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PubMed2026

Phylogenomics of Desulfuromonadia supports reclassification of Geobacter psychrophilus as Irobacter psychrophilus comb. nov. and proposal of Geosyntrophus gen. nov.

Genome-resolved phylogenomics reveals widespread misclassification of metal-reducing bacteria historically assigned to Geobacter based on 16S rRNA gene phylogeny, and highlights species that persist only as 16S rRNA entries without genomes for robust taxonomic resolution. Here, we resolve two such lineages by integrating whole-genome phylogeny with average amino acid identity (AAI) and percentage of conserved proteins (POCP) across 418 dereplicated genomes of Desulfuromonadia. We report a draft genome of the psychrophilic iron-reducing bacterium Geobacter psychrophilus (100% completeness). Phylogenomic analyses place both Geobacter psychrophilus and the GTDB placeholder genus g__JACRCG01 within the family 'Pseudopelobacteraceae', outside Geobacteraceae sensu stricto. Within this framework, G. psychrophilus forms a distinct, well-supported lineage separated from neighbouring genera by discontinuities in AAI and POCP, supporting its reclassification as Irobacter psychrophilus comb. nov. Additionally, we show that Geosyntrophus acetoxidans, a non-axenic syntrophic bacterium, forms a coherent genus with 51 other environmental genomes (placeholder genus g__JACRCG01), for which we propose the replacement name Geosyntrophus gen. nov. Comparative genome analysis revealed conserved family-level metabolic traits together with genus-specific differences in respiratory metabolism, while ANI-based clustering identified substantial species-level diversity within both proposed genera. Metagenome and 16S rRNA-gene survey data further show that Geosyntrophus and Irobacter occur in broadly similar aquatic and subsurface habitats spanning from the Arctic to the Antarctic. Together, these results resolve the taxonomy of two previously ambiguous Desulfuromonadales lineages and shed light on their environmental distribution.

AAI↗

PubMed2026

The longitudinal expression of P. aeruginosa reference genes in infection-mimicking media.

Quantitative reverse transcription PCR (RT-qPCR) is a popular and reliable tool for monitoring fluctuations in functional bacterial gene expression. A necessary step of the qRT-qPCR process is the use of a reference gene, which acts to distinguish between technical bias and true biological variation. Many reference genes have been defined for bacterial species; however, few studies have validated their stability across strain types and environmental test conditions. In this study of Pseudomonas aeruginosa, the expression consistency of seven commonly used reference genes (rpoD, proC, rpoS, 16S, algD, gyrA and ampC) was assessed in P. aeruginosa laboratory (PAO1) and clinical (LESB65) isolates grown in Lysogeny broth, synthetic cystic fibrosis (CF) media 2 (SCFM2) and CF lung media (CFLM) at various growth time points (2, 6, 24 and 72 h). The stability of the reference genes was then ranked using the RefFinder programme, and three differentially ranked (rpoS, 16S and ampC) were used to interpret the expression of a Pseudomonas virulence-related gene (exoS). The results showed that 16S was the only reference gene that was quantifiably expressed by both P. aeruginosa strains grown in all media types at all growth times. Furthermore, analysing the expression of exoS with different reference genes significantly influenced the calculated expression of exoS in SCFM2 and CFLM. This study has identified a suitable reference gene for RT-qPCR with P. aeruginosa grown in complex respiratory-mimicking media. The results presented here also highlight the importance of validating reference gene expression under the chosen experimental conditions and increase our understanding of how pathogen biology can fluctuate across diverse conditions. Such knowledge is paramount for the development of novel therapeutics, including antimicrobials and anti-virulence agents.

Pseudomonas aeruginosa↗

PubMed2025

Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.

Most microbiome studies to date rely on sequencing short amplicons of the 16S rRNA gene on Illumina's platforms. Because of the short read length, sequences often can be identified reliably only to the family or genus levels. Long read sequencing with whole-length 16S rRNA sequencing can improve taxonomic resolution, but often only to the species level. StrainID is an alternative approach that amplifies a large segment of the ribosomal operon, including the entire 16S rRNA gene, internal transcribed spacer, and a portion of the 23S rRNA gene. This longer amplicon is designed to allow ribotype-level classification. Although studies have demonstrated the utility of StrainID for several sample types, it has not yet been validated for saliva. Here, we compared the performance of StrainID to short read amplicons with saliva samples as well as a synthetic mock DNA community and human and mouse fecal samples. Short reads were amplified with primer pairs appropriate for the corresponding sample type, and were classified with two different taxonomic databases. For both saliva and fecal samples, we found that StrainID performed similarly to short reads overall and demonstrated a key benefit with phylogenetic-based beta diversity tests and taxonomic classification. Our results further build on establishing StrainID as a valid method and specifically validate its use with saliva samples.

Journal Article↗

PubMed2026

Routine methods misidentify Serratia spp.: Limitations of MALDI-TOF MS revealed by whole-genome sequencing.

Accurate species-level identification within the genus Serratia remains challenging due to extensive phenotypic overlap and high genomic relatedness among closely related and recently described taxa. This study presents an evaluation of routine and genome-based identification approaches applied to clinical Serratia isolates, integrating phenotypic assays, MALDI-TOF MS (Bruker Daltonics), 16S rRNA gene sequencing, and Whole-Genome Sequencing (WGS). A total of 103 isolates collected from a teaching hospital were analyzed. WGS was performed on a subset of isolates. Conventional biochemical methods classified all isolates as Serratia marcescens, whereas MALDI-TOF MS identified 60.1% as S. marcescens, 11.6% as S. ureilytica, and 28.1% just at the genus level. Peak analysis from MALDI-TOF MS revealed specific peaks associated with S. marcescens and S. ureilytica, but limited discriminatory power. WGS of six isolates initially identified as S. ureilytica by MALDI-TOF MS revealed reclassification as Serratia sarumanii (n = 5) and Serratia montpellierensis (n = 1), supported by Average Nucleotide Identity (ANI), Average Amino Acid Identity (AAI), and Digital DNA-DNA Hybridization (dDDH) thresholds. In contrast, 16S rRNA analysis showed limited species-level resolution. Phylogenomic and SNP-based analyses confirmed these classifications with strong support. Overall, this study underscores the critical role of high-resolution genomic approaches for precise species identification and highlights the need for continuous expansion and curation of MALDI-TOF MS reference databases to support reliable clinical diagnostics and epidemiological surveillance of emerging Serratia species.

Spectrometry, Mass, Matrix-Assisted Laser Desorpti↗

PubMed2026

Ecological and methodological insights from genetic and coprological profiling of gastrointestinal communities in wild howler monkeys.

The gastrointestinal tract hosts a complex community of microorganisms and helminth parasites that collectively contribute to host health and fitness. Analysis of these communities provides insight into diverse aspects of host dietary ecology, immunity, nutrition, and host-parasite interactions. However, research methodologies, such as sample preservation and sequencing approach, can influence how we understand and characterize these features. Here, we profiled the gastrointestinal microbial and helminth communities in different groups of wild Costa Rican mantled howler monkeys (Alouatta palliata palliata). We compared samples stored in ethanol versus directly flash frozen, and contrasted conclusions drawn from 16S versus shotgun sequencing approaches. Bacterial, archaeal, and eukaryotic taxa associated with the digestion of plant material dominated the GI communities. Storage and sequencing methods influenced microbial profiles: ethanol-stored samples exhibited higher diversity than frozen samples, and 16S sequencing detected lower diversity than shotgun. Helminths were detected via coprological microscopy in 71% of individuals, whereas metagenomic detection was inconsistent. This study provides new data on the microorganisms and their putative digestive functions in the gut of a folivorous primate, and highlights the pros and cons of different methodological choices when profiling host-microbiome and host-parasite interactions.

Animals↗

PubMed2025

Comparison of whole-genome sequencing-based analysis methods for taxonomic classification of isolates unclassified by MALDI-TOF MS.

Taxonomic identification of clinical isolates is routinely achieved using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). If the species cannot be reliably identified, whole-genome sequencing can be applied. The aim of this study was to compare the results of approaches for taxonomic assignment for classification of isolates that are difficult to identify. Fifty-seven isolates were included in the study. The isolates were whole-genome sequenced and de novo assembled. Assembly-based classification was performed with the Genome Taxonomy Database Toolkit (GTDB-Tk), BLAST against 16S rRNA gene databases, the Type (Strain) Genome Server (TYGS), and ribosomal MLST (rMLST). Read-based classification was performed with MetaPhlAn4 and Kraken2. Thirty-two isolates were assigned to the same species with all four assembly-based classifiers, while the remaining 25 showed diverging assignments. When evaluating the results for the latter isolates, GTDB-Tk performed better than the other classifiers regarding which assignments were most likely correct. Of the read-based classifiers, MetaPhlAn4 performed better than Kraken2. Our evaluation identified GTDB-Tk to be the strongest tool for taxonomic assignment of isolates that are difficult to identify. Disagreements between classifiers are likely due to database limitations, wrongly assigned taxonomy, or unreliable 16S rRNA gene-based assignments.

Spectrometry, Mass, Matrix-Assisted Laser Desorpti↗

PubMed2026

Albidovulum molybdatiresistens sp. nov., a molybdate-resistant bacterium isolated from river water.

A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, white rod-shaped strain, RF13T, was isolated from water samples of the Qingliang River in Fucheng County, Hebei Province, China, and was grown at 15-42 °C (optimum 35 °C), pH 6.0-8.0 (optimum pH 7), and 0-0.5% (w/v) NaCl (optimum concentration 0%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RF13T belonged to the genus Albidovulum, with closest sequence similarity to Albidovulum salinarum MCCC 1K0602T (97.2%), Frigidibacter oleivorans CGMCC 1.3778T (97.2%), Allgaiera indica MCCC 1A01802T (96.8%), and Pseudothioclava arenosa KCTC 52190T (96.4%). The genome size of strain RF13T was 3.7 Mb, and the DNA G+C content was 64.6%. The DNA-DNA hybridisation value (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) between strain RF13T and the reference strain were less than 20.0%, 78.8%, and 72.8%, respectively. Chemotaxonomic analysis revealed Summed feature 8 (48.4%) (C18:1 ω6c and/or C18:1 ω7c), C18:1 ω7c 11-methyl (22.1%), C18:0 3OH (7.9%), and C10:0 3OH (5.0%) as predominant fatty acids. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminolipids, two unidentified phospholipids, and three unidentified lipids. The predominant isoprenoid quinone was ubiquinone-10 (Q-10), and a small amount of Q-9 was also detected. In addition, strain RF13T exhibited a minimum inhibitory concentration (MIC) of 20 mM for molybdate in R2A broth medium and was capable of reducing molybdate to molybdenum blue. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with 16S rRNA gene sequence analyses and draft genome sequence comparisons, strain RF13T was considered to represent a novel species of the genus Albidovulum, and was therefore named Albidovulum molybdatiresistens sp. nov. The type strain was RF13T (= GDMCC 1.3414T= JCM 35643T).

Phylogeny↗

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

Comparative performance of sponge versus flocked swabs for culture-based and metagenomic detection of microbial contamination in the healthcare environment.

BACKGROUND: Identifying optimal methods for sampling surfaces in the healthcare environment is critical for future research requiring the identification of multidrug-resistant organisms (MDROs) on surfaces. METHODS: We compared 2 swabbing methods, use of a flocked swab versus a sponge-stick, for recovery of MDROs by both culture and recovery of bacterial DNA via quantitative 16S polymerase chain reaction (PCR). This comparison was conducted by assessing swab performance in a longitudinal survey of MDRO contamination in hospital rooms. Additionally, a laboratory-prepared surface was also used to compare the recovery of each swab type with a matching surface area. RESULTS: Sponge-sticks were superior to flocked swabs for culture-based recovery of MDROs, with a sensitivity of 80% compared to 58%. Similarly, sponge-sticks demonstrated greater recovery of Staphylococcus aureus from laboratory-prepared surfaces, although the performance of flocked swabs improved when premoistened. In contrast, recovery of bacterial DNA via quantitative 16S PCR was greater with flocked swabs by an average of 3 log copies per specimen. CONCLUSIONS: The optimal swabbing method of environmental surfaces differs by method of analysis. Sponge-sticks were superior to flocked swabs for culture-based detection of bacteria but inferior for recovery of bacterial DNA.

Humans↗

PubMed2025

The Effect of Colesevelam on the Microbiome in Postoperative Crohn's Disease.

BACKGROUND: While surgery plays a pivotal role in the management of ileal Crohn's disease, the risk of endoscopic recurrence following an ileocaecal resection can be greater than 65% within 12 months of surgery. More than 90% of patients with Crohn's disease have a concomitant diagnosis of bile acid diarrhea following an ileal resection. This pilot study aimed to assess whether the use of bile acid sequestrants in patients with Crohn's disease who have undergone a primary terminal ileal resection with concomitant bile acid diarrhea can alter the microbiome and prevent disease recurrence. METHODS: Patients with Crohn's disease who underwent a primary terminal ileal resection and had symptoms of diarrhea within 1-3 months of surgery underwent 75SeHCAT testing for bile acid diarrhea. If positive (75SeHCAT ≤ 15%), patients were treated with colesevelam and stool samples were collected at 4 weeks, 8 weeks, and 6-12 months posttreatment. If negative (75SeHCAT > 15%), treatment was not given and were reviewed in the clinic as per local guidelines. All patients underwent a 6-12 month postoperative colonoscopy where further stool samples and mucosal biopsies were taken. Disease activity was established using the endoscopic Rutgeert's score, with disease remission defined as Rutgeert's score <i2 and disease recurrence ≥i2. 16S ribosomal RNA gene analysis was undertaken for the collected fecal and mucosal samples to assess α/β-diversity and microbial composition. RESULTS: A total of 14 patients who completed the study, 10 of whom had a 75SeHCAT positive diagnosis of bile acid diarrhea and were started on treatment with colesevelam. Four patients did not require treatment as 3 were asymptomatic and 1 had a negative 75SeHCAT scan. Three of the fourteen patients had disease recurrence at their 6-12 month postoperative colonoscopy assessment, of which 1 patient was taking colesevelam and 2 patients were not taking colesevelam. A total of 44 fecal samples and 44 mucosal biopsies underwent 16S ribosomal RNA gene analysis to assess α/β-diversity and microbial composition. In the colesevelam treated patients there was no significant difference in α/β-diversity pre- and posttreatment. Pretreatment, the 3 most abundant bacterial classes in all patients were Bacteroidia, Clostridia, and Gammaproteobacteria. Following 6-12 months of treatment, out of the 9 patients on colesevelam, 5/9 (55.6%) had a reduction in Bacteroidia, 9/9 (100%) had an increase in Clostridia, and 7/9 (77.8%) had a reduction in Gammaproteobacteria. Of the 2 patients not given colesevelam, one showed a reduction in Bacteroidia, increase in Clostridia and a reduction in Gammaproteobacteria. CONCLUSIONS: This small pilot study demonstrated that patients who were given colesevelam, were more likely to be in disease remission at their 6-12 months colonoscopy review compared with those not treated. Furthermore, treatment with colesevelam may have a role in altering the microbiome to help maintain remission states in postoperative Crohn's disease. Larger mechanistic studies are now needed to confirm these findings and demonstrate statistical significance as well as investigate whether this benefit may be present even in those patients with 75SeHCAT negative disease.

Humans↗

PubMed2026

Description of two nitrogen-fixing bacteria, Azospirillum mesophilum sp. nov. and Azospirillum terrae sp. nov., isolated from paddy soils.

Two novel aerobic, rod-shaped, motile bacterial strains, designated as sgz302134T and sgz301742T, were isolated from paddy soil in Fujian Province. Strains sgz302134T and sgz301742T shared the highest 16S rRNA gene sequence similarities with the type strains Azospirillum isscasi C340-1T (98.2%) and Azospirillum thiophilum DSM 21654T (97.4%), respectively. The phylogenetic tree based on 16S rRNA gene sequences showed that two strains clustered with members of the genus Azospirillum. Growth of strains sgz302134T and sgz301742T was observed at 10-45 °C, pH 5.0-9.5 and 0-0.5% (w/v) NaCl and 15-37 °C, pH 6.0-9.0 and 0-1.0% (w/v) NaCl, respectively. Strains sgz302134T and sgz301742T contained Q-10 as the main quinone. The main fatty acids (>10%) of both strains were summed feature 2 (C12 : 0 aldehyde), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The genomic DNA G+C content of strains sgz302134T and sgz301742T was 68.4 and 68.3%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values between the two strains and their related reference strains were 27.8 and 87.4% and 22.0 and 84.3%, respectively. Both strains possessed nif genes nifBDEHKN. Based on the above results, these two strains represent two novel species of the genus Azospirillum, for which the names Azospirillum mesophilum sp. nov. and Azospirillum terrae sp. nov. are proposed. The type strains are sgz302134T (=MCCC 1K09520T=KCTC 8840T) and sgz301742T (=MCCC 1K09804T=KCTC 18149T), respectively.

Soil Microbiology↗

PubMed2026

Emerging food- and waterborne pathogen Arcobacter in wastewater: diversity and antibiotic resistance.

Arcobacter spp. are emerging food- and waterborne pathogens frequently detected in wastewater. Despite their high abundance in wastewater, Arcobacter diversity, antibiotic resistance, and genomic traits remain poorly characterized. To address these knowledge gaps, we conducted a comprehensive study of Arcobacter spp. in influent, effluent, and activated sludge from a Finnish wastewater treatment plant using full-length 16S rRNA gene sequencing, isolate-based genomics, and phenotypic antibiotic susceptibility testing. Arcobacter spp. were highly abundant in raw sewage but substantially removed during treatment. Four Arcobacter species were identified, dominated by Arcobacter cryaerophilus and Arcobacter suis. A proportion of amplicon sequence variants unclassified to species-level revealed potentially unexplored Arcobacter diversity. For the first time, we observed intragenomic variability in 16S rRNA gene copies of A. cryaerophilus, highlighting the importance of integrating culture-based and culture-independent approaches. Phenotypic testing revealed high proportions of non-wild-type isolates for clinically relevant antibiotics, including ampicillin, cefotaxime, tetracycline, and erythromycin. Genomic analyses showed that antibiotic resistance profiles were primarily mediated by chromosomally encoded determinants, including β-lactamases, efflux systems, and point mutations. Additionally, a broad arsenal of chromosomal and plasmid-borne resistance genes to heavy metals, biocides, and organic solvents was detected, reflecting adaptations to the wastewater environment. These findings provide novel insights into Arcobacter species-level diversity, resistance mechanisms, and ecological adaptations in anthropogenically influenced environments. The study highlights the significance of Arcobacter for public health and establishes a foundation for further research.IMPORTANCEArcobacter spp. are emerging human and animal pathogens that exhibit increasing resistance to clinically relevant antibiotics. Most community-acquired infections are linked to exposure through contaminated food and water, yet studies investigating their occurrence and diversity in wastewater remain scarce. Here, we focus on wastewater as an abundant source of Arcobacter spp. and a potential dissemination route contributing to downstream contamination of surface waters, irrigated soils, and possibly the food chain. By characterizing the species-level diversity, genomic traits, and antibiotic resistance profiles of Arcobacter spp. in wastewater, this study provides critical insights into the ecology and epidemiology of this ubiquitous genus.

Arcobacter↗

PubMed2026

Longitudinal dynamics of respiratory microbiome composition in infants after new tracheostomy placement.

OBJECTIVES: This prospective longitudinal study characterised respiratory microbiome dynamics following new tracheostomy placement among infants. SETTING: A tertiary care paediatric hospital system in the United States. PARTICIPANTS: Fifteen infants ≤12 months of age contributed 84 tracheal aspirate samples collected from day 1 through 3-4 months post-placement. PRIMARY AND SECONDARY OUTCOME MEASURES: Bacterial composition, including abundance, from 16S rRNA gene sequencing; alpha and beta diversity measures over time. RESULTS: 16S rRNA gene sequencing revealed immediate and sustained bacterial community shifts. Staphylococcus abundance increased and alpha diversity decreased in the first 30 days post-tracheostomy (p<0.05) before returning to baseline. Beta diversity demonstrated compositional changes immediately and with ongoing divergence through 3-4 months. Time and clinical factors (prematurity, ventilation and neurologic impairment) were significantly associated with microbiome structure (p=0.001). CONCLUSIONS: This study provides novel evidence that new tracheostomy placement induces rapid and prolonged airway microbiome disruption in infants, highlighting a previously uncharacterised window of vulnerability with implications for respiratory health.

Humans↗

PubMed2024

Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens.

The present study was undertaken to profile and compare the cecal microbial communities in conventionally (CONV) grown and raised without antibiotics (RWA) broiler chickens. Three hundred chickens were collected from five CONV and five RWA chicken farms on days 10, 24, and 35 of age. Microbial genomic DNA was extracted from cecal contents, and the V4-V5 hypervariable regions of the 16S rRNA gene were amplified and sequenced. Analysis of 16S rRNA sequence data indicated significant differences in the cecal microbial diversity and composition between CONV and RWA chickens on days 10, 24, and 35 days of age. On days 10 and 24, CONV chickens had higher richness and diversity of the cecal microbiome relative to RWA chickens. However, on day 35, this pattern reversed such that RWA chickens had higher richness and diversity of the cecal microbiome than the CONV groups. On days 10 and 24, the microbiomes of both CONV and RWA chickens were dominated by members of the phylum Firmicutes. On day 35, while Firmicutes remained dominant in the RWA chickens, the microbiome of CONV chickens exhibited am abundance of Bacteroidetes. The cecal microbiome of CONV chickens was enriched with the genus Faecalibacterium, Pseudoflavonifractor, unclassified Clostridium_IV, Bacteroides, Alistipes, and Butyricimonas, whereas the cecal microbiome of RWA chickens was enriched with genus Anaerofilum, Butyricicoccu, Clostridium_XlVb and unclassified Lachnospiraceae. Overall, the cecal microbiome richness, diversity, and composition were greatly influenced by the management program applied in these farms. These findings provide a foundation for further research on tailoring feed formulation or developing a consortium to modify the gut microbiome composition of RWA chickens.

Animals↗

PubMed2026

First report of tomato spotted wilt virus (Orthotospovirus tomatomaculae) and phytoplasma in China aster and development of duplex PCR, LAMP, and qPCR assays for rapid detection.

UNLABELLED: China aster (Callistephus chinensis) is an economically important ornamental crop widely cultivated for cut flowers and landscaping. During field surveys conducted in three districts of Karnataka, India, China aster plants exhibiting chlorotic and necrotic ring spots, leaf deformation, and witches' broom symptoms were collected and analyzed to determine the causal agents. Mechanical inoculation of symptomatic leaf sap onto cowpea (Vigna unguiculata cv. C-152) produced characteristic chlorotic and necrotic ring spots on newly emerging leaves indicating the presence of an infectious viral agent. Serological assay by DAC-ELISA followed by RT-PCR confirmed the presence of tomato spotted wilt virus (TSWV, Orthotospovirus tomatomaculae) in symptomatic plants. Similarly the plants exhibiting witches' broom symptoms tested positive for phytoplasma infection using universal and Nested primers PCR assays targeting the 16S rRNA gene. Sequence analysis of TSWV CP gene revealed more than 97% nucleotide identity with TSWV isolates reported from India and other countries. Based on these results, one representative isolate was selected for complete genome sequencing. The complete sequences of the L, M, S RNA segements were amplified cloned, and sequenced showing more than 97% nucleotide identity with global TSWV isolates available in database. Sequence analysis of 16S rRNA gene of the phytoplasma associated with witches' broom symptoms was identified as 'Candidatus Phytoplasma australasiaticum' belonging to the 16SrII-D subgroup, sharing 99.2% nucleotide identity with previously reported isolates. Phylogenetic analysis further supported the placement of both the TSWV and phytoplasma isolates within their respective taxonomic groups. To facilitate rapid and sensitive diagnosis, quantitative PCR (qPCR) and RT-LAMP assays were developed for TSWV detection. In addition a duplex PCR assay was optimized for simultaneous detection of TSWV and phytoplasma from infected China aster plants in a single reaction. This study represents the first reports of the complete genome characterization of TSWV and phytoplasma infection in China aster in India along with the development of sensitive qPCR, RT-LAMP, and duplex PCR assays for rapid detection of these pathogens providing valuable tools for disease diagnosis, epidemiological studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13205-026-05038-w.

China aster↗

PubMed2024

Antimicrobial resistance landscape in a metropolitan city context using open drain wastewater-based metagenomic analysis.

One Health concept recognizes the inextricable interactions of diverse ecosystems and their subsequent effect on human, animal and plant health. Antimicrobial resistance (AMR) is a major One Health concern and is predicted to cause catastrophes if appropriate measures are not implemented. To understand the AMR landscape in a south Indian metropolitan city, metagenomic analysis of open drains was performed. The data suggests that in January 2022, macrolide class of antibiotics contributed the highest resistance of 40.1% in the city, followed by aminoglycoside- 24.4%, tetracycline- 11.3% and lincosamide- 6.7%. The 'mutations in the 23S rRNA gene conferring resistance to macrolide antibiotics' were the major contributor of resistance with a prevalence of 39.7%, followed by '16s rRNA with mutation conferring resistance to aminoglycoside antibiotics'- 22.2%, '16S rRNA with mutation conferring resistance to tetracycline derivatives'- 9.2%, and '23S rRNA with mutation conferring resistance to lincosamide antibiotics'- 6.7%. The most prevalent antimicrobial resistance gene (ARG) 'mutations in the 23S rRNA gene conferring resistance to macrolide antibiotics' was present in multiple pathogens including Escherichia coli, Campylobacter jejuni, Acinetobacter baumannii, Streptococcus pneumoniae, Pseudomonas aeruginosa, Neisseria gonorrhoeae, Klebsiella pneumoniae and Helicobacter pylori. Most of the geographical locations in the city showed a similar landscape for AMR. Considering human mobility and anthropogenic activities, such an AMR landscape could be common across other regions too. The data indicates that pathogens are evolving and acquiring antibiotic resistance genes to evade antibiotics of multiple major drug classes in diverse hosts. The outcomes of the study are relevant not only in understanding the resistance landscape at a broader level but are also important for identifying the resistant drug classes, the mechanisms of gaining resistance and for developing new drugs that target specific pathways. This kind of surveillance protocol can be extended to regions in other developing countries to assess and combat the problem of antimicrobial resistance.

Cities↗

PubMed2026

Application of PathoChip to urine-derived nucleic acids for broad microbial profiling in men with suspected prostate cancer: setup of a methodological workflow and pilot feasibility study.

BACKGROUND: Urine-based liquid biopsy is an attractive non-invasive source of prostate cancer (PCa) biomarkers, but urinary microbiome studies have mainly relied on 16S rRNA sequencing or shotgun metagenomics. This pilot study optimized and evaluated a practical workflow using PathoChip - a broad-spectrum microarray designed to detect bacterial, viral, fungal, and parasitic signatures - for microbial profiling of urine sediments from men with suspected PCa, an application not previously established. METHODS: First-morning urine was collected without prostatic massage from 35 men scheduled for biopsy; 19 were diagnosed with PCa and 16 were biopsy-negative. Different urine volumes and extraction strategies were evaluated to optimize DNA/RNA recovery. A setup phase compared 25 ng versus 50 ng of urine DNA and RNA input. DNA/RNA isolated from human B cells was used as reference control. An analysis pipeline was developed to detect outlier probes and create a presence/absence matrix. Reproducibility was assessed via library yield, Pearson correlation, blank-control subtraction, outlier probe detection. Prevalence comparisons were performed between clinical groups. RESULTS: An 8 mL starting volume was chosen as consistently available from self-collected urine. Sequential DNA/RNA extraction using the AllPrep DNA/RNA Micro Kit from sediment provided the best balance between nucleic-acid recovery, purity, and clinical compatibility. Reducing the input from 50 ng to 25 ng preserved highly concordant hybridization profiles, with matched samples clustering together with strong correlations. Exploratory analysis revealed PCa- and grade-associated patterns involving Actinomycetaceae, Aerococcaceae, and Streptococcaceae, with Streptococcaceae enriched in PCa of higher grades (ISUP GG ≥ 2). Other signatures, including Mobiluncus, Prevotella, Rhodotorula, Hymenolepis, and JC polyomavirus, were broadly detected but not PCa-discriminating. CONCLUSIONS: PathoChip can be adapted to urine sediments, generating reproducible microbial profiles from limited DNA/RNA input without prostatic massage. This platform provides a quick and accessible approach to broad screening, extending beyond 16S rRNA sequencing by enabling simultaneous multi-kingdom detection. The observed PCa- and grade-associated patterns are hypothesis-generating and require validation in larger independent cohorts.

Pathochip↗

PubMed2026

The mechanism by which long-term exposure to TDCIPP promotes cognitive impairment in 3 ×Tg-AD mice: Insights from multi-omics studies.

Tri(1,3-dichloro-2-propyl) phosphate (TDCIPP) is a commonly used organophosphate ester that has the potential to adversely affect human health. Although previous studies have closely associated TDCIPP with cognitive impairment, the underlying mechanisms remain unclear. To elucidate the neurotoxic effects of TDCIPP and its mechanistic contribution to cognitive impairment in 3 ×Tg-AD mice, a multi-omics approach incorporating proteomics, untargeted metabolomics, and 16S ribosomal RNA (rRNA) gene sequencing was employed to evaluate the impact of TDCIPP exposure on neurobehavioral function. TDCIPP exposure promoted cognitive impairment in 3 ×Tg-AD mice. Proteomic analyses revealed that this promotion is associated with disturbances in the hippocampal mitochondrial autophagy pathway. Furthermore, TDCIPP may interfere with the PINK1/Parkin-mediated mitophagy pathway at the functional level, without altering PINK1 protein abundance. Untargeted metabolomic analysis of urine samples demonstrated that TDCIPP exposure altered the metabolic profile of 3 ×Tg-AD mice, with 58 metabolites upregulated and 11 downregulated. Additionally, 16S rRNA sequencing revealed substantial modifications in gut microbiome composition following exposure to TDCIPP. Notably, significant correlations were identified between the perturbed bacterial genera and the differential metabolites. In conclusion, exposure to TDCIPP promotes cognitive impairment in 3 ×Tg-AD mice, which is associated with the interference with the PINK1/Parkin-mediated mitophagy pathway, as well as alterations in the urinary metabolome and gut microbiota. These findings suggest the potential to mitigate such cognitive impairment by targeting the microbiota-gut-brain axis.

Animals↗