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PubMed2026

Exploring Actinobacteria for new insecticides and their delivery in crop protection.

Crop protection is essential for agricultural production systems, safeguarding yields and product quality. Chemical controls are a mainstay of protection; however, regulatory and consumer demands, environmental concerns and a general overreliance resulting in resistance development in pest populations have led to increased interest in biopesticides and environmentally friendly alternatives. Biopesticides targeting insects include micro-organisms and their derivatives, such as peptides and specialized metabolites. Their target specificity, structural complexity, modes of action and environmental safety are key differentiators to chemical controls, and when used in integrated pest management programmes, biopesticides can reduce reliance on chemical pesticides and promote sustainable agriculture. As the demand for bioinsecticides grows, so too has the research and application of micro-organisms, alongside their taxonomic diversity and isolation sources. Of key interest are Actinobacteria as both promising and well-tested alternatives for managing insect pests in various agricultural settings, with several products commercialized for use across a variety of crops and target pests. Recent advances and investigations in metabolomics and genomics highlight the untapped and significant biochemical potential and value of Actinobacteria for natural product discovery. This review covers a broad spectrum of published literature that has reported on insecticidal biological activity data associated with Actinobacteria or their natural products. We also report on Actinobacteria-derived nematicides and acaricides that are significant for crop protection. The origin of these natural products, their structural diversity and notable substructures are discussed, along with new areas for discovery and avenues for enhancing screening methods and metabolo-genomics approaches.

Insecticides↗

PubMed2026

[Exploring the mechanism underlying the efficacy differences of "Tiaojing Cuyun Acupuncture"for premature ovarian failure based on vaginal microbiota structure].

OBJECTIVE: To observe the efficacy of "Tiaojing Cuyun Acupuncture" combined with hormone replacement therapy in the treatment of premature ovarian failure (POF), and to investigate differences in vaginal microbiota among patients with different therapeutic responses, thereby preliminarily exploring the mechanism underlying efficacy differences. METHODS: Ninety-eight patients with POF were randomly divided into an observation group (49 cases, 1 case was eliminated)and a control group (49 cases, 1 case dropped out). The control group was treated with hormone replacement therapy with Femoston, one tablet each time, once daily. On the basis of the control group, the observation group was additionally treated with "Tiaojing Cuyun Acupuncture". Acupoint group 1 included Baihui (GV20), Zhongwan (CV12), Guanyuan (CV4), and bilateral Tianshu (ST25), Zigong (EX-CA1), Dahe (KI12), Zusanli (ST36), Sanyinjiao (SP6), and Taichong (LR3). Acupoint group 2 included Baihui (GV20), bilateral Shenshu (BL23), Ciliao (BL32), and Taixi (KI3). The two acupoint groups were used alternately, beginning with acupoint group 1. Treatment was administered once every other day, three times per week.Both groups were treated for three menstrual cycles. Serum follicle-stimulating hormone (FSH), luteinizing hormone (LH),estradiol (E2), and anti-M ü llerian hormone (AMH) levels on days 3-5 of the menstrual cycle were measured before and after treatment in the two groups. Self-rating anxiety scale (SAS) scores were assessed before and after treatment, and clinical efficacy was evaluated in the two groups. Five effective patients (G0 subgroup) and five ineffective patients (G1 subgroup)were randomly selected from each group, and their vaginal microbiota structure was analyzed using 16S rRNA sequencing. RESULTS: After treatment, FSH levels in both groups were lower than those before treatment (P<0.05); SAS scores in both groups were lower than those before treatment (P<0.05), and the observation group had lower SAS score than the control group (P<0.05). The total effective rate was 77.1% (37/48) in the observation group, which was higher than 56.3% (27/48) in the control group (P<0.05). Vaginal microbiota analysis showed that at the phylum level, the relative abundance of Firmicutes in the G0 subgroup of the control group was higher than that in the G1 subgroup, while the relative abundances of Bacteroidetes, Actinobacteria and Proteobacteria were lowed in the G0 subgroup. In contrast, the observation group exhibited an opposite trend: the G0 subgroup had lower Firmicutes abundance but higher abundances of Actinobacteria, Bacteroidetes and Proteobacteria compared with the G1 subgroup. At the family and genus levels, Bifidobacterium was enriched in the G0 subgroups of both groups, whereas Lactobacillus predominated in the G1 subgroups. The G0 subgroup of the control group showed higher abundance of Gardnerella, while both Lactobacillus and Gardnerella were concurrently elevated in the G1 subgroup of the observation group. Additionally, in the observation group indicated that Clostridiales and Rikenellaceae were significantly more abundant in the G0 subgroup than in the G1 subgroup (P<0.05). CONCLUSION: The "Tiaojing Cuyun Acupuncture" combined with hormone replacement therapy is superior to hormone replacement therapy alone in improving anxiety. There are differences in vaginal microbiota structure among patients with different theraputic efficacy, suggesting that the vaginal microecological environment may be involved in the mechanism of treatment response in POF.

Humans↗

PubMed2024

Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (Panicum virgatum L.) significantly impacts plant microbiomes.

UNLABELLED: Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-impact growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remain unclear. To address this, wild-type and QsuB-engineered switchgrass were grown in switchgrass field soils, and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wild-type, QsuB-engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB-engineered plants had a lower relative abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB-engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both AMF and Actinobacteriota similarly or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing nontarget impacts of engineered plant traits on the plant microbiome. IMPORTANCE: Bioenergy crops provide an important strategy for mitigating climate change. Reducing the lignin in bioenergy crops could improve fermentable sugar yields for more efficient conversion into bioenergy and bioproducts. In this study, we assessed how switchgrass engineered for low lignin impacted aboveground and belowground switchgrass microbiome. Our results show unexpected reductions in mycorrhizas and actinobacteria in belowground tissues, raising questions on the resilience and function of genetically engineered plants in agricultural systems.

Panicum↗

PubMed2026

Metagenomic Insights Into Microbial Diversity of Tea Rhizosphere of the Kangra Valley.

This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.

Rhizosphere↗

PubMed2024

Metagenomic Analysis of Gut Microbiome of Persistent Pulmonary Hypertension of the Newborn.

Persistent pulmonary hypertension of the newborn (PPHN) is one of the most common diseases in the neonatal intensive care unit which severely affects neonatal survival. Gut microbes play an increasingly important role in human health, but there are rarely reported how gut microbiota contribute to PPHN. In our study, the metagenomic sequencing of feces from 12 PPHN's neonates and 8 controls were performed to expose the relation between neonatal gut microbes and PPHN disease. Firstly, we found that the abundance of Actinobacteria, Proteobacteria, Bacteroidetes were significantly increased in PPHN compared with controls, but the Firmicutes components was reduced. And some pathogenic strains (like Vibrio metschnikovii) were significantly enriched in the PPHN compared with controls. Secondly, functional annotation of genes found that PPHN up-regulated transmembrane transport, but down-regulated ribosome and ATP binding. Lastly, microbial metabolic pathway enrichment analysis indicated that some metabolic pathway in PPHN were conflicting and contradictory, showed that an abnormally increased metabolism, disturbed protein synthesis and genomic instability in the PPHN neonate. Our results contribute to understanding the changes in the species and function of gut microbiota in PPHN, thus providing a theoretical basis for the explanation and treatment of PPHN.

Gastrointestinal Microbiome↗

PubMed2026

Microbial allies in a cotton pest: A descriptive account of associated microbiota dynamics in Dysdercus cingulatus across development.

BACKGROUND: Hemipteran insects harbour several symbiotic partners, mainly bacteria, which play pivotal roles for hosts like dietary provision, support overall physiology, xenobiotic degradation and manipulate/regulate behaviour. Most of these symbionts usually reside and operate from the digestive tracts of the animals. Cotton is one of the major cash crops in India and Dysdercus cingulatus (D. cingulatus) though a secondary pest, is causing significant destruction of cotton bolls, poor lint quality and reduce oil content of seeds. Premature opening of cotton bolls often leads to bacterial and fungal infections, thus resulting in extensive economic loss worldwide. D. cingulatus is a hemimetabolous insect that comprises of developmental stages like egg, nymph (5 instar stages), and adult. The present work explored the ontogeny specific diversity in the associated microbiota and predicted their probable functional inputs in D. cingulatus. RESULTS: The data obtained using 16S rRNA gene sequencing (NovaSeq 6000) revealed presence of members of Proteobacteria (65.83%), Firmicutes (24%), Actinobacteria (10%) phyla throughout the ontogeny of D. cingulatus. Highest alpha diversity of these symbiotic bacteria was recorded in the third instar nymphs in contrast to rest of the developmental stages. Among all the observed genera, Stenotrophomonas, Hungatella and Glutamicibacter were predominant from egg to adult stages. MicFunPred, a tool used for predicting the probable functional inputs of these symbionts, hinted at their probable stage specific contribution in crucial biochemical pathways such as polyketide biosynthesis, ascorbate/aldarate metabolism, pentose phosphate and glyoxylate cycles, steroid hormone and peptidoglycan biosynthesis, and glycolysis/pyruvate metabolism. CONCLUSIONS: The primary investigations on the ontogenetic composition and diversity of associated microbiota, suggest dynamic shifts in D. cingulatus, concurrent with their probable functions/roles in the host development and metabolism. To the best of our knowledge, this is the first report on symbiotic microbiota variation across the developmental stages of D. cingulatus that provides preliminary descriptive observations that may guide future functional and experimental investigations into microbiota-based pest management.

Animals↗

PubMed2026

Large-scale discovery platform enables identification of peptides targeting drug-resistant candidiasis.

Natural products have an unparalleled track record as sources of clinical drugs. Among them, nonribosomal peptides (NRPs) stand as one of the most therapeutically significant classes, encompassing numerous approved anti-infective and anticancer agents. Yet, discovering bioactive NRPs remains profoundly challenging due to their complex biosynthesis and chemical architecture. Here, we present NPDiscover, a pathogen-oriented, scalable bioinformatics platform that integrates genome mining, metabolomics, and machine learning to identify NRPs active against drug-resistant pathogens. Applying NPDiscover to Actinobacteria datasets, we discovered edaphochelin A, a previously unreported NRP that kills multi-drug-resistant Candida auris and Candida glabrata by disrupting respiratory chain proteins. Structural elucidation via nuclear magnetic resonance and mass spectrometry, alongside in vitro and in vivo validation, confirmed its efficacy, safety, and a mode of action distinct from existing antifungals-establishing edaphochelin A as a compelling drug candidate and NPDiscover as a powerful engine for scalable natural product discovery.

CP: biotechnology↗

PubMed2024

Land use conversion to uplands significantly increased the risk of antibiotic resistance genes in estuary area.

Land use conversion in estuary wetlands may affect the transmission of antibiotic resistance genes (ARGs), while the risk rank of the ARGs and the change of clinically relevant ARGs under various land-use types are not well understood. This study used metagenomics to reveal the diversity and abundance of ARGs across five distinct land uses: reed wetland, tidal flat, grassland, agricultural land and fallow land, as well as their distribution and potential health risks. Results showed that high numbers of ARG subtypes and classes were detected irrespective of land-use types, notably higher in agricultural land (144 ARG subtypes). The most shared ARG subtypes were multidrug resistance genes across all the land uses (29 subtypes, 4.7 × 10-2-1.5 × 10-1 copies per 16S rRNA gene copy). Proteobacteria and Actinobacteria were primary ARG hosts, with 18 and 15 ARGs were found in both of them, respectively. The ARG subtype mdtB was the most dominant clinical ARG detected with 90 % amino acid identity. The change of ARGs exhibited a consistent trend across land uses in terms of health risk ranks, with the highest observed in fallow land and the lowest in reed wetland. This study reveals the distribution pattern of ARGs across various land-use types, and enhances our understanding of the potential health risks associated with ARGs in the context of coastal wetland conversion in estuary areas.

Estuaries↗

PubMed2024

Soil keystone viruses are regulators of ecosystem multifunctionality.

Ecosystem multifunctionality reflects the capacity of ecosystems to simultaneously maintain multiple functions which are essential bases for human sustainable development. Whereas viruses are a major component of the soil microbiome that drive ecosystem functions across biomes, the relationships between soil viral diversity and ecosystem multifunctionality remain under-studied. To address this critical knowledge gap, we employed a combination of amplicon and metagenomic sequencing to assess prokaryotic, fungal and viral diversity, and to link viruses to putative hosts. We described the features of viruses and their potential hosts in 154 soil samples from 29 farmlands and 25 forests distributed across China. Although 4,460 and 5,207 viral populations (vOTUs) were found in the farmlands and forests respectively, the diversity of specific vOTUs rather than overall soil viral diversity was positively correlated with ecosystem multifunctionality in both ecosystem types. Furthermore, the diversity of these keystone vOTUs, despite being 10-100 times lower than prokaryotic or fungal diversity, was a better predictor of ecosystem multifunctionality and more strongly associated with the relative abundances of prokaryotic genes related to soil nutrient cycling. Gemmatimonadota and Actinobacteria dominated the host community of soil keystone viruses in the farmlands and forests respectively, but were either absent or showed a significantly lower relative abundance in that of soil non-keystone viruses. These findings provide novel insights into the regulators of ecosystem multifunctionality and have important implications for the management of ecosystem functioning.

Soil Microbiology↗

PubMed2024

Assessment of antibiotic resistance genes in soils polluted by chemical and technogenic ways with poly-aromatic hydrocarbons and heavy metals.

Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.

Soil Pollutants↗

PubMed2026

Environmental coupling between metal resistance genes and bacterial communities in Beijing urban green-space soils.

Urban green spaces are intensively managed ecosystems exposed to chronic, multisource, low-intensity anthropogenic inputs. These inputs may alter soil microbial communities and influence the distribution of metal resistance genes (MRGs). However, MRG distributions and their relationships with environmental conditions and bacterial communities remain unclear under the complex, non-extreme pollution conditions typical of these ecosystems. We investigated Beijing urban green spaces as a representative system using metagenomic sequencing and metagenome-assembled genome (MAG) analysis. We characterized soil MRG composition, its environmental associations, and the distribution of potential hosts. MRG composition differed significantly among ecological conservation (EC), transitional urban (TU), and central urban (CU) zones. These differences were closely associated with soil physicochemical properties and bacterial community structure. Available phosphorus (AP) was significantly associated with variation in both bacterial community structure and MRG composition. MAG-based analysis identified distinct potential-host compositions across the three functional zones. Proteobacteria were more frequently represented among dereplicated MAGs from EC soils, whereas Actinobacteria were more frequent in TU and CU soils. Heavy metal concentrations correlated with MRG composition. However, variation partitioning analysis did not identify an independent contribution from heavy metals after accounting for soil physicochemical properties and bacterial community structure. These findings indicate that urban green-space soil monitoring should incorporate environmental conditions and microbial community characteristics rather than rely solely on total metal concentrations.

Soil Microbiology↗

PubMed2026

Description and genomic characterization of Aquipuribacter aurantiacus sp. nov., isolated from saline lake sediment.

Strains MA13-6T and MA13-13, two Gram-stain-positive, aerobic, short rod-shaped actinobacteria, were isolated from a saline lake in Ngari Prefecture, Xizang Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these two strains belonged to the genus Aquipuribacter, with the closest relationship to Aquipuribacter hungaricus IV-75T (98.47% sequence similarity) and Aquipuribacter nitratireducens AMV4T (97.36% sequence similarity). Phylogenetic analysis based on genomes further confirmed their classification as a distinct cluster within the genus Aquipuribacter. The average nucleotide identity and digtal DNA-DNA hybridization values between these two strains and their closest relative Aquipuribacter hungaricus IV-75T, were 82.44-82.49% and 23.00%, respectively, clearly indicating that strains MA13-6T and MA13-13 represent a novel species. The 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA-DNA hybridization values between these two strains were 99.79%, 99.97% and 99.40%, respectively, unequivocally confirming their classification within the same species. However, DNA fingerprinting analysis distinguished them as non-clonal variants. The polar lipids comprised phosphatidylglycerol, two unidentified phospholipids, two unidentified glycolipids, and two unidentified lipids. The predominant respiratory quinone was MK-10 (H4). The major fatty acids were anteiso-C15:0, C18:1ω9c, isoC16:0 and anteiso-C17:0. The cell wall diagnostic diamino acid was meso-diaminopimelic acid. Based on phylogenetic analyses combined with phenotypic and chemotaxonomic characterization, strains MA13-6T and MA13-13 represent a novel species of the genus Aquipuribacter, for which the name Aquipuribacter aurantiacus sp. nov. is proposed. The type strain is MA13-6T (=MCCC 1K10045T = KCTC 59572T).

Phylogeny↗

PubMed2025

Metagenomic and Transcriptomic Datasets of Plateau Brown Frogs (Rana kukunoris) from the Helan Mountains.

Global climate change has become a primary driving factor behind the biodiversity crisis in amphibians, making it crucial to understand how climate change affects species and their potential responses. The plateau brown frog (Rana kukunoris) is often regarded as an ideal ecological indicator species, yet research on its environmental adaptation mechanisms based on transcriptomic and microbiomic studies remains limited. Therefore, this study investigates the adaptation strategies of the plateau brown frog to environmental changes, providing extensive transcriptomic and the first comprehensive metagenomic dataset from two distinctly different environmental regions (eastern and western slopes of the Helan Mountains). We gathered transcriptomic data from three tissues (blood, liver, and muscle), resulting in 294,962 unigenes and 570,192 transcripts. Metagenomic sequencing identified major bacterial groups, including Firmicutes, Proteobacteria, Bacteroidetes, Spirochetes, and Actinobacteria. In summary, the results of this study can be used to further explore the associations among microbiota, host, and environment, which are crucial for comprehending the mechanisms of environmental adaptation in this species and contributing to the conservation of amphibian biodiversity.

Animals↗

PubMed2025

Nutritional modulation of host physiology, behavior, and gut microbiome in the captive rodent Octodon degus.

Diet is a key determinant of health by affecting nutrient metabolism, energy balance, body weight regulation, and mental health. The gut-brain axis is a critical pathway through which dietary factors influence cognitive function and behavior via microbial metabolites. While this relationship has been extensively studied in traditional laboratory models, diet-microbiome-cognition interactions remain largely unexplored in Octodon degus, an emerging model for aging, neurodegeneration, and cognitive research. Here, we compared two widely used rodent diets-LabDiet and Champion-to evaluate their effects on digestive efficiency, behavior, and gut microbiome composition. We also examined the relationships between these variables using piecewise structural equation modeling (pSEM). Our results indicated that LabDiet-fed degus exhibited enhanced nutrient absorption, higher fecal acetic acid levels, and a higher abundance of Actinobacteria (particularly Bifidobacterium), likely driven by its vitamin C supplementation. These animals also showed improved working memory and social motivation, but they displayed increased anxiety-like behavior. In contrast, Champion-fed degus, which consumed a more fiber-diverse, plant-based diet, showed lower anxiety traits and significantly greater gut microbial richness, with higher abundance of Bacteroidota and Tenericutes. Innate behaviors, such as burrowing and nesting, remained unaffected by the diet. SEM analysis revealed that diet explained most of the variance in microbial activity and identified a positive association between acetic acid levels and cognitive performance. This emphasizes a strong relationship among diet, microbiome, and brain function. Overall, our results suggest that dietary composition is a key factor influencing experimental outcomes in degus, with important implications for physiology, cognition, and microbial ecology. Standardizing dietary inputs is essential to ensure reproducibility in behavioral and biomedical studies using this model. Additionally, our results reinforce the microbiome's role as a mediator of diet-driven brain function via SCFAs, underscoring degus as a powerful system for investigating diet-microbiome-neurobehavioral interactions relevant to aging and mental health.

Animals↗

PubMed2026

Streptomyces xingningensis sp. nov. and Streptomyces rhizosphaerae sp. nov. isolated from the rhizosphere soil of Camellia oleifera.

Two novel actinobacteria strains, designated YCB024T and YCB041T, were isolated from rhizosphere soil samples of Camellia oleifera collected from Xingning City, Guangdong Province, PR China. Both strains exhibited mycelial filaments and intertwined hyphal cells. Phylogenetic analysis revealed that strain YCB024T exhibited the highest 98.8% 16S rRNA gene similarity with Streptomyces yogyakartensis NBRC 100779T, Streptomyces javensis NBRC 100777T and Streptomyces violaceusniger NBRC 13459T, and strain YCB041T exhibited the highest 98.9% similarity with Streptomyces albospinus NBRC 13846T. The average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values among the two strains and their closely related species indicated that they were clearly different from other known Streptomyces species. The draft genome sizes of the two strains were 6.9 Mbp and 9.5 Mbp with DNA G+C contents of 70.4 mol% and 71.7 mol%. The major cellular fatty acids in strain YCB024T included iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0, and strain YCB041T included iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. The major polar lipids of the two strains were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside or unidentified aminophospholipid. The respiratory quinones of both strains included MK-9 (H6), MK-9 (H8) and MK-10 (H4). Based on phylogenetic analysis, ANI and dDDH values, physiological and chemical properties, strains YCB024T and YCB041T represent two novel species of the genus Streptomyces, for which the names Streptomyces xingningensis sp. nov. (type strain YCB024T=GDMCC 4.314T=JCM 36249T) and Streptomyces rhizosphaerae sp. nov. (type strain YCB041T=GDMCC 4.469T=JCM 38170T) are proposed, respectively.

Streptomyces↗

PubMed2025

WhiB6 Transduces Contact-Dependent Signaling in Mycobacterium smegmatis and Coordinately Induces Both ESX-1 and ESX-4.

Bacteria have evolved complex conditional pathways that respond to environmental stresses and signals. We use conjugation in Mycobacterium smegmatis to identify contact-recognition and response pathways that mediate interactions between donor and recipient cells. Contact with a compatible donor cell initiates a response in the recipient that requires the ESX-1 secretion system and subsequently activates the dormant ESX-4 secretion system. The links of this signal transduction pathway, the mechanism of coordination and dependency between ESX-1 and ESX-4 secretion systems, are unknown. Previous studies identified SigM as a cell-contact responsive sigma factor dedicated to activating ESX-4. WhiB proteins are iron-sulfur-binding stress-response transcription factors exclusively found in Actinobacteria. WhiB6 has been shown to regulate ESX-1 associated gene expression in other mycobacteria. Here, we show that WhiB6 is required both for conjugation and for transducing cell-contact dependent signaling in the recipient cell. Our RNA-seq, ChIP-seq, and proteomic profiling data define a WhiB6 regulon that supports conjugative cell-cell interaction. The WhiB6 regulon includes genes encoding ESX-1, ESX-4, SigM, as well as dispersed operons that likely support ESX secretion. Our data demonstrate that WhiB6 is epistatic to SigM and ESX-4 in this signal transduction pathway. This work shows that WhiB6 functions as a signal transduction node in recipient cells: it coordinates the expression of two ESX systems and it also induces uncharacterized proteins that collectively constitute a complete secretion response to recipient contact with a donor cell.

Mycobacterium smegmatis↗

PubMed2026

Causal Effects of Gut Microbiota on Morning Chronotype, Insomnia and Sleep Duration: A Two-Sample Mendelian Randomization Study.

BACKGROUND: The gut microbiota has been shown to be closely associated with brain function; however, whether it exerts a causal influence on sleep traits remains to be further explored. Mendelian randomization (MR) is an emerging epidemiological approach that uses whole-genome sequencing data to infer causal relationships. In this study, we conducted a two-sample MR analysis to investigate the causal effects of gut microbiota on three domains of sleep traits: morning chronotype, insomnia, and sleep duration. METHODS: Single nucleotide polymorphisms strongly associated with 196 gut microbiota taxa were selected as instrumental variables. Morning chronotype, insomnia, and sleep duration were used as outcomes. MR and sensitivity analyses were performed to assess the causal relationships between gut microbiota and sleep traits. RESULTS: Three taxa (Bifidobacteriales, Bifidobacteriaceae, and Bifidobacterium) were negatively associated with morning chronotype, while Tyzzerella 3 showed a positive causal effect on morning chronotype. Oscillibacter was negatively associated with insomnia, whereas four taxa (Negativicutes, Selenomonadales, the Clostridium innocuum group, and Lachnoclostridium) were identified as risk-increasing factors for insomnia. Lentisphaerae and Victivallaceae were positively associated with sleep duration. Actinobacteria and Alistipes had negative effects on long sleep duration, whereas Ruminiclostridium 6 was positively associated with long sleep duration. Four taxa (Victivallales, Anaerofilum, Lentisphaerae, and Lentisphaeria) were negatively associated with short sleep duration. CONCLUSIONS: Our findings suggest that specific gut microbiota taxa may be positively or negatively associated with sleep traits. These results offer new insights into the potential role of gut microbiota in sleep regulation and provide a basis for future studies aimed at understanding whether modulating microbial composition could influence sleep health.

Mendelian randomization↗

PubMed2026

Genome analysis and antagonistic activity of Streptomyces sp. strain J36 against Phytophthora cactorum.

The Phytophthora blight of Panax notoginseng, caused by Phytophthora cactorum, is a devastating oomycete disease. Biocontrol strategies hold immense potential for inhibiting the spread of P. cactorum. We isolated 72 actinobacteria from soil and screened their antagonistic activity against P. cactorum. Both strain J36 and its cell-free filtrate exhibited strong antagonistic activity against P. cactorum and were therefore selected. Based on the 16S rRNA gene phylogenetic tree, strain J36 formed a well supported subclade with Streptomyces zaomyceticus NRRL B-2038 (bootstrap value 100%). However, because 16S rRNA sequences often lack sufficient resolution for species-level discrimination, we performed multilocus sequence analysis (MLSA) using three housekeeping genes (rpoB, recA, and atpD). The MLSA results consistently placed strain J36 within the same cluster as S. zaomyceticus NRRL B-2038, with a bootstrap support of 99%, indicating a close phylogenetic relationship. To further clarify the taxonomic status, we calculated the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain J36 and the type strain of S. zaomyceticus NBC-00415T. The ANI value was 90.91% and the dDDH value was 39.30%, both well below the accepted thresholds for species demarcation (ANI < 95%, dDDH < 70%). These genomic indices therefore strongly support that strain J36 represents a novel species within the genus Streptomyces. Through whole-genome sequencing and CAZymes analysis, a total of 98 carbohydrate-active enzymes (CAZymes) were detected, including 2 cellulase and 2 β-1,3-glucanases. The cell-free filtrate, which exhibited strong antagonistic activity against P. cactorum, also showed high activities of cellulase and β-1,3-glucanase, suggesting that these enzymes may be involved in its anti-oomycete activity. These findings suggest that J36 has potential as a biocontrol candidate, although further in vivo evaluation is needed to confirm its efficacy against Phytophthora blight of P. notoginseng.

Panax notoginseng↗