fastp: an ultra-fast all-in-one FASTQ preprocessor

Revisiting the emergence of the Chikungunya virus in Alagoas, Northeast of Brazil

Chikungunya virus (CHIKV), an Alphavirus, emerged in the Americas in 2013 and was first documented in Brazil in September 2014, in the states of Pará and Bahia. Although Alagoas state officially reported its first case in late 2015, this study investigated potential earlier unreported cases by analyzing samples from a 2013-2014 Orthoflavivirus serological survey. We screened sera from patients with acute febrile illness, initially suspected of dengue but negative in molecular tests for the genus Orthoflavivirus, using ELISA (IgM/IgG), viral isolation, PCR, and next-generation sequencing. Two samples collected in June and August 2014 tested positive for anti-CHIKV IgM, and four additional samples collected between June and September 2014 tested positive for anti-CHIKV IgG antibodies. From one sample IgM-positive (630H) collected in August 2014, we isolated and sequenced a nearly complete genome (95.53% coverage, 2714× depth) classified as the East-Central-South-African (ECSA) genotype. Phylogenetic analyses revealed that the Alagoas-2014 genome formed a distinct, well-supported clade separate from the Bahia 2014 lineage. Temporal inference dated this lineage's origin to October 2013 (90% CI: April 2013-March 2014), suggesting a new introduction of ECSA into Alagoas. This genomic evidence, along with serological data, confirms the undetected early circulation of CHIKV in Alagoas and suggests a possible introduction of ECSA in Brazil in 2014, distinct from the well-documented introduction in Bahia.

Chromosome-level genome assembly of scalloped spiny lobster Panulirus homarus homarus

Lobsters, aquatic organisms of significant economic value, hold an important position in the global aquaculture and fisheries industries. However, due to overfishing and ecological change, the populations of certain lobster species have declined dramatically, prompting conservation efforts in various countries. However, limited genomics research has restricted our capacity to conserve and exploit lobster germplasm resources. Here, we present a chromosome-level reference genome for Panulirus homarus homarus constructed using PacBio long-read sequencing and Hi-C data. The genome assembly size was 2.61 Gb, with a contig N50 of 5.43 Mb, and a scaffold N50 of 36.69 Mb. The assembled sequences were anchored to 73 chromosomes, covering 96.05% of the total genome. A total of 25,580 protein-coding genes were predicted, and 99.98% of the genes were functionally annotated using various protein databases. The high-quality genome assembly provides a valuable resource for studying the biology and evolutionary history of P. h. homarus, and could facilitate sustainable resource management, aquaculture, and conservation of the species.

The Great Barrier Reef, a center for Pelagophyceae (Heterokontophyta) diversity, including a new genus and seven new species

The pelagophytes are a morphologically diverse class of marine heterokont algae defined by deoxyribonucleic acid (DNA) gene sequences, the presence of a multilayered, perforated theca (PT), and the novel role of the Golgi apparatus in the formation and secretion of the PT, as well as materials for the synthesis of the outer extracellular layers (e.g., cell walls and mucilage). We established clonal cultures of sand-dwelling pelagophytes collected from intertidal and subtidal locations at Heron Island on the Great Barrier Reef (GBR), Australia, and established phylogenetic trees based on nuclear 18S rDNA and plastid rbcL, psaA, psaB, psbA, and psbC gene sequences that led to the discovery of seven new species and several interesting range extensions. The new genus and species, Revolvomonas australis, is sister to Pituiglomerulus and Chrysocystis in the Chrysocystaceae (Sarcinochrysidales, Pelagophyceae). Additional new species are Sarcinochrysis kraftii, Sa. guiryi, Arachnochrysis pilardiaziae, A. cassiotisii, Sungminbooa capricornica, and Su. tropica; also identified and cultured from the GBR were Sa. marina, Aureoumbra geitleri, Chrysoreinhardia giraudii, Chrysocystis fragilisi, and the planktonic Pelagomonas calceolata. Revolvomonas was studied in detail and has several unusual features for sand-dwelling pelagophytes. In just three short collecting trips to Heron Island, we were able to isolate and identify over 40% of the pelagophyte genera discovered to date. This study substantiates the diverse nature of pelagophytes and suggests tropical reef sand may be a center for pelagophyte diversity.

Are reads required? High-precision variant calling from bacterial genome assemblies

Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related Staphylococcus aureus isolates sequenced on Illumina and Oxford Nanopore Technologies platforms. By benchmarking multiple assembly and variant-calling pipelines against a ground truth dataset, we found that read-based methods consistently achieved high accuracy. Assembly-based approaches performed well in some cases but were highly dependent on assembly quality, as errors in the assembly led to false-positive variant calls. These findings underscore the need for improved assembly techniques before the potential benefits of assembly-based variant calling (such as reduced computational requirements and simpler data management) can be realized.

Defining three dimensional chromatin structures of pediatric and adolescent B cells using primary B cell and EBV-immortalized B cell reference genomes

BACKGROUND/PURPOSE

Knowledge of the 3D genome is essential to elucidate genetic mechanisms driving autoimmune diseases. The 3D genome is distinct for each cell type, and it is uncertain whether cell lines faithfully recapitulate the 3D architecture of primary human cells or whether developmental aspects of the pediatric immune system require use of pediatric samples. We undertook a systematic analysis of B cells and B cell lines to compare 3D genomic features encompassing risk loci for juvenile idiopathic arthritis (JIA), systemic lupus (SLE), and type 1 diabetes (T1D).

METHODS

We isolated B cells from four healthy individuals, ages 9-17. HiChIP was performed using a CTCF antibody, and CTCF peaks were called within each sample separately. Peaks observed in all four samples were identified. CTCF loops were called within the pediatric samples using three CTCF peak datasets: 1) self-called CTCF consensus peaks called within the pediatric samples, 2) ENCODE's publicly available GM12878 CTCF ChIP-seq peaks, and 3) ENCODE's primary B cell CTCF ChIP-seq peaks from two adult females. Differential looping was assessed within the pediatric samples and each of the three peak datasets.

RESULTS

The number of consensus peaks called in the pediatric samples was similar to that identified in ENCODE's GM12878 and primary B cell datasets. We observed < 1% of loops that demonstrated significantly differential looping between peaks called within the pediatric samples themselves and when called using ENCODE GM12878 peaks. Significant looping differences were even fewer when comparing loops of the pediatric called peaks to those of the ENCODE primary B cell peaks. When querying loops found in juvenile idiopathic arthritis, type 1 diabetes, or systemic lupus erythematosus risk haplotypes, we observed significant differences in only 2.2%, 1.0%, and 1.3% loops, respectively, when comparing peaks called within the pediatric samples and ENCODE GM12878 dataset. The differences were even less apparent when comparing loops called with the pediatric vs ENCODE adult primary B cell peak datasets.

CONCLUSION

The 3D chromatin architecture in B cells is similar across pediatric, adult, and EBV-transformed cell lines. This conservation of 3D structure includes regions encompassing autoimmune risk haplotypes. Thus, even for pediatric autoimmune diseases, publicly available adult B cell and cell line datasets may be sufficient for assessing effects exerted in the 3D genomic space.

Whole-genome sequencing of global forest pathogen Diplodia sapinea causing pine shoot blight

OBJECTIVE

The pathogenic fungus Diplodia sapinea is of significant importance due to its primary role inducing tip dieback on various Pinus species which are widely distributed throughout the world. The objective of this study is to further provide comprehensive and specific resources for genome assembly and sequence annotation of this important forest pathogen from China, thereby establishing a robust foundation for future studies on its systematics, population genetics, genomics and global movement.

DATA DESCRIPTION

A high-quality genome of D. sapinea strain ZXD319 was sequenced utilizing the Nanopore PromethION and BGI DNBSEQ-T7 platforms. The assembled genome spans a total length of 36.81 Mb, comprising 14 contigs, with a GC content of 56.80% and an N50 value of 2,972,533 bp. It encompasses 11,200 protein-coding genes and 252 noncoding RNAs. The predicted genes were annotated against multiple public databases, and 1,611 potential virulence genes were identified through the Pathogen Host Interactions (PHI) database. Furthermore, the genome comparative analysis of D. sapinea and related species revealed 11,568 gene clusters and 3,436 single-copy clusters. Phylogenetic analysis indicated a close evolutionary relationship between D. sapinea with D. corticola and D. seriata. The genomic data presented herein serve as a valuable resource for future studies on this globally important pathogen.

Chromosome-level assemblies of the White bream Parabramis pekinensis

White bream Parabramis pekinensis is an omnivorous fish belong to Cyprinidae that is widespread in Asia. In this study, we presented chromosome-level genome assemblies of P. pekinensis by using PacBio HiFi long reads and Hi-C technology. We assembled high-quality genome of 1.03 Gb with scaffold N50 length of 40.04 Mb, and a total of 98.31% of the assembled sequences were anchored to 24 chromosomes. BUSCO analysis revealed that the genome assembly has a high-level completeness of 98.35% gene coverage. A total of 26,542 protein-coding genes were predicted, of which 92.61% were functionally annotated. The phylogenetic analysis indicated that the lineage leading to P. pekinensis was diverged from the lineage to Megalobrama amblycephala approximately 7.6 million years ago. The high-quality genome assembly provide valuable resources for evolutionary study and genetic breeding of genus Parabramis.

From Rare to Common: Genetic Insights into TLR7 Variants in a Multicentric Spanish Study on COVID-19 Severity

TLR7, which encodes a key receptor for single-stranded RNA (ssRNA) virus of the innate immune system, was recently associated with X-linked immunodeficiency and COVID-19 susceptibility. This study investigates the association between TLR7 variants and susceptibility to severe COVID-19 in a multicentric Spanish cohort. The TLR7 gene was sequenced in a cohort of 365 COVID-19 patients, stratified into two groups: one comprising mild and asymptomatic patients, considered as controls (n = 87), and the other consisting of moderate to severely affected patients hospitalized due to COVID-19 pneumonia, considered as cases (n = 278). A total of 152 unique TLR7 variants were identified, of note, six rare variants were identified in 11 cases (3.96%), all of whom belonged to the case group. The functional impact of rare TLR7 variants was assessed using a luciferase reporter assay and revealed that N215S is a loss-of-function (LOF) variant, while D332G exhibits an hypomorphic behavior. Conversely, H90Y, V219I, A448V, and R902K maintained normal signaling. No skewed X-inactivation was observed in female carriers of N215S or D332G. In addition, the common variants Q11L (rs179008), c.4-151A>G (rs179009) and c.*881C>G (rs3853839) were associated with severe pneumonia, while c.4-151A>G (rs179009) was specifically linked to Intensive Care Unit (ICU) admission. These findings highlight the role of TLR7 in antiviral immune response and its association with severe COVID-19 in men. The luciferase assay proves to be a reliable tool for evaluating TLR7 signaling, effectively distinguishing between neutral, LOF, and gain-of-function (GOF) variants. Further research is needed to better understand TLR7 variants and its implications in immunodeficiency and immune dysregulation.

A foodborne outbreak caused by atypical enteropathogenic Escherichia coli O45:H15 in the Kinki region of Japan

Atypical enteropathogenic Escherichia coli (aEPEC) mainly causes sporadic diarrhea and occasional outbreaks. However, the genetic determinant of aEPEC causing large outbreaks is still unknown. In June 2022, 171 of 934 people presented with diarrhea and abdominal pain after eating a lunch box in the Kinki region of Japan. We investigated 44 fecal samples from persons who ate the cuisine and isolated enteropathogenic Escherichia coli (EPEC) serotype O45:H15 from 38 of them. The same pathogen was also isolated from the feces of two employees and a leftover sample (mashed tofu salad with spinach). Pulsed-field gel electrophoresis and whole genome sequencing supported the clonality of the isolates. The isolates were negative for bfpA, encoding the bundle-forming pilus, and were accordingly identified as aEPEC. Whole genome sequencing revealed the presence of a plasmid-encoded type 3 secretion system effector gene, espT, involving the invasive phenotype of EPEC. Finally, we concluded that this was a foodborne outbreak caused by aEPEC O45:H15. Since the food poisoning case caused by aEPEC O45:H15 harboring espT has not been reported previously, the current study broadens our understanding of aEPEC food poisoning and its genetic background.IMPORTANCEaEPEC causes diarrhea in humans, despite the reported asymptomatic carriers of aEPEC worldwide. Several outbreaks caused by aEPEC also support that this pathogen is a diarrheagenic agent; however, the genetic determinant of aEPEC causing large outbreaks is still unclear. In 2022, a large foodborne outbreak by aEPEC O45:H15 affected more than 170 people in the Kinki region of Japan. We sequenced the whole genomes of the etiological agents and identified a potential virulent plasmid carrying espT, which is a virulence factor of aEPEC O111 that caused diarrhea in more than 600 people in Finland. Our data strengthen the importance of espT as a virulence factor of aEPEC outbreaks.

Urolithin A alleviates radiation pneumonitis by activating PINK1/PRKN-mediated Mitophagy

BACKGROUND

Radiation pneumonitis (RP) is a common and severe complication of radiotherapy, whose pathogenesis involves complex inflammatory responses and cellular damage. Despite its clinical significance, effective treatments remain limited. This study investigates the role of radiation-induced PINK1/PRKN-mediated mitophagy and type I interferon responses in RP and evaluates the therapeutic potential of Urolithin A (UA) in regulating inflammation through mitophagy activation.

METHODS

We established RP mouse models (20 Gy thoracic irradiation) and radiation-induced BEAS-2B cell models (6 Gy). We systematically investigated mitochondrial damage, mtRNA release, RIG-I/MDA5-MAVS pathway activation, and PINK1/PRKN-mediated mitophagy changes. Moreover, the effects of UA and the mitophagy inhibitor Mdivi-1 on inflammation and lung injury were analyzed.

RESULTS

Radiation significantly caused mitochondrial damage in lung tissues, inducing mtRNA release and RIG-I/MDA5-MAVS-mediated type I interferon response. PINK1/PRKN-mediated mitophagy was significantly enhanced, clearing damaged mitochondria and reducing cytosolic mtRNA release, thereby suppressing inflammation. Pharmacological activation of mitophagy with UA markedly improved lung pathology, reduced inflammatory cytokine levels, and inhibited excessive activation of the RIG-I/MDA5-MAVS pathway. Conversely, the knockdown of PINK1 or PRKN weakened the protective effects of UA. Both in vitro and in vivo, UA reduced radiation-induced inflammation and improved lung tissue structure and function through mitophagy.

CONCLUSIONS

Radiation-induced mtRNA release activates the RIG-I/MDA5-MAVS-mediated type I interferon response, driving inflammation in RP. PINK1/PRKN-mediated mitophagy significantly alleviates inflammation by reducing cytosolic mtRNA release. As a mitophagy inducer, UA demonstrates therapeutic potential for RP, providing a new direction for the development of anti-inflammatory strategies.

ROS homeostasis and cell wall biosynthesis pathway are involved in female inflorescence development of birch (Betula platyphylla)

BACKGROUND

Female inflorescence development from megasporogenesis to gametogenesis, and mature female gametophyte (FG), is a complex and important event in plant sexual reproduction. However, how this essential developmental process is regulated in birch remains obscure. This study conducted extensive morphological and transcriptomic analyses to reveal possible regulatory mechanisms during birch female inflorescence development.

RESULTS

Histological analyses showed that birch exhibits a Polygonum-type embryo sac. During early ovule development, the ovule primordium emerges and subsequently differentiates into the archesporial cell (ASC), initiating megasporogenesis. The megaspore mother cell (MMC) then undergoes meiosis, generating a functional megaspore (FM) that develops into the mature embryo sac (MES). Transcriptomic profiling revealed upregulation of reactive oxygen species (ROS)-scavenging genes, including BpGSTU17, BpGSTU19, BpAPX1, BpPRXIIE-1, BpSODCP, and BpFDX3, at the MMC stage. At the MES stage, genes involved in both ROS synthesis and scavenging, such as BpACX, BpCuAOγ1, BpGLO1, BpRBOHH, BpUOX2, BpFSD2, BpCAT3, BpGRX, BpNRX, and BpTRX, were significantly expressed. BpPAL, BpC4H, BpCSE, BpCoMT, BpCCoAOMT, BpCAD, BpF5H, BpLAC, BpXTH23, and BpCESA, genes involved in the cell wall biosynthesis pathways including lignin, cellulose, hemicellulose and pectin, were also upregulated.

CONCLUSION

Our results suggest that ROS homeostasis affects the process of birch megasporogenesis. Genes related to ROS signaling and cell wall synthesis participate in embryo sac maturation.

Chitin/cellulose nanofiber complex from spent mushroom substrate systemically induces plant disease resistance through its cellulose-derived function

Spent mushroom substrate (SMS) is a major agricultural waste generated as a by-product of industrial mushroom cultivation. To valorize SMS, we developed a method to convert it to a form of nanofiber dispersion, chitin/cellulose nanofiber complex (CCNFC), via nanofibrillation. CCNFC application induces plant disease resistance, local immune response, and systemic disease resistance. Because chitin nanofibers (NF) also induce these defense responses, their function has been proposed to contribute to CCNFC-induced disease resistance. Here, we aimed to determine the precise mode of action of CCNFC in inducing plant disease resistance. The local immune response and systemic disease resistance induced by CCNFC were not compromised in Arabidopsis and rice mutants for lysin motif-type pattern recognition receptors involved in chitin perception. Transcriptome analysis revealed similar systemic transcriptional responses in CCNFC- and cellulose NF-treated Arabidopsis plants. Cellulose NF-induced systemic disease resistance but not local immune response. Thus, the local immune response triggered by CCNFC also requires another component(s) in CCNFC other than cellulose, accompanied by chitin. In contrast, the systemic disease resistance induced by CCNFC could be caused mainly by cellulose NF.

Chromosome-scale genome assembly of the fire blight resistant Malus fusca accession MAL0045, donor of FB_Mfu10

The wild apple, Malus fusca accession MAL0045, is highly resistant to fire blight disease, caused by the bacterial pathogen, Erwinia amylovora. A major resistance locus, FB_Mfu10 was identified on chromosome 10 of MAL0045 including other contributory loci on chromosomes 16, 4, and 15. Here, we report a chromosome-scale genome assembly of MAL0045 to facilitate the studies of its fire blight resistance. PacBio sequencing and Illumina sequencing for Hi-C contig anchorage were employed to obtain the genome. A total of 669.46 Mb sequences were anchored onto 17 chromosomes, taking up 99.75% of total contig length. Contigs anchored onto chromosomes were further ordered and orientated, where a total of 637.67 Mb sequences were anchored onto chromosomes in proper order and orientation, resulting in a final anchoring ratio of 95.25%. The BUSCO score of this assembly is 97.46%. Further, a total of 47,388 genes were predicted via ab initio, homology-based, and RNAseq methodologies. The availability of this genome will facilitate functional and comparative genomics studies, especially about the donors of fire blight resistance in Malus.

Unlocking the agro-physiological potential of wheat rhizoplane fungi under low P conditions using a niche-conserved consortium approach

Plant growth-promoting fungi (PGPF) hold promise for enhancing crop yield. This study delves into the fungal diversity of the wheat rhizoplane across seven Moroccan agricultural regions, employing a niche-conserved strategy to construct fungal consortia (FC) exhibiting higher phosphorus (P) acquisition and plant growth promotion. This study combined culture-independent and culture-dependent methods exploring taxonomic and functional diversity in the rhizoplane of wheat plants obtained from 28 zones. Twenty fungal species from eight genera were isolated and confirmed through internal transcribed spacer (ITS) Sanger sequencing. P solubilization (PS) capacity was assessed for individual species, with Talaromyces sp. (F11) and Rhizopus arrhizus CMRC 585 (F12) exhibiting notable PS rates, potentially due to production of organic acids such as gluconic acid. PGPF traits and antagonism activities were considered when constructing 28 niche-conserved FC (using isolates from the same zone), seven intra-region FC (different zones within a region), and one inter-region FC. Under low P conditions, in planta inoculation with niche-conserved FC (notably FC14 and FC17) enhanced growth, physiological parameters, and P uptake of wheat, in both vegetative and reproductive stages. FC14 and FC17, composed of potent fungi such as F11 and F12, demonstrated superior plant growth benefits compared with intra- and inter-region constructed FC. Our study underscores the efficacy of the niche-conserved strategy in designing synthetic fungal community from isolates within the same niche, proving significant agro-physiological potential to enhance P uptake and plant growth of wheat.

Dynamic changes of dental plaque and saliva microbiota in OSCC progression

OBJECTIVES

To elucidate the changes in microbial composition and genomics in saliva and dental plaque during the progression of Oral Squamous Cell Carcinoma (OSCC), and to identify virulence factors and pathways associated with tumor differentiation in OSCC patients.

MATERIALS AND METHODS

Using metagenomic sequencing, 64 saliva and dental plaque samples from OSCC patients at different stages of differentiation were examined.

RESULTS

The results showed notable differences in the microbial composition and genomic profiles across ecological regions and differentiation degrees. Notably, the relative abundance of specific microbes, such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Haemophilus parainfluenzae, increased in poorly differentiated OSCC. Microbial alpha diversity in dental plaque and saliva correlates with tumor T staging. Dental plaque microbiota shows higher specialization, especially in poorly differentiated tumors. Both microbiota types become more stable with advanced T staging. Genomic analysis reveals increased virulence factors in poorly differentiated stages.Subsequently, functional pathway analysis and tracing of pathogens reveal specific microbial mechanisms in oral cancer pathogenesis. Certain oral pathogens may promote tumorigenesis by secreting factors like GAPDH (glyceraldehyde-3-phosphate dehydrogenase), GspG (a gingipain precursor), and AllS (a lysine-specific gingipain precursor).

CONCLUSIONS

OSCC progression is associated with altered microbial composition, diversity, and genomic profiles in saliva and dental plaque. Poorly differentiated stages show higher abundance of pathogens and virulence factors, implicating them in tumorigenesis.

CLINICAL RELEVANCE

Understanding the microbial and genomic changes in saliva and dental plaque during OSCC progression could aid in developing new diagnostic biomarkers and targeted therapies, potentially enhancing early detection, treatment efficacy, and patient prognosis. Maintaining oral microbiota homeostasis may also help prevent oral cancer.

AFB1 exacerbates testicular and intestinal inflammation by increasing stearoyl ethanolamide and homocysteine levels

In environmental toxicology, aflatoxin B1 (AFB1) is recognized for its detrimental effects on reproductive and intestinal health. This study elucidates how AFB1-induced elevations in stearoyl ethanolamide (SEA) and homocysteine (HCY) impact male fertility and intestinal function in mice. AFB1 was found to markedly reduce sperm concentration and exacerbate sperm damage in mice, primarily by increasing serum SEA and HCY levels. These metabolites compromise testicular structure and function, disrupt the blood-testicular barrier, and downregulate critical testicular proteins including DAZL, SYCP1, SYCP2, StAR, and CYP17A1. Transcriptomic analysis revealed that SEA and HCY broadly alter testicular gene expression, activate NOD-like receptor signaling pathways, induce testicular inflammation, and promote apoptosis. Additionally, SEA and HCY impair intestinal barrier function by reducing the expression of tight junction proteins ZO-1 and Occludin. Functional network analysis indicated that SEA and HCY regulate intestinal immune responses by promoting M1 macrophage polarization and the upregulation of pro-inflammatory cytokines, while simultaneously inhibiting anti-inflammatory factors. This study underscores the multifaceted adverse effects of SEA and HCY on male reproductive health and gut integrity, and highlights the need for further research into mechanisms and potential interventions to mitigate these harmful outcomes.

Cellular hierarchies of embryonal tumors with multilayered rosettes are shaped by oncogenic microRNAs and receptor-ligand interactions

Embryonal tumor with multilayered rosettes (ETMR) is a pediatric brain tumor with dismal prognosis. Characteristic alterations of the chromosome 19 microRNA cluster (C19MC) are observed in most ETMR; however, the ramifications of C19MC activation and the complex cellular architecture of ETMR remain understudied. Here we analyze 11 ETMR samples from patients using single-cell transcriptomics and multiplexed spatial imaging. We reveal a spatially distinct cellular hierarchy that spans highly proliferative neural stem-like cells and more differentiated neuron-like cells. C19MC is predominantly expressed in stem-like cells and controls a transcriptional network governing stemness and lineage commitment, as resolved by genome-wide analysis of microRNA-mRNA binding. Systematic analysis of receptor-ligand interactions between malignant cell types reveals fibroblast growth factor receptor and Notch signaling as oncogenic pathways that can be successfully targeted in preclinical models and in one patient with ETMR. Our study provides fundamental insights into ETMR pathobiology and a powerful rationale for more effective targeted therapies.

Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics

The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bronchoalveolar lavage fluid and sputum samples from 116 COVID-19 patients, categorized into mild, severe, and critical groups. Our analysis revealed significant differences in viral genotypes across disease stages. As disease severity increased, the Chao index also rose. The mild group was predominantly dominated by Firmicutes, while the severe group showed an increase in Bacteroidetes. The critical group was characterized by a higher abundance of Actinobacteria and Proteobacteria. Notably, the abundance of Streptococcus and Rothia decreased as the disease progressed. Additionally, the Shannon index correlated with mortality risk, while the Chao index was associated with ICU admission, mechanical ventilation, and patient survival. These findings highlight the strong link between microbial composition and COVID-19 severity, providing valuable insights for assessing disease progression.

Population genomics uncovers loci for trait improvement in the indigenous African cereal tef (Eragrostis tef)

Tef (Eragrostis tef) is an indigenous African cereal that is gaining global attention as a gluten-free "superfood" with high protein, mineral, and fibre contents. However, tef yields are limited by lodging and by losses during harvest owing to its small grain size (150× lighter than wheat). Breeders must also consider a strong cultural preference for white-grained over brown-grained varieties. Tef is relatively understudied with limited "omics" resources. Here, we resequence 220 tef accessions from an Ethiopian diversity collection and also perform multi-locational phenotyping for 25 agronomic and grain traits. Grain metabolome profiling reveals differential accumulation of fatty acids and flavonoids between white and brown grains. k-mer and SNP-based genome-wide association uncover important marker-trait associations, including a significant 70 kb peak for panicle morphology containing the tef orthologue of rice qSH1-a transcription factor regulating inflorescence morphology in cereals. We also observe a previously unknown relationship between grain size, colour, and fatty acids. These traits are highly associated with retrotransposon insertions in homoeologues of TRANSPARENT TESTA 2, a known regulator of grain colour. Our study provides valuable resources for tef research and breeding, facilitating the development of improved cultivars with desirable agronomic and nutritional properties.

Genomic insights into Neopusillimonas aestuarii sp. nov., a novel estuarine bacterium with adaptations for ectoine biosynthesis and stress tolerance

A novel Gram-stain-negative, aerobic rod-shaped bacterial strain, which was catalase- and oxidase-positive, designated as DMV24BSW_DT, was isolated from the estuarine waters of the Bhavnagar (India) coast of the Arabian Sea. Its 16S rRNA gene exhibited 99.52% similarity with Neopusillimonas maritima 17-4AT, followed by 97.95% similarity with the Pusillimonas caeni strain EBR-8-1 and 97.4% similarity with the P. noertemannii strain BN9T. Phylogenomic analysis using BPGA (14,332 aa) and UBCG (90,261 bp) tools revealed a unique phylogenetic position within the genus Neopusillimonas. The genome exhibited a G + C content of 53.25%. In comparison with N. maritima 17-4AT, the strain demonstrated an average nucleotide identity (ANIb) of 94.47% and a digital DNA-DNA hybridization (dDDH) value of 60.1%, indicating distinct genomic divergence. The genome of DMV24BSW_DT contains several unique metabolic genes that facilitate efficient electron transfer during aerobic respiration. Additionally, it harbours one intact prophage and four defective prophages, indicating ongoing viral interactions. The genome encodes a complete pathway for ectoine biosynthesis and transportation. Strain DMV24BSW_DT tested positive for gelatin hydrolysis and demonstrated the ability to utilize a wide range of carbohydrates, including α-D-glucose, D-melibiose, D-fructose, L-rhamnose, and various organic acids, such as methyl pyruvate and propionic acid, along with tolerance to fluctuating pH (5 to 10) and salinity (0-4% NaCl). The major polar lipids included phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine, while fatty acid analysis revealed C12:0, C16:0, C17:0 cyclo, and summed feature 2 (C12:0 aldehyde/unknown) as major components. The respiratory quinones identified were MK-7 and MK-8. These comprehensive phenotypic, chemotaxonomic, and genomic characteristics support the unique taxonomic position of DMV24BSW_DT within the genus Neopusillimonas and the proposal of a novel species of the genus Neopusillimonas, for which the name Neopusillimonas aestuarii sp. nov. (Type strain DMV24BSW_DT = MCC 2506 T = KCTC 72453 T = JCM 34508 T) is proposed.

A consortium of seven commensal bacteria promotes gut microbiota recovery and strengthens ecological barrier against vancomycin-resistant enterococci

BACKGROUND

Vancomycin-resistant enterococci (VRE) often originate from the gastrointestinal tract, where their proliferation precedes dissemination into the bloodstream, and can lead to systemic infection. Uncovering the actors and mechanisms reducing the intestinal colonisation by VRE is essential to control infection. We aimed to identify commensal bacteria that interfere with VRE gut colonisation or act as an ecological barrier.

RESULTS

We performed a 3-week longitudinal analysis of the gut microbiota composition and VRE carriage levels during microbiota recovery in mice colonised with VRE after antibiotic-induced dysbiosis. By combining biological data and mathematical modelling, we identified 15 molecular species (OTUs) that negatively correlated with VRE overgrowth. Six strains representative of these OTUs were collected, cultivated and used in mixture with a seventh strain (Mix7) in two different mouse lines challenged with VRE. Of the seven strains, three belonged to Lachnospiraceae, one to Muribaculaceae, one to Ruminococcaceae and two to Lactobacillaceae. We found that Mix7 led to a better recovery of the gut microbiota composition and reduced VRE carriage. Differences in the effect of Mix7 were observed between responder and non-responder mice. These differences were associated with variations in the composition of the initial microbiota and during recovery and represent potential biomarkers for predicting response to Mix7. In a mouse model of alternative stable state of dysbiosis, response to Mix7 was associated with higher concentrations of short-chain fatty acids (acetate, propionate, butyrate) and a range of metabolites including bile acids, reflecting the recovery of the microbiota back to initial state. Furthermore, Muribaculum intestinale strain was required to obtain the Mix7 effect on VRE reduction in vivo, but the presence of at least one of the other six strains was needed. None of the supernatant of the seven strains, alone or in combination, inhibited VRE growth in vitro. Interestingly, five strains belong to species shared among humans and mice, and the other two have human functional equivalents.

CONCLUSIONS

An innovative approach based on mathematical modelling of the microbiota composition permitted to identify a mixture of commensal bacterial strains, which improves the ecological barrier effect against VRE. The mechanisms are dependent on the recovery and initial composition of the microbiota. Ultimately, this work will enable a move towards a personalised medicine by targeting predisposed patients presenting a risk of infection, such as neutropenic or bone-marrow transplant patients, and likely to respond to supplementation with commensal strains, providing new live biotherapeutic products and biomarkers to predict response to supplementation. Video Abstract.

Potential role of key rumen microbes in regulating host health and growth performance in Hu sheep

BACKGROUND

Average daily gain (ADG) is an important component affecting the profitability of sheep. However, research on the relationship between rumen microbes and sheep growth phenotype is still very lacking. Therefore, in this study, 16 Hu sheep were selected from a cohort of 318 sheep assigned to the same feeding and management conditions, and divided into high growth rate (HADG, n = 8) group and low growth rate (LADG, n = 8) group according to the extreme ADG value. Then, the differences in rumen microbes, rumen fermentation and animal immune parameters were further compared between groups to explore the potential role of rumen key microbes in regulating the health and growth performance of Hu sheep hosts.

RESULTS

The results showed that specific pathogenic bacteria associated with ADG, including Anaerotruncus, Sediminibacterium and Glaesserella, exhibited significant correlations with interleukin-6 (IL-6) and immunoglobulin G (IgG). These interactions disrupt immune homeostasis in the host, leading to a metabolic prioritization of energy resources toward immune responses, thereby impairing growth and development. Succinivibrio_dextrinosolvens was enriched in HADG sheep and exhibited a significant positive correlation with propionate levels. This promoted propionate production in the rumen, enhancing the metabolic activity of carbohydrate, amino acid and energy metabolism, ultimately contributing to higher ADG in sheep. Importantly, random forest analysis results showed that Succinivibrio_dextrinosolvens could classify sheep into HADG and LADG with a prediction accuracy of 81.2%. Additionally, we identified 34 bacteria belonged to connectors in the HADG co-occurrence network, including Alloprevotella, Phascolarctobacterium, Anaerovibrio, Butyricicoccus, Ruminococcaceae_noname, and Roseburia, etc., which play an important role in the degradation of carbohydrates and convert them into short-chain fatty acids (SCFAs), maintaining rumen health, and modulating inflammation.

CONCLUSIONS

In summary, key microbes in the rumen affect the overall healthy homeostasis and rumen fermentation of the host, leading to changes in energy utilization, which in turn affects the average daily gain of Hu sheep. Succinivibrio_dextrinosolvens is a promising biomarker for selecting high growth rate sheep in the future. This study provides a new method to manipulate rumen bacteria to improve growth performance in sheep.

deepTFBS: Improving within- and Cross-Species Prediction of Transcription Factor Binding Using Deep Multi-Task and Transfer Learning

The precise prediction of transcription factor binding sites (TFBSs) is crucial in understanding gene regulation. In this study, deepTFBS, a comprehensive deep learning (DL) framework that builds a robust DNA language model of TF binding grammar for accurately predicting TFBSs within and across plant species is presented. Taking advantages of multi-task DL and transfer learning, deepTFBS is capable of leveraging the knowledge learned from large-scale TF binding profiles to enhance the prediction of TFBSs under small-sample training and cross-species prediction tasks. When tested using available information on 359 Arabidopsis TFs, deepTFBS outperformed previously described prediction strategies, including position weight matrix, deepSEA and DanQ, with a 244.49%, 49.15%, and 23.32% improvement of the area under the precision-recall curve (PRAUC), respectively. Further cross-species prediction of TFBS in wheat showed that deepTFBS yielded a significant PRAUC improvement of 30.6% over these three baseline models. deepTFBS can also utilize information from gene conservation and binding motifs, enabling efficient TFBS prediction in species where experimental data availability is limited. A case study, focusing on the WUSCHEL (WUS) transcription factor, illustrated the potential use of deepTFBS in cross-species applications, in our example between Arabidopsis and wheat. deepTFBS is publically available at https://github.com/cma2015/deepTFBS.

Transcriptome analysis reveals the mechanisms underlying petal growth during the flower opening process in Phalaenopsis orchids

BACKGROUND

Phalaenopsis orchids, belonging to the Orchidaceae family, one of the largest groups of angiosperms, possess significant commercial value due to their fascinating flowers. Petal size is a vital trait that directly determines flower size and shape of Phalaenopsis. However, the genetic and developmental regulation of petal size in Phalaenopsis remains unexplored.

RESULTS

In this study, we tracked the petal growth pattern through five stages of flower opening, discovering that cell division stops at stage 2 and stages 3 to 5 are the critical periods of rapid petal expansion. RNA-seq was then conducted to further reveal the molecular mechanisms underlying petal size regulation. Gene ontology (GO) analysis indicated that the differentially expressed genes (DEGs) from the four comparable groups were both enriched in terms related to cell expansion. Endogenous hormone assays showed that auxin, cytokinin, and gibberellin were implicated in the petal growth of Phalaenopsis. Moreover, six auxin signaling pathway genes, 11 cell expansion-related genes, and 30 transcription factors (TFs) identified through trend analysis were abundantly expressed during the critical period of petal expansion, suggesting that they may influence petal size by regulating cell expansion. In contrast, 18 TFs exhibited the highest expression levels at the S1 stage, indicating their potential role in petal cell proliferation. Based on weighted gene co-expression network analysis (WGCNA), six hub genes (PaLOF2, PaSWEET11, PaVNI2, PaHDA3, PaPMEI3, PaXTH30) were screened from the green and yellow module which was highly associated with the petal size.

CONCLUSION

Our results lay a foundation for further exploration of the molecular mechanisms regulating petal size development and are significant for molecular breeding programs aimed at generating novel Phalaenopsis with desirable traits.

Identification of key modules and genes in response to high-temperature stress in Platostoma palustre based on WGCNA

Platostoma palustre (Blume) A. J. Paton is one of the important medicinal and edible plants in China, and it is widely cultivated in tropical and subtropical regions of southern China. In these areas, high-temperature stress (HTS) is often one of the unfavorable environmental factors affecting the growth and yield of P. palustre. Nevertheless, the molecular mechanism underlying the response of P. palustre to HTS remains unclear. In this study, we used two varieties of P. palustre, LSL and MDG, as experimental materials to identify key genes involved in the response of P. palustre to HTS by employing transcriptome sequencing technology, thereby revealing the molecular mechanism underlying its adaptation to HTS. The results showed that HTS significantly influenced the plant height, above-ground fresh weight, root fresh weight, root growth, chlorophyll a, chlorophyll b, chlorophyll a + b, and carotenoid content of P. palustre plants. MDG exhibited stronger high-temperature tolerance compared to LSL. Under HTS, 8352 DEGs were up-regulated and 9201 DEGs were down-regulated in HT_LSL_vs_CK_LSL, while 5433 DEGs were up-regulated and 6325 DEGs were down-regulated in HT_MDG_vs_CK_MDG, suggesting a significant difference in gene expression levels between LSL and MDG under HTS. KEGG enrichment analysis showed the pathways possibly involved in HTS responses in P. palustre, such as plant hormone signal transduction, brassinosteroid biosynthesis, phenylpropanoid biosynthesis, pentose and glucuronate interconversions, diterpenoid biosynthesis, flavonoid biosynthesis, etc. Further weighted gene co-expression network analysis (WGCNA) identified 14 modules and 61 hub genes closely related to the response to HTS in P. palustre. The hub genes included peroxidase 51-like (TRINITY_DN34017_c0_g1), UDP-glucuronate 4-epimerase 1-like (GAE1, TRINITY_DN815_c0_g3), NAC domain-containing protein 1 (NAC, TRINITY_DN328_c0_g1), UGT73A13 (TRINITY_DN8437_c0_g2), universal stress protein 7 (USP7, TRINITY_DN6361_c0_g2), malonyl-coenzyme: anthocyanin 5-O-glucoside-6'''-O-malonyltransferase-like (5MaT1, TRINITY_DN3589_c0_g1), ent-kaurene synthase 5 (KSL5, TRINITY_DN5126_c0_g1), ABC transporter (TRINITY_DN39495_c0_g1, TRINITY_DN10383_c0_g1), etc. This study investigated the molecular mechanism of heat tolerance in P. palustre at the gene expression level, providing a scientific basis for heat-tolerant breeding of P. palustre.

RNA-seq Analysis of the Mechanisms Underlying Chalky Grain and Characterization of Two IAA Receptor Proteins OsAFB3 and OsAFB5 in Chalkiness Formation in Oryza sativa

Grain chalkiness is an undesirable agronomic trait that negatively affects both the yield and quality of rice (Oryza sativa). The molecular mechanisms underlying chalky grain phenotype have remained largely unclear. In this study, we selected the rice variety HK300 with a high chalkiness, and ZR24D with a low chalkiness, as experimental materials and systematically characterized the reasons of grain chalkiness formation at molecular level by means of RNA-seq analysis. Analysis results revealed that the differentially expressed genes (DEGs) in these two rice varieties were significantly enriched in transcriptional regulation, sucrose and starch metabolism, and phytohormone signal transduction. Moreover, we found the expression of 13 genes related to trehalose pathway (4 out of 14 TPS genes and 9 out of 13 TPP genes in rice genome) were significantly different between the two varieties, indicating trehalose synthesis pathways may contribute to the increased chalkiness formation. Notably, the number of DEGs associated with the signal transduction pathway for indole-3-acetic acid (IAA), which has been rarely studied for its involvement in chalkiness formation, was the highest among those associated with plant hormone signal transduction. Among them, the expression of two IAA receptor genes, OsAFB3 and OsAFB5, were significantly lower in HK300 than that in ZR24D through RNA-seq and qRT-PCR. Furthermore, we newly validated the two genes negatively regulated the formation of chalkiness through gene knockout. Our findings provided the theoretical basis and novel gene resources for molecular breeding aimed at improving rice quality.

Spatio-Temporal Regulation of Gibberellin Biosynthesis Contributes to Optimal Rhizome Bud Development

The perennial life cycle involves the reiterative development of sexual and asexual organs. Asexual structures such as rhizomes are found in various plant species, fostering extensive growth and competitive advantages. In the African wild rice Oryza longistaminata, we investigated the formation of rhizomes from axillary buds, which notably bend diagonally downward of the main stem, as the factors determining whether axillary buds become rhizomes or tillers are unclear. Our study revealed that rhizome buds initiate between the third and fifth nodes of seedlings beyond the 6-leaf stage, while the buds above the sixth node develop into tillers. We propose that precise regulation of gibberellin (GA) biosynthesis plays a pivotal role in optimal rhizome bud development, as demonstrated by a comparative transcriptome analysis between tiller buds and rhizome buds and quantification of phytohormones. Furthermore, GA4 treatment upregulated the expression of genes associated with flowering repression and cell wall modification. These findings highlight the integration of GA biosynthesis and flowering repression genes as crucial in asexual organ development, shedding new light on the molecular mechanisms governing rhizome bud development in O. longistaminata and deepening our understanding of asexual reproduction regulation in perennial plants.

Ancient Microbiomes as Mirrored by DNA Extracted From Century-Old Herbarium Plants and Associated Soil

Numerous specimens stored in natural history collections have been involuntarily preserved together with their associated microbiomes. We propose exploiting century-old soils occasionally found on the roots of herbarium plants to assess the diversity of ancient soil microbial communities originally associated with these plants. We extracted total DNA and sequenced libraries produced from rhizospheric soils and roots of four plants preserved in herbaria for more than 120 years in order to characterise the preservation and taxonomic diversity that can be recovered in such contexts. Extracted DNA displayed typical features of ancient DNA, with cytosine deamination at the ends of fragments predominantly shorter than 50 bp. When compared to extant microbiomes, herbarium microbial communities clustered with soil communities and were distinct from communities from other environments. Herbarium communities also displayed biodiversity features and assembly rules typical of soil and plant-associated ones. Soil communities were richer than root-associated ones with which they shared most taxa. Regarding community turnover, we detected collection site, soil versus root and plant species effects. Eukaryotic taxa that displayed a higher abundance in roots were mostly plant pathogens that were not identified among soil-enriched ones. Conservation of these biodiversity features and assembly rules in herbarium-associated microbial communities indicates that herbarium-extracted DNA might reflect the composition of the original plant-associated microbial communities and that preservation in herbaria seemingly did not dramatically alter these characteristics. Using this approach, it should be possible to investigate historical soils and herbarium plant roots to explore the diversity and temporal dynamics of soil microbial communities.

Microplastic exposure induces preeclampsia-like symptoms via HIF-1α/TFRC-mediated ferroptosis in placental trophoblast cells

Microplastic (MP) pollution is an emerging environmental concern with potential health risks, yet its impact on pregnancy remains largely unexplored. This study investigated the effects of polystyrene microplastic (PS-MP) exposure on placental function and its role in preeclampsia (PE) pathogenesis. Pregnant rats were exposed to PS-MP, which induced PE-like symptoms including elevated blood pressure, increased proteinuria, and altered expression of angiogenic factors. Transcriptomic and molecular analyses revealed PS-MP triggered ferroptosis in placental trophoblast cells by activating the HIF-1α/TFRC axis, resulting in iron overload and oxidative stress. PS-MP exposure impaired trophoblast migration, invasion, and angiogenesis; these effects were ameliorated by ferroptosis inhibition. These findings identified PS-MP-induced ferroptosis as a critical mechanism underlying placental dysfunction, highlighting PS-MP as a potential environmental risk factor for PE. Understanding the impact of MP on pregnancy provides crucial insights into their reproductive toxicity and underscores the need for further research on mitigating their effects.

Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer

Determining response to therapy for patients with pancreatic cancer can be challenging. We evaluated methods for assessing therapeutic response using cell-free DNA (cfDNA) in plasma from patients with metastatic pancreatic cancer in the CheckPAC trial (NCT02866383). Patients were evaluated before and after initiation of therapy using tumor-informed plasma whole-genome sequencing (WGMAF) and tumor-independent genome-wide cfDNA fragmentation profiles and repeat landscapes (ARTEMIS-DELFI). Using WGMAF, molecular responders had a median overall survival (OS) of 319 days compared to 126 days for nonresponders [hazard ratio (HR) = 0.29, 95% confidence interval (CI) = 0.11-0.79, P = 0.011]. For ARTEMIS-DELFI, patients with low scores after therapy initiation had longer median OS than patients with high scores (233 versus 172 days, HR = 0.12, 95% CI = 0.046-0.31, P < 0.0001). We validated ARTEMIS-DELFI in patients with pancreatic cancer in the PACTO trial (NCT02767557). These analyses suggest that noninvasive mutation and fragmentation-based cfDNA approaches can identify therapeutic response of individuals with pancreatic cancer.

Global spatiotemporal patterns of demographic fluctuations in terrestrial vertebrates during the Late Pleistocene

Demographic fluctuations are crucial for assessing species' threat levels, yet their global spatiotemporal patterns and historical drivers remain unknown. Here, we used single whole-genome sequence data for 527 extant and widespread terrestrial vertebrates to investigate their demographic fluctuations during the Late Pleistocene. Effective population size (Ne) simulations indicated that all taxa experienced a population decline from the Last Interglacial to the Last Glacial Maximum (LGM). After the LGM, birds and amphibians underwent population expansion, whereas mammals and reptiles' populations declined. Regions with high Ne shifted from Neotropical to Afrotropical and to Palearctic, some overlapping with recognized glacial refugia and biodiversity hotspots. In addition, climate-related factors exerted long-term effects on Ne, while human disturbances might confine to specific regions around the Pleistocene-Holocene boundary. This study underscores the significance of quantifying vertebrate genetic vulnerability to guide biodiversity conservation in response to environmental changes.

Gut microbiota mediates semaglutide attenuation of diabetes-associated cognitive decline

Diabetes-associated cognitive decline (DACD), characterized by cognitive impairment, is a serious complication of diabetes mellitus (DM). Research has shown that semaglutide, a novel glucagon-like peptide-1 receptor agonist, has neurotrophic and neuroprotective properties. However, a comprehensive understanding of the specific effects and underlying mechanisms of semaglutide treatment in patients with DACD remains lacking. In this study, we evaluated the potential of semaglutide to alleviate DACD in mice with DM. Eight-week-old mice fed a high-fat diet with streptozotocin-induced DM were subcutaneously injected with semaglutide (30 ​nmol/kg qd) for 12 weeks. Semaglutide administration significantly alleviated cognitive impairment, inhibited hippocampal neuron loss, improved the hippocampal synaptic ultrastructure, and effectively mitigated neuroinflammation. Furthermore, semaglutide treatment increased the relative abundances of g_Alistipes, g_norank_f_Eubacterium_coprostanoligenes, g_Bacteroides, and g_Parabacteroides, while decreasing the relative abundances of g_ faecalibaculum, g_Colodertribacter, g_GCA-900066575, g_Erysipelatoclostridium, and g_norank_f_Lachnospiraceae. Semaglutide also induced alterations in fecal and serum metabolites, as well as transcriptomic changes in brain tissue, with significant common enrichment in neuroactive ligand-receptor interactions. Furthermore, strong correlations were observed among semaglutide-affected genes, metabolites, and microbiota, as assessed by correlation analysis and integrative modeling. In conclusion, these findings suggest a correlation between the protective effects of semaglutide against DACD and the microbiota-gut-brain axis.

Genomic and chromosomal architectures underlying fertility maintenance in the testes of intergeneric homoploid hybrids

The remarkable diversity of the Cyprinidae family highlights the importance of hybridization and gene flow in generating genetic variation, adaptation, and even speciation. However, why do cyprinid fish frequently overcome postzygotic reproductive isolation, a mechanism that normally prevents successful reproduction after fertilization? To address this gap in knowledge, we conducted comparative studies using reciprocal F1 hybrid lineages derived from intergeneric hybridization between the cyprinid species Megalobrama amblycephala and Culter alburnus. Utilizing long-read genome sequencing, ATAC-seq, Hi-C, and mRNA-seq technologies, we identified rapid genomic variations, chromatin remodeling, and gene expression changes in the testicular cells of F1 hybrid individuals. By analyzing the distribution of these alterations across three gene categories (allelic genes, orphan genes, and testis-specific genes), we found that changes were less pronounced in allelic and testis-specific genes but significantly more pronounced in orphan genes. Furthermore, we hypothesize that rnf212b is a crucial testis-specific gene that regulates spermatogenesis. Our findings suggest that allelic and testis-specific genes potentially mitigate "genomic shock" on reproductive function following hybridization. This research offers potential insights into the formation mechanisms of homoploid hybridization by demonstrating the coordinated interplay of genomic variations, chromatin remodeling, and gene expression changes during testicular development and spermatogenesis.

Complete African swine fever virus genome isolated from the 2023 outbreak in Cameroon

African swine fever virus has been endemic in Cameroon since the early 1980s. Here, we report on the genotype I Cameroon/2023/SBP30 genome collected from a domestic pig during the 2023 outbreak.

PARylation of POLG Mediated by PARP1 Accelerates Ferroptosis-Induced Vascular Calcification via Activating Adora2a/Rap1 Signaling

BACKGROUND

Vascular calcification (VC) is associated with diabetes, chronic kidney disease, and aging. VC is found to be a powerful and independent risk factor for cardiovascular mortality. Vascular smooth muscle cell (VSMC) ferroptosis, a form of cell death, is known to be involved in VC. However, whether VSMC ferroptosis is regulated by posttranslational modifications remains undefined.

METHODS

We explored the potential role and mechanism of PARP1 (poly[ADP-ribose] polymerase 1)-mediated poly(ADP-ribosyl)ation (PARylation) in VSMC ferroptosis during VC. Mouse VSMCs were treated with β-glycerophosphate, and Parp1flox/flox Tagln Cre+ calcified mice were generated with AAV9-sh-POLG (DNA polymerase gamma) injected to establish in vitro and in vivo models, respectively. RNA-sequencing analysis was performed to determine the transcriptomic alterations in VSMCs overexpressing POLG and treated with β-glycerophosphate.

RESULTS

Both PARP1 expression and PARylation levels were increased in β-glycerophosphate-induced VC, with PARP1 knockdown mitigating VC by improving mitochondrial function and inhibiting the subsequent VSMC ferroptosis. Mechanistically, POLG PARylation levels were increased in calcified VSMCs from PARP1 activation, triggering PARylation-dependent ubiquitination of POLG that resulted in POLG downregulation. This led to mitochondrial dysfunction and Adora2a (adenosine receptor A2A)/Rap1 (Ras-associated protein 1) signaling pathway activation to induce VSMC ferroptosis, which ultimately aggravated VC.

CONCLUSIONS

Our study establishes the critical role of PARP1-mediated PARylation-dependent ubiquitination of POLG in VSMC ferroptosis-induced VC. These findings suggest that PARP1 inhibitors could potentially serve as novel therapeutic strategies for VC.

Glucose release kinetics of different feed ingredients and their impact on short-term growth of pigs by influencing carbon-nitrogen supply synchronization

BACKGROUND

Pigs fed diets with different ingredients but identical nutritional levels show significant differences in growth performance, indicating that growth may also be influenced by the synchronicity of dietary carbon and nitrogen supply. Therefore, this study aimed to determine glucose release kinetics of various feed ingredients, to investigate a glucose release pattern that is conducive to synchronized carbon-nitrogen supply, and to elucidate the underlying mechanisms by which this synchronization optimizes growth of pigs.

RESULTS

We analyzed the glucose release kinetics of 23 feed ingredients in vitro and found that their glucose release rates and amounts varied greatly. Based on this, a nitrogen-free diet and 5 purified diets, which represented the observed variations in glucose release rates and quantities among feed ingredients, were designed for 18 ileal-cannulated pigs. The results demonstrated that slower glucose release pattern could disrupt the synchrony of dietary carbon and nitrogen supply, reducing the growth of pigs and increasing nitrogen losses. Specifically, the diet with slower and moderate amounts of glucose release showed a relatively slower release of amino acids. Pigs fed this diet had the lower amino acid digestibility and the enrichment of harmful bacteria, such as Streptococcus, in the terminal ileum. Conversely, the diets with slower and lower glucose release exhibited a relatively rapid release of amino acids but also resulted in poor growth. They increased glucogenic amino acid digestibility and potentially enriched bacteria involved in nitrogen cycling and carbon metabolism. Notably, only the diet with rapid glucose release achieved synchronized and rapid release of nutrients. Pigs fed this diet exhibited higher amino acid digestibility, decreased harmful bacteria enrichment, improved nutrient utilization, and enhanced short-term growth performance.

CONCLUSIONS

Our research analyzed significant differences in glucose release kinetics among swine feed ingredients and revealed that slow glucose release disrupted dietary carbon-nitrogen supply synchrony, shifting amino acid utilization and enriching pathogens, negatively impacting growth and nutrient utilization. Consequently, choosing feed ingredients releasing glucose at a rapid rate to balance dietary carbon and nitrogen supply helps promote pig growth, and ensures efficient feed utilization.

HPV-associated squamous cell carcinoma and adenocarcinoma in distinct cervical sites: a case report

BACKGROUND

The synchronous occurrence of adenocarcinoma and squamous cell carcinoma in distinct cervical regions is exceptionally rare. This report highlights a case of HPV-associated adenocarcinoma and squamous cell carcinoma at distinct sites in a patient with primary stage IA1 cervical cancer.

CASE PRESENTATION

A 54-year-old female tested HPV type 18 positive in a routine physical exam. Cervical Liquid - based Cytology Test (LCT) showed Atypical Squamous Cells of Undetermined Significance (ASCUS). Colposcopy-directed biopsies revealed moderately differentiated squamous cell carcinoma at multiple sites (3, 6, 9, 12 o'clock positions and the ECC), with a clinical diagnosis of stage IA1. Preoperative abdominal MRI (including contrast enhancement) showed no lymph node enlargement, and urinary CT urography was normal. Squamous cell carcinoma antigen levels were within the normal range.

Characterisation of Heavy Metals and Microbial Communities in Urban River Sediments: Interactions and Pollution Origin Analysis

Urbanisation has significantly impacted urban rivers, by introducing substantial amounts of heavy metals and altering microbial communities in the river sediments. This study investigated the characteristics, interactions, and pollution sources of heavy metals and microbial communities in the sediments of two typical urban rivers in Xi'an, China. The analytical results showed significant differences in heavy metal concentrations between the two rivers, with higher levels of copper, zinc, and antimony in the Chan River, and higher levels of cadmium, lead and arsenic in the Ba River. The geoaccumulation index indicated that selenium reached moderate-to-heavy pollution levels in the sediments. The microbial communities in the sediments were dominated by Proteobacteria, Firmicutes, and Actinobacteria, with similar compositions in both rivers. However, the Ba River exhibited more abundant indicator taxa. Correlation analysis revealed complex interactions between the heavy metals and the microbial communities, with copper having the most significant effect on the microbial diversity, and arsenic the least. Principal component analysis and Pearson correlation analyses identified the pollution sources of heavy metals, which were mainly influenced by agricultural activities, whereas the Chan River was primarily affected by industrial activities. This study provides scientific evidence for the environmental management and pollution control of urban rivers.

COVID-19 Alters Inflammatory, Mitochondrial, and Protein Clearance Pathway Genes: Potential Implications for New-onset Parkinsonism in Patients

Several preclinical and clinical studies have shown that SARS-CoV-2 infection is associated with new-onset Parkinson's disease (PD). The overall goal of this study is to uncover how the COVID-19 severity gradient impacts the conventional pathological pathway of PD to inform the identification of at-risk patients and the development of personalized treatment strategies. Transcriptomics analysis of 43 PD pathogenic genes was conducted on nasopharyngeal swabs from 50 COVID-19 patients with varying severity including 17 outpatients, 16 non-ICU, and 17 ICU patients, compared to 13 SARS-CoV-2 negative individuals. The study shows that COVID-19 severity gradient differentially dysregulates PD pathological genes. Dysfunctional lysosomal and mitochondrial processes in outpatients and non-ICU COVID-19 patients was identified as the convergent network of COVID-19-PD interactions. These dysfunctions were later abrogated by the upregulation of the ubiquitin-proteasome system and autophagy-lysosome system in ICU COVID-19 patients. A potential synergistic co-expression and clustering of protein clearance pathway genes with other pathological genes was observed in ICU patients, indicating a possible overlap in biological pathways. Dysregulation of the PD pathopharmacogene, SLC6A3 was observed in ICU patients, suggesting potential COVID-19-gene-drug interactions. Nasopharyngeal swabs express major PD pathological genes as well as clinically relevant drug processing genes, which could advance studies on PD, including diagnosis, pathogenesis, and the development of disease-modifying treatments. Outpatients and non-ICU COVID-19 patients may face a higher risk of developing new-onset PD, whereas ICU COVID-19 patients may be more susceptible to COVID-19-gene-drug interactions.

Gut opportunistic pathogens contribute to high-altitude pulmonary edema by elevating lysophosphatidylcholines and inducing inflammation

Gut microbiota have been found to promote hypoxia-induced intestinal injury. However, the role of gut microbiota in high-altitude pulmonary edema (HAPE), the preventive effect of synbiotic on HAPE, and the mechanisms by which they might work remain unknown. In this study, we aimed to investigate the role of gut microbiota in the pathogenesis of HAPE and to explore the underlying mechanisms involved. We performed a fecal microbiome analysis and found a significant decrease in intestinal Klebsiella and Escherichia-Shigella, along with a notable increase in intestinal Bifidobacterium and Lactobacillus, as volunteers recovered from acute mountain sickness (AMS). Gavage colonization with Klebsiella pneumoniae and Escherichia coli induced plasma inflammation, increased plasma lysophosphatidylcholine (LPC) levels, and contributed to HAPE in rats at a simulated altitude of 6,500 m. Conversely, a synbiotic containing Bifidobacterium, Lactiplantibacillus, fructooligosaccharides, and isomaltose-oligosaccharides significantly reduced the severity of HAPE. Cellular experiments and molecular dynamics simulations revealed that LPCs can cause damage and permeability to human pulmonary microvascular endothelial cell (HPMEC) and human pulmonary alveolar epithelial cell (HPAEpiC) monolayers under hypoxic conditions by disrupting cell membrane integrity. In addition, tail vein injection of LPCs promoted HAPE in mice at a simulated altitude of 6,500 m. In conclusion, this study describes a gut microbiota-LPCs/inflammation-HAPE axis, an important new insight into HAPE that will help open avenues for prevention and treatment approaches.

IMPORTANCE

The role of the gut microbiota in high-altitude pulmonary edema (HAPE) is currently unknown. This study found that intestinal Klebsiella pneumoniae and Escherichia coli contribute to HAPE by inducing inflammation and increasing lysophosphatidylcholine (LPC) levels under hypoxic conditions. Conversely, a synbiotic containing Bifidobacterium, Lactiplantibacillus, fructooligosaccharides, and isomaltose-oligosaccharides significantly reduced the severity of HAPE. Further investigation revealed that LPCs can cause damage and permeability to human pulmonary microvascular endothelial cell (HPMEC) and human pulmonary alveolar epithelial cell (HPAEpiC) monolayers under hypoxic conditions by disrupting cell membrane integrity. These findings contribute to the understanding of the pathogenesis of HAPE and will benefit populations living at high altitude or traveling from low to high altitude.

Comparative analysis of homology of carbapenem-resistant Klebsiella pneumoniae based on pulsed-field gel electrophoresis and whole genome sequencing

OBJECTIVE

This study was conducted to compare the homology of carbapenem- resistant Klebsiella pneumoniae (CRKP) obtained based on different methods. Methods A total of 44 CRKP strains were collected from a Class A tertiary hospital in China from 2017 to 2023. The homology of these CRKP strains was analyzed based on pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Besides, the sequence types (STs), drug resistance genes, genome islands, and prophages of different clonal strains were comparatively analyzed. Moreover, the homology of these CRKP strains was comparatively analyzed using the average nucleotide identity (ANI), BLAST score ratio (BSR) scatter plots, homologous gene heatmaps, phylogenetic trees based on 16S rRNA gene sequences, phylogenetic trees based on core genes, phylogenetic trees based on whole-genome single nucleotide polymorphism (SNP), SNP distance heatmaps, and minimum spanning trees based on SNP and STs. Results The ANI between two homologous strains was greater than 99.99 %, and the BSR scores of homologous strains were close to the center line. The results of phylogenetic trees based on 16S rRNA gene sequences were significantly different from those of PFGE. In contrast, the results of phylogenetic trees based on core genes and whole-genome SNP were similar to those of PFGE. There were significant differences in the SNP between the homologous strains of ST11. Conclusion The ST11CRKP strain demonstrates polymorphism. Furthermore, WGS can be employed to distinguish between the genetic variations of clonal strains and analyze the homology of CRKP strains via various comparative genomic methods from multiple perspectives.

Draft genome sequence of Agarivorans albus strain S3 capable of utilizing nori as a nutrient source

We sequenced the draft genome of Agarivorans albus strain S3, a bacterium capable of utilizing nori (Pyropia yezoensis), a polysaccharide-rich seaweed, as a nutrient source. The genome revealed approximately 100 genes involved in the degradation of starch, β-glucans including cellulose, galactans including agar/porphyran, mannans, xylan, and other polysaccharides.

Metatranscriptomic analysis of colonic mucosal samples exploring the functional role of active microbial consortia in complicated diverticulitis

In this study, we investigated complicated diverticulitis, an inflammatory condition associated with abscesses, fistulas, intestinal obstructions, perforations, and primarily affects adults over the age of 60. Although the exact etiology remains unclear, the gut microbiome has been suggested as a contributing factor. Previous studies have used 16S rRNA gene analysis from patient fecal samples, which is limited to identifying the bacterial communities present. Herein, we employed shotgun metatranscriptomics on 40 patient-matched samples of diseased and adjacent normal colonic mucosal tissues from 20 patients with complicated diverticulitis to gain a more comprehensive understanding of active microbial taxa and gene expression patterns that may be involved in this disease state. Our findings revealed distinct beta diversity and a conglomerate of pathogenic microbiota in the diseased tissues, including Staphylococcus cohnii, Corynebacterium jeikeium, Kineococcus, Talaromyces rugulosus, Campylobacteraceae, and Ottowia, among others. The adjacent normal tissues were a stark contrast, harboring anti-inflammatory taxa such as Streptococcus salivarius and housekeeping genes and pathways such as the ABC-2 type transport system ATP-binding protein. These results align with previous amplicon sequencing studies and provide novel functional insights that may be crucial for understanding the etiology of complicated diverticulitis.IMPORTANCEComplicated diverticulitis is a virulent condition with no clear cause other than the association with colonic diverticulosis. We assessed the microbial gene expression in complicated diverticulitis patients using colonic tissue samples, revealing microbes in the diseased tissue known to exacerbate the diverticular condition and to live in extreme places, and microbes in patients' normal tissue known to maintain normal bodily functions. This functional information is therefore important for understanding what microbial taxa are present and what they are doing. It is possible clinicians could someday harness this information to more effectively treat complicated diverticulitis symptoms. For example, clinicians may suggest dietary changes and prescribe probiotics to increase beneficial bacteria. Clinicians may also prescribe targeted antibiotics or consider the emerging treatment option of fecal transplants in complicated diverticulitis patients. While not curing complicated diverticulitis, each potential treatment option mentioned addresses balancing out dysbiosis of the gut microbiome, therefore alleviating associated symptoms.

Secondary bacterial infections of Carbapenem-Resistant Acinetobacter baumannii in patients with COVID-19 admitted to Chinese ICUs

BACKGROUND

A significant proportion of patients who are hospitalized with coronavirus disease 2019 (COVID-19), particularly those being admitted to ICUs, exhibit the development of secondary bacterial infections (SBIs). However, there is a lack of detailed epidemiological investigations and genetic information of Carbapenem-Resistant Acinetobacter baumannii (CRAB) based on whole genome sequencing (WGS), which is one of the frequently detected bacteria among COVID-19 patients, to confirm alterations in the clonal structure and infection mechanism.

RESULTS

A total of 37 unique CRAB strains, sourced from patients, along with an additional 2 CRAB strains form the environment, were isolated. Among the cohort of 37 patients, 22 individuals succumbed to CRAB infection, resulting in a mortality rate of 54.46%. The median duration of illness for these patients was 7.95 days, highlighting the severity and rapid progression of CRAB infections in this patient population. A total of 22 CRAB strains, isolated from deceased individuals, in addition to two strains isolated from the environment, were subjected to further investigation. All 24 CRAB isolates exhibited a high ability to form biofilm and displayed a similar spectrum of resistance. Except for two isolates from patients with COVID-19, all the remaining CRAB isolates were categorized as ST195 and demonstrated highly close genetic background based on analysis of WGS. The ST195 strain of CRAB harbored three copies of the blaOXA-23 gene located on the chromosome, each of which was carried by Tn2006. Notably, one Tn2006 element was integrated within Tn6022, leading to the formation of AbaR4-like resistance islands Tn6166-I.

CONCLUSIONS

Our findings underscore the significance of SBIs in the COVID-19 pandemic, particularly those caused by CRAB and specifically those belonging to MLST types that were previously prevalent in ICUs.

Identification of novel gene expression patterns and pathways involved in PARP-1 inhibitor resistance

US-FDA has approved PARP-1 inhibitors (Talazoparib, Olaparib, Rucaparib, and Niraparib) as the first line of treatment for many cancer types (e.g., breast, ovarian, pancreatic, and prostate) caused by mutations in breast cancer gene 1 and 2 (BRCA1/2). However, developing resistance to PARP-1 inhibitors is a major concern, which limits therapeutic effectiveness. In the present study, we identified novel gene signatures implicated in developing resistance to Olaparib. Meta-analysis was performed on publicly available RNA-Seq data related to ovarian and breast cancers from the GEO (Gene Expression Omnibus) database. Differential gene expression analysis, gene ontology, KEGG pathway enrichment, and protein-protein interaction (PPI) networking analyses were performed. A total of 139 Common DEGs (Differentially Expressed Genes) were identified, comprising 69 and 70 genes that were upregulated and downregulated respectively. KEGG Pathways "P53 signaling pathway" and "Positive regulation of developmental process(BP)", "endoplasmic reticulum lumen(CC)," and "growth factor binding(MF)", were found to be potentially associated with Olaparib resistance. Five hub genes were identified using PPI networking of which FN1, CCN2, and JUN may play a significant role in the development of Olaparib resistance and could be promising therapeutic and diagnostic biomarkers for dealing with Olaparib resistance in BRCA1/2 mutant breast and ovarian cancer.

Effects of USP25 knockout on the gut microbial diversity and composition in mice

BACKGROUND

The gut microbiota plays a crucial role in host health. Recent study revealed that ubiquitin-specific protease 25 (USP25) deficiency affected colonic immune responses and resistance to certain bacterial infection. This study aimed to investigate the impact of USP25 gene deletion on the gut microbiota of mice, utilizing 16 S rRNA amplicon sequencing and metagenomic sequencing to provide a comprehensive analysis of microbial diversity, composition and functional characteristics.

METHODS

We collected fecal samples from 10 wild type (WT) C57BL/6J mice and 10 USP25-/- mice (C57BL/6J-Usp25em1cyagen) for 16 S rRNA amplicon sequencing. Subsequently, the 6 of the 20 samples underwent further analysis using metagenomic sequencing.

RESULTS

Our results revealed significant differences in the gut microbiota between USP25 knockout (KO) mice and wild-type (WT) controls, with KO mice exhibiting 1,858 unique amplicon sequence variants (ASVs) compared to 1,723 in WT mice. Notably, the KO group displayed a higher tendency for biofilm formation and a greater proportion of gram-negative bacteria, while the WT group demonstrated enhanced stress tolerance and a higher presence of gram-positive bacteria. Functional prediction analyses indicated an increase in antibiotic resistance genes in the KO mice, particularly for tetracycline, cephalosporin, and sulfonamides, suggesting a potential risk for clinical antibiotic treatment efficacy. Moreover, KEGG pathway enrichment analysis revealed significant enrichment for fructose and mannose metabolism, streptomycin biosynthesis in the KO group. Furthermore, an increase in protective microbes alongside a decrease in potential pathogens in the KO microbiota hinted at altered immune responses due to USP25 deletion.

CONCLUSION

Our findings elucidate the essential role of USP25 in modulating gut microbiota composition and function, providing insights for future therapeutic strategies targeting gut microbiota in disease contexts.

CLINICAL TRAIL NUMBER

Not applicable.

Nuclear m6A modification regulates satellite transcription and chromosome segregation

The precise location and functions of N6-methyladenosine (m6A) modification on mammalian nuclear noncoding RNA remain largely unknown. Here we developed nuclear-m6A-label-seq to directly map human and mouse cell nuclear RNA m6A methylome at single-base resolution. Specifically, m6A modifications have been identified on abundant human γ satellite DNA II (GSATII) RNA transcripts, a type of repeat RNA, transcribed from SST1-TAR1-GSATII satellite arrays in the pericentromeric region of chromosome 9. GSATII RNA m6A positively regulates the transcription of GSATII-located satellite arrays as well as trans-associated peri/centromeric satellites, typically chromosome 3 centromeric higher-order repeat α satellite. Dysregulation of this circuit renders a phenotype of abnormal chromosome segregation. Mechanistic study reveals that YTHDC1 reads GSATII RNA m6A marks and recruits bromodomain protein 4 (BRD4) to promote transcriptions of the associated satellites via an m6A-YTHDC1-BRD4-H3K27ac axis. These results uncover a mechanism governing the transcription of cis- and trans-associated pericentromeric and centromeric satellites via cross-talk between epitranscriptomic and epigenomic marks.

Gut microbiota variations over the lifespan and longevity in rabbit's maternal lines

In rabbit breeding, selection for production efficiency traits has been successful but has reduced rabbit functional longevity. The gut microbiota, which influences host health, is linked to longevity and undergoes significant changes with age. While previous studies have focused on young rabbits, research on gut microbiota changes in adult rabbits is limited. Understanding how gut microbiota evolves with age and its impact on longevity of does during reproductive life could offer insights into improving productivity, health and welfare. This study aims to investigate the evolution of gut microbiota through age and to compare different functional longevity groups between and within two maternal rabbit lines with different longevities; a standard commercial line (A) and another founded using longevity criteria (LP). Our analysis demonstrated a significant impact of age on the gut microbiome of does during their reproductive lifespan, with a decline in alpha diversity and change in beta diversity composition as age progressed. Differential abundance analysis revealed that 20% and 16% of taxa in lines A and LP, respectively, were influenced by age, predominantly showing a negative correlation. In terms of functional longevity, differences in abundance between groups were more pronounced within line A, with up to 16% of taxa differing between high-longevity HL (females with more than 10 parities) and low-longevity LL (females died/culled before 5th parity) groups, compared to only 4% within line LP, highlighting the role of genetic background in shaping microbiota composition and its potential influence on longevity. Finally, differences in microbiome between the two lines A and LP were consistent and maintained through their lifespan independently from their longevity. This study reveals that age significantly influences gut microbiome diversity and composition in adult female rabbits, leading to decreased alpha diversity and notable shifts in composition. Microbiome also differs according to functional longevity, with differences varying by genetic line. This suggests that using microbiome through selection or using specific taxa within it as biomarkers could be a promising avenue for improving longevity. Moreover, microbiome differences between genetic lines persist throughout life, even among animals with the same longevity.

The superoxide dismutase (SOD) gene family in perennial ryegrass: Characterization and roles in heat stress tolerance

Perennial ryegrass (Lolium perenne) is a cool-season forage and turfgrass widely cultivated in warm and subtropical regions worldwide due to its ease of cultivation, resilience, and low maintenance costs. However, high temperatures severely impact its growth. Superoxide dismutase (SOD) is a key enzyme in plant stress responses, playing a crucial role in regulating reactive oxygen species (ROS) homeostasis. In this study, eight SOD genes were identified in perennial ryegrass. Bioinformatics analyses provided detailed insights into their chromosomal locations, phylogenetic relationships, conserved motifs, and cis-acting regulatory elements. Transcriptomic data revealed that these LpSOD genes exhibit distinct tissue-specific expression patterns and temperature response profiles. The enzymatic activity experiments of the purified LpSOD proteins revealed the effects of pH and temperature on the superoxide dismutase activity of LpSODs. Functional complementation tests using yeast mutants demonstrated that LpMSD1.1, LpCSD1, LpCSD2, and LpCSD3 rescue the high-temperature-sensitive phenotypes of yeast SOD gene deletion mutants. This study represents the first genome-wide analysis of the LpSOD gene family, laying a foundation for a better understanding of their functional roles in the high-temperature response of perennial ryegrass.

The TetR-like regulator Sco4385 and Crp-like regulator Sco3571 modulate heterologous production of antibiotics in Streptomyces coelicolor M512

Heterologous expression in well-studied model strains is a routinely applied method to investigate biosynthetic pathways. Here, we pursue a comparative approach of large-scale DNA-affinity-capturing assays (DACAs) coupled with semi-quantitative mass spectrometry (MS) to identify putative regulatory proteins from Streptomyces coelicolor M512, which bind to the heterologously expressed biosynthetic gene clusters (BGCs) of the liponucleoside antibiotics caprazamycin and liposidomycin. Both gene clusters share an almost identical genetic arrangement, including the location of promoter regions, as detected by RNA sequencing. A total of 2,214 proteins were trapped at the predicted promoter regions, with only three binding to corresponding promoters in both gene clusters. Among these, the overexpression of a yet uncharacterized TetR-family regulator (TFR), Sco4385, increased caprazamycin but not liposidomycin production. Protein-DNA interaction experiments using biolayer interferometry confirmed the binding of Sco4385 to Pcpz10 and PlpmH at different locations within both promoter regions, which might explain its functional variance. Sequence alignment allowed the determination of a consensus sequence present in both promoter regions, to which Sco4385 was experimentally shown to bind. Furthermore, we found that the overexpression of the Crp regulator, Sco3571, leads to a threefold increase in caprazamycin and liposidomycin production yields, possibly due to an increased expression of a precursor pathway.IMPORTANCEStreptomycetes are well-studied model organisms for the biosynthesis of pharmaceutically, industrially, and biotechnologically valuable metabolites. Their naturally broad repertoire of natural products can be further exploited by heterologous expression of biosynthetic gene clusters (BGCs) in non-native host strains. This approach forces the host to adapt to a new regulatory and metabolic environment. In our study, we demonstrate that a host regulator not only interacts with newly incorporated gene clusters but also regulates precursor supply for the produced compounds. We present a comprehensive study of regulatory proteins that interact with two genetically similar gene clusters for the biosynthesis of liponucleoside antibiotics. Thereby, we identified regulators of the heterologous host that influence the production of the corresponding antibiotic. Surprisingly, the regulatory interaction is highly specific for each biosynthetic gene cluster, even though they encode largely structurally similar metabolites.