorts. These insights pave the way for more targeted and efficient approaches in poultry disease control, enhancing both the efficacy of vaccines and the overall health of poultry populations.
VSV infection and LPS treatment alter serum bile acid profiles, bile acid biosynthesis, and bile acid receptors in mice
Authors: Li Yamei , Luo Yan , Wang Chao , Xu Lei , Dai Xinhua , An Yunfei , He Lin , Zeng Dongmei , Bai Yangjuan , Zhang Hua 
Published: September 2024

ABSTRACT

Pathogen infections remain a significant public health problem worldwide. Accumulating evidence regarding the crosstalk between bile acid (BA) metabolism and immune response reveals that BA metabolism regulates host immunity and microbial pathogenesis, making it an attractive target for disease prevention and infection control. However, the effect of infection on circulating BA profiles, the biosynthesis-related enzymes, and their receptors remains to be depicted. Here, we investigated the effect of viral (vesicular stomatitis virus, VSV) and bacterial (lipopolysaccharide, LPS) infections on BA metabolism and signaling. Infection models were successfully established by intraperitoneally injecting VSV and LPS, respectively. VSV and LPS injection significantly changed the circulating BA profiles, with highly increased levels of taurine-conjugated BAs and significant decreases in unconjugated BAs. Consistent with the decreased levels of circulating cholic acid (CA) and chenodeoxycholic acid (CDCA), the expression of BA biosynthesis-related rate-limiting enzymes (
Cyp7a1
,
Cyp27a1
,
Cyp8b1,
and
Hsd3b7
) were significantly reduced. Furthermore, hepatic and pulmonary BA receptors (BARs) expression varied in different infection models. LPS treatment had an extensive impact on tested hepatic and pulmonary BARs, resulting in the upregulation of TGR5, S1PR2, and VDR, while VSV infection only promoted VDR expression. Our study provides insights into the involvement of BA metabolism in the pathophysiology of infection, which may provide potential clues for targeting BA metabolism and BAR signaling to boost innate immunity and control infection.

IMPORTANCE
This study focuses on the crosstalk between bile acid (BA) metabolism and immune response in VSV infection and LPS treatment models and depicts the effect of infection on circulating BA profiles, the biosynthesis-related enzymes, and their receptors. These findings provide insights into the effect of infection on BA metabolism and signaling, adding a more comprehensive understanding to the relationship between infection, BA metabolism and immune responses.
Trends in sex differences in neurodevelopmental outcomes among extremely preterm infants
Authors: Boghossian Nansi S , Mack Nicole A , Bell Edward F , Tan Sylvia , Stoll Barbara J , Rysavy Matthew A , Ambalavanan Namasivayam , Tyson Jon E , Das Abhik , Hintz Susan R 
Published: September 2024

ObjectiveTo examine whether changes in survival without moderate or severe neurodevelopmental impairment (NDI) at 18–26 months’ corrected age from 1999 to 2018 differed between male and female infants.DesignThis retrospective cohort study used data from the NICHD Neonatal Research Network hospitals. Robust Poisson regression models were used to estimate adjusted relative risks (aRRs) and 95% CIs for survival without moderate or severe NDI between males and females. Interactions between sex and time were assessed to evaluate temporal differences in the outcome by sex. Variables adjusted for included centre, maternal age, ethnicity/race, gestational age and small for gestational age.PatientsInborn infants with gestational age of 22–26 weeks at NICHD Neonatal Research Network hospitals from 1999 to 2018.Main outcome measureChange over time in survival without moderate or severe NDI at 18–26 months’ corrected age between male and female infants.ResultsOf 26 307 infants, 13 045 (49.6%) were male. Survival without moderate or severe NDI declined for both sexes over time, from 32.9% to 30.6% for males and from 47.4% to 40.0% for females, between 1999–2003 and 2014–2018. Males were less likely than females to survive without moderate or severe NDI (aRR=0.80; 95% CI 0.78 to 0.83). Changes in survival without moderate or severe NDI did not differ between males and females.ConclusionThere were no differential changes in survival without moderate or severe NDI between male and female infants.
Use of CFTR modulators in pregnancy: new information for neonatal, paediatrics and midwifery teams
Authors: Khan Haji Sheeraz , Tran Paula 
Published: September 2024

Cystic fibrosis (CF) is common, multisystem, life-limiting genetic condition, predominantly in the Caucasian population. There have been recent advances in the management of CF, in particular in the last 5 years following approval of cystic fibrosis transmembrane conductance regulator (CFTR) protein modulators by the National Health Service (NHS) for use in people with CF (pwCF).
Traditionally, almost 40% of female patients with CF (fwCF) and over 95% of male patients with CF (mwCF) have issues with subfertility or infertility. CFTR modulators have transformed the lives of pwCF who have the specific genetic variants that respond to the treatment.
Women taking CFTR modulators, particularly highly effective CFTR modulators (elexacaftor, tezacaftor and ivacaftor), have shown resolution of infertility and successful pregnancies without fertility treatment. At present male patients taking CFTR modulators have not shown improvement in infertility. Unplanned pregnancies are on the increase in fwCF. fwCF have had significantly improved general health when taking CFTR modulators. Subsequently many fwCF now become pregnant and choose to continue their pregnancies to term, with positive outcomes.
Clinical and biochemical status of the newborn babies with CF, who are born to fwCF on CFTR modulators, can be very different when compared with the other babies with CF who are unexposed to CFTR modulators in utero.
New opportunities bring new challenges. This review highlights how infants exposed to CFTR modulators in utero can be affected, and suggests how they should be monitored.
Cumulative live birth rate of a blastocyst versus cleavage stage embryo transfer policy during in vitro fertilisation in women with a good prognosis: multicentre randomised controlled trial
Authors: Cornelisse Simone , Fleischer Kathrin , van der Westerlaken Lucette , de Bruin Jan-Peter , Vergouw Carlijn , Koks Carolien , Derhaag Josien , Visser Jantien , van Echten-Arends Jannie , Slappendel Els , Arends Brigitte , van der Zanden Moniek , van Dongen Angelique , Brink-van der Vlugt Janneke , de Hundt Marcella , Curfs Max , Verhoeve Harold , Traas-Hofmans Maaike , Wurth Yvonne , Manger Petra , Pieterse Quirine , Braat Didi , van Wely Madelon , Ramos Liliana , Mastenbroek Sebastiaan 
Published: September 2024

Abstract

Objectives
To evaluate whether embryo transfers at blastocyst stage improve the cumulative live birth rate after oocyte retrieval, including both fresh and frozen-thawed transfers, and whether the risk of obstetric and perinatal complications is increased compared with cleavage stage embryo transfers during in vitro fertilisation (IVF) treatment.

Design
Multicentre randomised controlled trial.

Setting
21 hospitals and clinics in the Netherlands, 18 August 2018 to 17 December 2021.

Participants
1202 women with at least four embryos available on day 2 after oocyte retrieval were randomly assigned to either blastocyst stage embryo transfer (n=603) or cleavage stage embryo transfer (n=599).

Interventions
In the blastocyst group and cleavage group, embryo transfers were performed on day 5 and day 3, respectively, after oocyte retrieval, followed by cryopreservation of surplus embryos. Analysis was on an intention-to-treat basis, with secondary analyses as per protocol.

Main outcome measures
The primary outcome was the cumulative live birth rate per oocyte retrieval, including results of all frozen-thawed embryo transfers within a year after randomisation. Secondary outcomes included cumulative rates of pregnancy, pregnancy loss, and live birth after fresh embryo transfer, number of embryo transfers needed, number of frozen embryos, and obstetric and perinatal outcomes.

Results

The cumulative live birth rate did not differ between the blastocyst group and cleavage group (58.9% (355 of 603)
v
58.4% (350 of 599; risk ratio 1.01, 95% confidence interval (CI) 0.84 to 1.22). The blastocyst group showed a higher live birth rate after fresh embryo transfer (1.26, 1.00 to 1.58), lower cumulative pregnancy loss rate (0.68, 0.51 to 0.89), and lower mean number of embryo transfers needed to result in a live birth (1.55
v
1.82; P<0.001). The incidence of moderate preterm birth (32 to <37 weeks) in singletons was higher in the blastocyst group (1.87, 1.05 to 3.34).

Conclusion
Blastocyst stage embryo transfers resulted in a similar cumulative live birth rate to cleavage stage embryo transfers in women with at least four embryos available during IVF treatment.

Trial registration
International Clinical Trial Registry Platform NTR7034.