16S rDNA Research Articles

An investigation of the role of wild rats in transmitting Leptospira spp. to stray cats and dogs in Malaysia

Stray cats and dogs have been reported to shed Leptospira spp., and wild rats are speculated to be involved. We aimed to elucidate the role of wild rats in transmitting Leptospira to stray cats and dogs in Malaysia. We tested sera from 124 wild rats with the microscopic agglutination test (MAT): 88 of 122 (72%) sera were positive (titer ≥1:100), with the predominant serovars Icterohaemorrhagiae, Bataviae, Ballum, Javanica, Lai, and Pomona. With a Leptospira -specific PCR assay, we detected pathogenic Leptospira spp. in 33 of 124 (27%) kidney samples and 13 of 79 (16%) urine samples. Isolates obtained by culture of rat kidney and urine were identified to the species level with MAT using hyperimmune sera and the PCR assay. From 29 isolates, 2 pathogenic species were identified: L. interrogans serovar Bataviae and L. borgpetersenii serovar Javanica. Phylogenetic analysis using partial 16S rDNA sequences of the Leptospira spp. from the wild rats indicated that the species were similar to isolates from stray cats and dogs in previous studies. We confirmed that wild rats carried pathogenic Leptospira spp. and were a potential source of leptospiral infection of stray cats and dogs in Malaysia.

Robertsonian rearrangements in the genome of the azure damselfish, Chrysiptera hemicyanea (Perciformes, Pomacentridae)

Cytogenetic studies on the azure damselfish, Chrysiptera hemicyanea (Weber, 1913), revealed a karyotype with 2n = 31 chromosomes (17 metacentric, 2 submetacentric, and 14 telocentric; FN = 52). The study found Robertsonian polymorphisms, which involve small heterochromatic regions at the centromeres. Nucleolar organizer regions (NORs) were observed near the ends of the long arms on the large metacentric chromosome pair (pair 2). FISH analysis, which detects specific DNA sequences, revealed notable variability in the distribution of ribosomal DNA (5S and 18S rDNAs) along the chromosomes. Specifically, the 18S rDNA was located at the ends of the long arms on the large metacentric chromosomes (pair 2), while the 5S rRNA genes were found near the centromere of another large metacentric chromosome pair (pair 3). The analysis also showed that repetitive DNA sequences (CA)15, (GA)15, and (CAA)10 were spread across the subtelomeric and telomeric regions of various chromosomes. The study suggests that the structure of the karyotype and chromosome number are linked to the Robertsonian rearrangements observed, highlighting their significant role in the evolutionary changes in the karyotype of the genus Chrysiptera.

Intermediate insights: tracing trematodes infecting amphibians via their first intermediate snail hosts

Abstract Background Amphibians are a prime example of the global biodiversity crisis, as they represent the most threatened group of vertebrates. Yet, amphibian macroparasites remain one of the most poorly described groups of parasites, with the majority of species lacking comprehensive morphological, molecular, or ecological data. Among these, digenean trematodes constitute a dominant group and feature multi-host life cycles. This study examines the first intermediate hosts of trematodes, aquatic gastropods, to assess the occurrence, prevalence, and seasonality of amphibian trematodes. Methods A total of 5362 snails from five families (Bithyniidae, Hydrobiidae, Lymnaeidae, Physidae, and Planorbidae) were collected in three stream systems in North Rhine-Westphalia, Germany and investigated for trematode infections. Detailed information on amphibian-infecting trematode cercarial morphology and measurements were provided via light microscopy and scanning electron microscopy (SEM). Comprehensive molecular analyses were conducted and novel sequences generated for multiple genetic markers (28S rDNA, ITS1-5.8S-ITS2, ITS2, cox1, and nad1). Results Three trematode taxa infecting amphibians as second intermediate and/or definitive hosts (Lecithopyge, Cephalogonimus, and Opisthioglyphe) were identified exclusively from lymnaeid snail hosts. A total of 79 novel sequences were generated for 21 trematode isolates. Phylogenetic analyses based on 28S and ITS1-5.8S-ITS2 sequences resulted in concordant taxonomies. Distinct seasonal infection patterns allowed for insights into the species’ life cycles. Conclusions Our findings highlight significant gaps in the knowledge of amphibian macroparasites and underline the value of studying cercariae occurrence in snail intermediate hosts as a method for monitoring amphibian trematode biodiversity without affecting amphibian populations. Graphical Abstract

How reliable is mitochondrial DNA for recovering the phylogeny of Chironomidae (Culicomorpha: Diptera)?

We examine mitochondrial DNA as a source of data to estimate phylogenetic relationships within the Chironomidae (Diptera). Previous studies have shown that mitogenomes often produce ambiguous phylogenetic topologies that are inconsistent with both morphological and multi-locus molecular data. In this study, we sequenced 18 new mitogenomes representing 5 subfamilies, including the first available sequence for Protanypodinae. These were combined with 65 previously annotated chironomids mitogenomes, 8 additional individuals assembled from SRA data, and 8 outgroup taxa. Phylogenetic reconstructions were performed using complete protein-coding genes (PCGs), the first and second codon positions of PCGs (PCG 12), with and without ribosomal genes (12S rDNA and 16S rDNA), and amino acid sequences (AA). Both Bayesian Inference and Maximum Likelihood approaches were implemented. Three alternative outgroup compositions were tested: (i) chironomids only, with restricted rooting on Podonominae; (ii) Ceratopogonidae and Culicidae; and (iii) a diverse selection of Culicomorpha. We found that the AA, PCG12, and PCG 12 + rDNA datasets, when coupled with the third outgroup combination, provide the strongest phylogenetic signal, with the highest effective sample size and log-likelihood scores. In most cases, the resulting tree topologieswere congruent between mitochondrial and multi-locus data. However, some consistent differences in topologies were observed, leading to differences in divergence time estimates. Our phylogenetic study indicates paraphyly of Orthocladiinae due to the positions of Brillia Kieffer and Abiskomyia Edwards, suggesting that a comprehensive integrative revision of this subfamily is required. We conclude that the reliability of the mitochondrial phylogenetic signal improves with the increased taxon sampling.

Examining gut microbiota and metabolites to clarify mechanisms of Dimocarpus longan Lour leaf components against type 2 diabetes

BACKGROUND Dimocarpus longan Lour leaf components (DLC) contain key active compounds such as quercetin, kaempferol, and quercitrin. They are effective for managing type 2 diabetes mellitus (T2DM), though the exact mechanism by which DLC acts remains unclear. AIM To investigate the material basis and mechanism underlying the therapeutic effect of DLC in T2DM. METHODS T2DM was triggered in rats using a high-sugar, high-fat diet alongside 35 mg/kg streptozotocin. The effect of DLC on the intestinal microbiota in T2DM rats was analyzed via 16S rDNA sequencing. Targeted metabolomics was conducted to evaluate the impact of DLC on the levels of nine short-chain fatty acids (SCFAs). Untargeted metabolomics examined DLC-induced alterations in fecal metabolites and associated metabolic pathways. Additionally, Spearman’s correlation analysis assessed gut microbiota and fecal metabolite relationships. RESULTS DLC significantly attenuated pathological weight loss, reduced fasting blood glucose levels, restored blood sugar homeostasis, and ameliorated dyslipidemia in T2DM rats. The 16S rDNA sequencing revealed that DLC enhanced microbial diversity and reversed intestinal dysbiosis. Targeted metabolomics indicated decreased acetic acid and propionic acid levels and increased butyric acid, isobutyric acid, and 2-methylbutyric acid levels after DLC treatment. Untargeted metabolomics revealed 57 metabolites with altered expression associated with amino acid, carbohydrate, purine, and biotin pathways. The Spearman analysis demonstrated significant links between specific gut microbiota taxa and fecal metabolites. CONCLUSION DLC may exert hypoglycemic effects by modulating intestinal flora genera, SCFA levels, and fecal metabolites.

Description of Ellipsomyxa prima n. sp. in the gallbladder of Gambusia yucatana (Cyprinodontiformes: Poeciliidae) from freshwater springs in the Yucatán Peninsula, Mexico

The Celestún Lagoon is located on the coast of the Yucatán Peninsula in southern Mexico. The peripheral margins of the lagoon are exposed to a constant influx of water from freshwater springs, where a wide diversity of freshwater fishes occurs. Simultaneously, these freshwater springs are mixing with marine water from the sea and brackish water from the lagoon. Gambusia yucatana is an endemic poeciliid freshwater fish of this coastal region, with no current parasitological records. In December 2023, 24 specimens from two freshwater springs near the Celestún Lagoon were examined for myxozoan infection. Disporic plasmodia containing mature myxospores floating freely within the bile were detected in all fish. The myxospores were ellipsoidal in the valvular and sutural views, measuring 9.5 ± 0.6 μm length and 6.5 ± 0.5 μm width. Two pyriform polar capsules discharging on opposite sides, 3.2 ± 0.4 μm length and 2.3 ± 0.2 μm width, and 5–6 polar filament coils. Polar tubule 31.3 μm long and coiled 5–6 times. The partial sequences of 18S rDNA and 28S rDNA displayed a similarity of ≤ 96.4% and ≤ 85.2% to all other available sequences from the genus Ellipsomyxa. Phylogenetic analyses revealed that the novel species named Ellipsomyxa prima n. sp. is closely related to other congeneric Ellipsomyxa parasites. This study describes the first parasite in G. yucatana and the first Ellipsomyxa species reported in a fish of the order Cyprinodontiformes and the family Poeciliidae.

A novel and simple workflow for investigating Mycoplasma spp. contamination in cell cultures.

Mycoplasma spp. contamination is a major concern in laboratories handling cell cultures, and routine detection methods are usually time-consuming, laborious and lack sensitivity. This study presents a streamlined workflow integrating rapid thermal DNA extraction (99°C-1min) with a SYBR Green-based qPCR for Mycoplasma detection. High-coverage primers targeting an 86-bp region of the 16S rDNA were designed using 109 Mycoplasma spp. sequences from GeneBank. In silico analysis confirmed full primer annealing to major cell culture contaminants (M. arginini, M. hominis, M. orale, and M. hyorhinis). Upon thermal lysis and qPCR optimization, the yield of the protocol was equivalent to that of phenol-chloroform extraction plus qPCR, with a detection limit of 64 bacterial cells. Finally, the performance of the protocol was confirmed in cell cultures with known Mycoplasma spp. contamination, accurately reproducing the contamination status. Thus, the developed protocol provides a simple, rapid, cost-effective, and sensitive method for monitoring Mycoplasma spp. in cell cultures.

Specific Nested PCR for the Detection of 16SrI and 16SrII Group Phytoplasmas Associated with Yellow Leaf Disease of Areca Palm in Hainan, China

Yellow leaf disease (YLD), caused by the areca palm yellow leaf phytoplasma (APYL), poses a significant threat to the sustainability of the areca palm industry. Timely and accurate detection is essential for effectively diagnosing and managing this disease. This study developed a novel nested PCR system using primers specifically designed from conserved regions of the phytoplasma 16S rDNA sequence to overcome limitations such as false positives often associated with universal nested PCR primers. The resulting primer pairs HNP-1F/HNP-1R (outer) and HNP-2F/HNP-2R (inner) consistently amplified a distinct 429 bp fragment from APYL strains belonging to the 16SrI and 16SrII groups. The detection sensitivity reached 7.5 × 10−7 ng/μL for 16SrI and 4 × 10−7 ng/μL for 16SrII. Field validation using leaf samples from symptomatic areca palms confirmed the high specificity and reliability of the new primers in detecting APYL. Compared to conventional universal primers (P1/P7 and R16mF2/R16mR1), this newly developed nested PCR system demonstrated higher specificity, sensitivity, and speed, making it a valuable tool for the early diagnosis and management of YLD in areca palms.

Seasonal dynamics and molecular phylogenetic studies on cercariae in Central Zone of Kashmir valley.

A total of 12103 snails examined in Central Kashmir for determining the population dynamics of cercariae revealed overall prevalence to be 4.03%. Gymnocephalus (0.13%), furcocercous (0.28%), echinostome (0.34%) and xiphido-cercaria (3.26%) were recorded. The prevalence of cercaria was recorded highest in summer (4.28%) followed by spring (4.05%) and autumn (3.32%). None of the cercaria was recorded during winter season. Morphologically identified cercariae of Veterinary importance were subjected to molecular analysis using genus (28S rDNA and ITS-2) specific primers. The isolates of gymnocephalus cercaria (FA28, FC28, FZ28, FC2) were identified as cercarial stages of Fasciola spp. The phylogenetic trees revealed that the isolates FA28 and FC28 belonged to Fasciola gigantica and FZ28 and FC2 isolate to F. hepatica. The isolate of Fasciola gigantica (FA28, FC28, FZ28) showed 2, 4 and 13 nucleotide polymorphisms. There was addition and deletion of 1 and 8 nucleotides at various positions in case of Fasciola isolates respectively. Besides this, there were nucleotide substitutions at 4 positions along with presence of nucleotide T at 475 position which confirmed it be Fasciola hepatica. The isolates of echinostome cercaria (B1, BD13 and GY) were identified as cercarial stages of Moliniella anceps, Echinoparyphium recurvatum and family Echinostomatidae respectively. The Moliniella anceps isolate showed prominent differences at 8 positions with respect to other Echinostomatidae spp. The insertion of C at position 612 confirmed it to be Moliniella anceps, while as other two isolates showed 2 nucleotide polymorphisms each after 28S gene amplification. On ITS-2 rDNA analysis, the isolate B1 showed 7 nucleotide polymorphisms and phylogenetic tree revealed that the isolate B1, also belonged to Echinoparyphium recurvatum. The study made it very clear that molecular characterization employing internal transcribed spacer (ITS-2) and 28S ribosomal DNA sequences are reliable approach for genetic differentiation of cercarial stages of trematodes. The phylogenetic taxonomy of echinostomes is still unclear and molecular diversity found in this study is perhaps the first study from India as well as in Indian subcontinent. So, focus should be made more on echinostomes for understanding their morphological, biological and molecular diversity for clarifying their taxonomic position.

Key findings from 15 years of Mangrovibacter research: a generalist bacterium beyond endophytes.

Since the discovery of Mangrovibacter plantisponsor in 2010, research on Mangrovibacters (MGBs) has stagnated. Although laboratories worldwide have isolated various MGB strains and deposited their 16S rDNA sequences in the NCBI database, a limited understanding of MGBs has resulted in only a few publications from these collections. Recent advancements in metagenomic technology have revealed the presence of MGBs in a broader range of habitats. Most microbiomes exhibit low MGB abundance (typically <1%). Even in environments with higher prevalence, such as salt-tolerant aerobic granular sludge (75%), the gut of superworms fed with polyurethane (22%), or fermented foods like mandai (16%), the functional roles of MGBs remain unclear. Through meticulous curation of publications and data from MicrobeAtlas and AMIBASE, MGBs can be classified as free living, endophytic, or zoonotic. Recent evidence suggests their presence in food sources and potential interactions with humans. Current studies confirm the coexistence of MGBs with humans. This review underscores the phenotypic features and genomic foundations of MGBs, highlighting attributes such as endophytic behavior, diverse metabolite utilization, tolerance to salinity and pH, metal homeostasis, biofilm formation, and bioremediation potential. Insights are derived from the analysis of four MGB genomes deposited in NCBI since 2014, along with three newly reported genomes in 2024. Experimental and genetic evidence suggests that MGBs act as "generalist microbes" capable of thriving in diverse nutrient sources and harsh environments. This review elucidates prospective research trajectories and highlights numerous potential commercial applications of MGBs, emphasizing the need for further investigation into their roles and benefits.

A droplet microfluidic strategy for cultivation, investigation, and high-throughput isolation of mouse gut microbiome bacteria.

Understanding the gut microbiome's intricate dynamics and its impact on host health necessitates the cultivation and isolation of its constituent microorganisms. Traditional culturing techniques often fall short in capturing the diversity of the gut microbiota, particularly for rare and slow-growing species. In this study, we present a droplet microfluidic platform as a high-throughput and efficient method for the cultivation and isolation of mouse gut microorganisms. Droplets, each encapsulating a single cell, were incubated under both aerobic and anaerobic conditions, thereby providing individual microenvironments without nutrient competition and facilitating the growth of a wide range of microorganisms. We validated the platform by successfully cultivating and isolating a diverse array of gut microorganisms, including strains with probiotic potential. A comparative analysis with traditional agar plating techniques revealed a higher number of unique isolates from the droplet cultivation method, demonstrating its enhanced capability to capture the cultivable fraction of the gut microbiome. Beyond isolation, 16S rDNA amplicon sequencing of the diverse microbial cultures in droplets demonstrated that our system reflects changes in microbial diversity induced by dietary interventions in mice. Droplet microfluidics offers a powerful and scalable tool for the high-throughput cultivation, evaluation, and isolation of gut microorganisms, paving the way for deeper insights into the gut microbiome's role in health and disease.IMPORTANCEThe gut microbiome plays a crucial role in health and disease, yet many of its microbial members remain difficult to cultivate using traditional methods. In this study, we present a droplet microfluidic platform that advances our ability to cultivate, isolate, and analyze mouse gut microorganisms. By providing individual microenvironments for single cells, this high-throughput method overcomes limitations of traditional culturing techniques, enhancing microbial diversity recovery compared to standard techniques. Furthermore, this platform can reflect changes in microbial diversity in response to dietary changes in mice, highlighting its potential for studying gut microbial dynamics.

Intestinal helminth Schyzocotyle acheilognathi Yamaguti, 1934 infection ameliorate lipid metabolism of grass carp (Ctenopharyngodon idella) through immune and gut microbiota regulation

Fats have been widely applied in aquaculture to promote growth performance and substitute partial protein in fish feeds. However, excessive dietary fat levels induce metabolic disorders harming the health of cultured fish. Helminth infection in mammals was inversely correlated with metabolic syndrome, but its effect in aquatic animals is unknown yet. Here, we evaluated the impacts of Schyzocotyle acheilognathi infection on lipid metabolism of grass carp fed with high-fat diet (HFD). By comparison with the uninfected grass carp, helminth infection significantly increased the concentration of high-density lipoprotein (HDL) and condition factor (CF), and significantly decreased the concentration of low-density lipoprotein (LDL), the activity of AST, perimeter ratio (PR) and the thickness of muscularis mucosa (MM). Helminth infection also significantly lowered the lipid accumulation in liver, which may attribute to the significant up-regulated expression levels of apolipoprotein E (ApoE) and down-regulated expression of peroxisome proliferator-activated receptor-gamma (PPAR-γ) and lipoprotein lipase (LPL). Meanwhile in the grass carp infected by tapeworm, there was significant down-regulated expression of pro-inflammatory genes, interleukin-1beta (IL-1β) and tumor necrosis factor-alpha (TNF-α), and significant up-regulated expression of anti-inflammatory genes, transforming growth factor-beta 1 (TGF-β1) and interleukin-10 (IL-10). 16S rDNA sequencing results showed that helminth infection didn’t affect the α diversity of the intestinal microbiota, but increased the relative abundance of Cetobacterium, and significantly changed the structure of intestinal microbiota by PERMANOVA analysis. Correlation analysis showed the relative abundance of Cetobacterium was significant positively correlated with the helminth infection in grass carp fed HFD. PICRUST2 analysis indicated that several lipid metabolism-related pathways were significantly altered after helminth infection. Consequently, the above results indicated that tapeworm infection could ameliorate abnormal lipid metabolism through immune and gut microbiota regulation.

Valorization of Rice-Bran and Corn-Flour Hydrolysates for Optimized Polyhydroxybutyrate Biosynthesis: Statistical Process Design and Structural Verification

The extensive environmental pollution caused by petroleum-based plastics highlights the urgent need for sustainable, economically viable alternatives. The practical challenge of enhancing polyhydroxybutyrate (PHB) production with cost-effective agro-industrial residues—rice-bran and corn-flour hydrolysates—has been demonstrated. Bacillus bingmayongensis GS2 was isolated from soil samples collected at the Pirana municipal landfill in Ahmedabad, India, and identified through VITEK-2 biochemical profiling and 16S rDNA sequencing (GenBank accession OQ749793). Initial screening for PHB accumulation was performed using Sudan Black B staining. Optimization via a sequential one-variable-at-a-time (OVAT) approach identified optimal cultivation conditions (36 h inoculum age, 37 °C, pH 7.0, 100 rpm agitation), resulting in a PHB yield of 2.77 g L−1 (66% DCW). Further refinement using a central composite response surface methodology (RSM)—varying rice-bran hydrolysate, corn-flour hydrolysate, peptone concentration, and initial pH—significantly improved the PHB yield to 3.18 g L−1(74% DCW), representing more than a threefold enhancement over unoptimized conditions. Structural validation using Fourier Transform Infrared spectroscopy (FTIR) and Proton Nuclear Magnetic Resonance spectroscopy (1H-NMR) confirmed the molecular integrity of the produced PHB. That Bacillus bingmayongensis GS2 effectively converts low-cost agro-industrial residues into high-value bioplastics has been demonstrated, indicating substantial industrial potential. Future work will focus on bioreactor scale-up, targeted metabolic-engineering strategies, and comprehensive sustainability evaluations, including life-cycle assessment.

Characteristics Analysis and Intestinal Effects of Probiotic‐Derived Nano‐Selenium by Lactobacillus bulgaricus CICC 20247

ABSTRACTThe bioproduction of selenium nanoparticles (SeNPs) is garnering increasing attention as an environmentally friendly method, given that many microorganisms inherently possess the ability to synthesize nano‐selenium. In the present study, Lactobacillus bulgaricus (L. bulgaricus) was selected to convert sodium selenite to SeNPs, the optimum conversion conditions were finally established, the morphology and structure of SeNPs were characterized as uniform distribution spherical particles with average size of 92.4 nm, in combination with field emission scanning electron microscope (FE‐SEM), transmission electron microscope (TEM), X‐ray photoelectron spectroscopy (XPS), and Fourier transform infrared spectroscopy (FTIR). 16S rDNA sequencing and genomic sequencing revealed that SeNPs influenced the composition of the gut microbiota, the abilities of immune and metabolism in mice were improved significantly after SeNPs supplement. The results corroborated the potential of SeNPs synthesized from probiotic L. bulgaricus CICC 20247 in intestinal health promotion and various biomedical even food processing applications.

The Herbal Pair Polygonum hydropiperL‐Coptis chinensis Franch Attenuate DSS‐Induced Ulcerative Colitis by Modulating Metabolism and Intestinal Flora

ABSTRACTUlcerative colitis (UC) is a chronic inflammatory bowel disease in which dysbiosis of the intestinal flora plays a critical role in its pathogenesis. Polygonum hydropiper L‐Coptis chinensis Franch (PH‐CC) known for its anti‐inflammatory properties and ability to regulate gut microbiota, has been demonstrated to alleviate UC. The aim of this study was to investigate the effects of PH‐CC on dysbiosis of intestinal flora and metabolic disorders in dextran sodium sulfate (DSS)‐induced UC mice. A UC mouse model was induced using a 3% DSS solution, and histopathological changes in the colon were assessed through hematoxylin and eosin staining. The composition and diversity of the intestinal flora were analyzed using 16S rDNA technology, whereas metabolomics was employed to identify potential differential metabolites and metabolic pathways through multivariate statistical analysis. Pearson correlation analysis was performed between metabolites, inflammatory factors, the NLRP3/Caspase‐1 pathway, and differential flora. The results revealed that treatment with PH‐CC improved the morphological structure of colon tissue and reduced damage in UC mice, while the model group exhibited significant damage to the crypt structure, exfoliation of the colonic mucosal epithelium, loss of glands, and infiltration of inflammatory cells. Analysis of 16S rDNA sequencing data indicated that PH‐CC regulated the DSS‐induced changes in gut microbiota, significantly decreasing the abundance of norank_f_norank_o_Rhodospirillales, norank_f_UCG‐010, Corynebacterium, and Eubacterium_nodatum_group. The differential microbiota exhibited a strong correlation with the NLRP3/Caspase‐1 pathway and downstream inflammatory factors. Additionally, 27 differential metabolites identified in fecal samples were primarily associated with phenylalanine metabolism and bile secretion, showing a high correlation with the differential microbiota. In conclusion, PH‐CC regulates dysbiosis in intestinal flora and metabolic disorders in UC mice by reducing the abundance of specific bacterial groups, thereby alleviating inflammatory damage to the colonic mucosa and improving the overall condition of UC.

Pine-fungal co-invasion alters whole-ecosystem properties of a native eucalypt forest.

Pine-fungal co-invasions into native ecosystems are increasingly prevalent across the southern hemisphere. In Australia, invasive pines slowly spread into native eucalypt forests, creating novel mixed forests. We sought to understand how pine-fungal co-invasions impact interconnected above- and belowground ecosystem characteristics. We sampled beneath mature Pinus radiata and Eucalyptus racemosa in a pine-invaded eucalypt forest in New South Wales, Australia. We measured microbial community composition via amplicon sequencing of 16S, ITS2, and 18S rDNA regions, microbial metabolic activity via Biolog plate substrate utilization, and soil, leaf litter, and understory plant characteristics. Pines were associated with decreased topsoil moisture, increased pine litter, and decreased eucalypt litter total phosphorus content. Soils and roots beneath pines had distinct microbial community composition and activity relative to eucalypts, including decreased bacterial diversity, decreased microbial utilization of several C- and N-rich substrates, and enrichment of pine-associated ectomycorrhizae. Introduced suilloid fungi were abundant across both pine and eucalypt soils and roots. Many ecosystem impacts increased with pine size. Invasive pines and their ectomycorrhizae have significant impacts on eucalypt forest properties as they grow. Interconnected impacts at the scale of individual trees should be considered when managing invaded forests and predicting effects of pine invasions.

Intestinal microbiota changes in early life of very preterm infants with bronchopulmonary dysplasia: a nested case–control study

Background and aimBronchopulmonary dysplasia (BPD) is one of the most important complications of very preterm infants. This study was to investigate changes in the intestinal microbiota of very preterm infants with BPD.MethodsWe enrolled 50 very preterm infants at the gestational age of 24+0–31+6 weeks, categorizing them into the BPD group and control group, and fecal samples were collected on days 1, 7, 14, 21, and 28, respectively. Finally, 30 preterm infants were left after excluding 20 preterm infants. We tested and analyzed 16S rDNA of bacteria and short-chain fatty acids (SCFAs) within the feces.ResultsThe BPD group possessed a higher abundance of Ureaplasma urealyticum (UU) and a lower abundance of Bacteroidota than the control on day 1. The differences in intestinal microbiota were reduced on days 7 and 14, and no difference in SCFAs existed on day 14. New differences emerged over time, with a significant decrease of Veillonella dispar in the BPD group than in the control group on day 28, which showed a continuous decline in the BPD group over time.ConclusionIntestinal microbiota dysbiosis existed in very preterm infants with BPD. The increased abundance of UU on day 1 and the decrease of Veillonella dispar on day 28 might increase the risk of BPD.

The human milk bacteriome and mycobiome and their inter-kingdom interactions viewed across geography

BackgroundThe human milk microbiota is one of the biologically active components of human milk, and factors affecting it and the effect size are not well understood. Assessments of human milk microbiota have mainly been done in small cohorts and/or in single geographical locations, and most have been restricted to the bacteriome. Here we assessed the bacterial, archaeal and fungal composition of human milk and the potential inter-kingdom interactions in milk collected from women living in a wide spectrum of countries, environments, and socio-economical settings.Materials and methodsAbout 518 human milk samples were collected in 16 countries. After DNA extraction, bacterial and fungal metataxonomic analyses were performed via amplification and sequencing of the 16S rDNA and the ITS2 genes, respectively. In parallel, the presence of methanogenic archaea was determined by qPCR.ResultsBacterial analysis revealed significant Country variations in human milk microbiota diversity and taxa distribution. Core genera such as Staphylococcus, Streptococcus, and Bifidobacterium were universally prevalent, and their abundance varied geographically. Methanogenic sequences were found in the amplicon sequences, mostly of Methanobrevibacter (11.8% of samples), while qPCR only detected 0.7% (2 out of 268) methanogens. Fungi—mostly Candida—were detected in 7% of samples, with wide country variations. Co-abundance network analysis revealed mostly positive bacterial correlations and negative inter-kingdom interactions.ConclusionThis study shows substantial global variation in the human milk microbiome with bacterial-fungal interactions, highlighting the importance of global-scale studies to understand the human microbiome and its role in maternal and infant health.

Propagule-Specific Bacteriome of Funneliformis mosseae Spores and Hyphae: Integrated High-Throughput and Culture-Dependent Insights.

Arbuscular mycorrhizal (AM) symbiosis is increasingly recognized as a tripartite interaction involving the fungal symbiont, the host plant, and a diverse assemblage of associated bacteria. Through this study, propagule-specific bacteriome of Funneliformis mosseae was explored, particularly its taxonomic composition and plant growth-promoting (PGP) potential. Using a polyphasic approach integrating Illumina high-throughput sequencing with culture-dependent techniques, bacterial communities associated with monosporal hyphae and spores were characterized. Sequencing analyses revealed distinct taxonomic profiles between two propagule types: spores were dominated by Pseudomonas, whereas hyphae harbored higher relative abundances of Sphingobium and Rhodococcus. Culture-dependent screening on NBRIP medium yielded 53 phosphate-solubilizing bacterial isolates-21 from spores and 32 from hyphae. While hyphae-associated propagules contained a greater number of phosphate-solubilizing isolates, those from spores exhibited significantly higher solubilization capacities, ranging from 16.87 to 273 µg mL⁻¹, with 47.6% exceeding 100 µg mL⁻¹. In contrast, hyphae-derived isolates ranged from 35.03 to 142.20 µg mL⁻¹, with 28.1% surpassing the 100-µg mL⁻¹ threshold. Functional screening further revealed that 38% of spore and 31% of hyphae-associated isolates exhibited diverse PGP traits. The five most potent strains were identified through 16S rDNA sequencing as Pseudomonas aeruginosa, Lactiplantibacillus plantarum, Bacillus haynesii, Bacillus licheniformis, and Enterococcus innesii. This study represents the first attempt to characterize a propagule-specific core bacteriome in Funneliformis mosseae, revealing clear taxonomic and functional divergence between spore and hyphae-associated bacterial communities. These findings highlight the specialized ecological roles of distinct propagule microbiomes and offer novel avenues for targeted manipulation of AM symbiosis to enhance plant nutrient acquisition and growth.

First Report of Xanthomonas sacchari Causing Bacterial Panicle Blight of Rice in the United States.

Rice (Oryza sativa) plants showing severe leaf and panicle blight symptoms were observed and collected from four field plots in Louisiana in summer 2023. As the observed symptoms looked like bacterial leaf and panicle blight caused by Pantoea ananatis (Bruno et al. 2025) or bacterial panicle blight caused by Burkholderia glumae and B. gladioli (Nandakumar et al. 2009), we presumptively attempted to isolate one of these bacterial pathogens as the causal agent. Bacteria were isolated from the symptomatic seeds, which were surface sterilized, dehulled and ground in sterile distilled water using a sterile mortar and pestle. The homogenate was spread on the CCNT medium (Kawaradani et al. 2000) and LB agar supplemented with nitrofurantoin (50 µg/ml) and cycloheximide (50 µg/ml). After 72 h incubation at 41⁰C, round, smooth and faint, yellow-colored bacterial colonies appeared on both CCNT and LB agar plates. Unexpectedly, all six bacterial isolates from rice samples were initially identified as Xanthomonas sacchari based on PCR-amplified 16S rDNA sequences using the primers fD1 (5'-CCGAATTCGTCGACAACAGAGTTTGATCCTGGCTCAG-3')/rD1 (3'-CCCGGGATCCAAGCTTAAGGAGGTGATCCAGCC-5') (Weisburg et al. 1991), regardless of their sampling locations. Whole genome sequencing analyses (NCBI Accession ID: PRJNA1223440) performed through a hybrid sequencing approach using Oxford Nanopore sequencer & Illumina NextSeq2000 system (Plasmidsaurus Inc., California, USA) further confirmed that all six strains belong to X. sacchari. To satisfy Koch's postulates, each of the six strains LXP-1780, LXP-1783, LXP-1790, LXP-1791, LXP-1792, and LXP-1793 was confirmed for its pathogenicity to rice through two inoculation methods, using one-month-old plants (cv. Kitaake) at tillering stage; 1) pricking the stems with a sterile toothpick touched to the overnight grown bacterial culture on LB agar (~ 5-8 x 105 bacterial cells per tip) and 2) clipping the leaves with scissors dipped in the bacterial suspension containing ~1 × 108 bacterial cells per mL of sterile distilled water. This virulence assay was conducted twice with three replications for each strain, and rice plants inoculated with sterile distilled water were included as the negative control. By twenty-seven days after inoculation (DAI), the inoculated plants developed symptoms on leaves and panicles, which were similar to the symptoms initially observed in the field. Besides blight symptoms and water-soaked lesions in the leaves, the most noticeable symptom observed was the blackening or darkening of the leaf tips, which appeared as dark spots or streaks. In panicles, panicle blight-like symptoms, such as grain discoloration and darkening of rice hulls, were observed. The bacteria were reisolated from each artificially inoculated plant and their identity were validated to be X. sacchari. To our knowledge, this is the first report of rice disease caused by X. sacchari in the United States. This finding strongly suggests the emergence of this disease as a new potential threat to U.S. rice industry. Furthermore, the strains of X. sacchari and their whole genome sequence information obtained from this study will serve as a foundation for future studies on this newly emerging disease.