16S Ribosomal RNA Gene Research Articles

Probiotics and Antibiotic-Induced Microbial Aberrations in Children

Probiotics are often considered in children to prevent antibiotic-associated diarrhea. However, the underlying mechanistic effects and impact of probiotics on antibiotic-induced microbiota changes are not well understood. To investigate the effects of a multispecies probiotic on the gut microbiota composition in children receiving antibiotics. This is a secondary analysis of a randomized, quadruple-blind, placebo-controlled clinical trial from February 1, 2018, to May 31, 2021, including 350 children receiving broad-spectrum antibiotics in the inpatient and outpatient settings. Patients were followed up until 1 month after the intervention period. Fecal samples and data were analyzed between September 1, 2022, and February 28, 2023. Eligibility criteria included 3 months to 18 years of age and recruitment within 24 hours following initiation of broad-spectrum systemic antibiotics. In total, 646 eligible patients were approached and 350 participated in the trial. Participants were randomly assigned to receive daily placebo or a multispecies probiotic formulation consisting of 8 strains from 5 different genera during antibiotic treatment and for 7 days afterward. Fecal stool samples were collected at 4 predefined times: (1) inclusion, (2) last day of antibiotic use, (3) last day of the study intervention, and (4) 1 month after intervention. Microbiota analysis was performed by 16S ribosomal RNA gene sequencing. A total of 350 children were randomized and collected stool samples from 88 were eligible for the microbiota analysis (54 boys and 34 girls; mean [SD] age, 47.09 [55.64] months). Alpha diversity did not significantly differ between groups at the first 3 times. Shannon diversity (mean [SD], 3.56 [0.75] vs 3.09 [1.00]; P = .02) and inverse Simpson diversity (mean [SD], 3.75 [95% CI, 1.66-5.82] vs -1.31 [95% CI, -3.17 to 0.53]; P = 1 × 10-4) indices were higher in the placebo group compared with the probiotic group 1 month after intervention. Beta diversity was not significantly different at any of the times. Three of 5 supplemented genera had higher relative abundance during probiotic supplementation, but this difference had disappeared after 1 month. The studied probiotic mixture had minor and transient effects on the microbiota composition during and after antibiotic treatment. Further research is needed to understand their working mechanisms in manipulating the microbiome and preventing antibiotic-associated dysbiosis and adverse effects such as antibiotic-associated diarrhea. ClinicalTrials.gov Identifier: NCT03334604.

Unravelling the genomic and environmental diversity of the ubiquitous Solirubrobacter.

Solirubrobacter, though widespread in soils and rhizospheres, has been relatively unexplored despite its ubiquity. Previously acknowledged as a common soil bacterium, our research explores its phylogenomics, pangenomics, environmental diversity, and interactions within bacterial communities. By analysing seven genomic sequences, we have identified a pangenome consisting of 19,645 protein families, of which 2644 are shared across all studied genomes, forming the core genome. Interestingly, despite the non-motility of reported isolates, we discovered genes for flagellin and a partial flagellum assembly pathway. Examining the 16S ribosomal RNA genes of Solirubrobacter revealed substantial diversity, with 3166 operational taxonomic units identified in Mexican soils. Co-occurrence network analysis further demonstrated its significant integration within bacterial communities. Through phylogenomic scrutiny, we conclusively excluded the NCBI's GCA_009993245.1 genome from being classified as a Solirubrobacter. Our research into the metagenomic diversity of Solirubrobacter across various environments confirmed its presence in rhizospheres and certain soils, underscoring its adaptability. The geographical ubiquity of Solirubrobacter in rhizospheres raises intriguing questions regarding its potential interactions with plant hosts and the biotic and abiotic factors influencing its presence in soil. Given its ecological significance and genetic diversity, Solirubrobacter warrants further investigation as a potentially crucial yet underappreciated keystone species.

A prospective evaluation of the prostate microbiome in malignant and benign tissue using transperineal biopsy.

The link between the prostate microbiome and prostate cancer remains unclear. Few studies have analyzed the microbiota of prostate tissue, and these have been limited by potential contamination by transrectal biopsy. Transperineal prostate biopsy offers an alternative and avoids fecal cross-contamination. We aim to characterize the prostate microbiome using transperineal biopsy. Patients with clinical suspicion for prostate cancer who were to undergo transperineal prostate biopsy with magnetic resonance imaging(MRI) fusion guidance were prospectively enrolled from 2022 to 2023. Patients were excluded if they had Prostate Imaging Reporting and Data System lesions with scores ≤ 3, a history of prostate biopsy within 1 year, a history of prostate cancer, or antibiotic use within 30 days of biopsy. Tissue was collected from the MRI target lesions and nonneoplastic transitional zone. Bacteria were identified using 16S ribosomal RNA gene sequencing. Across the 42 patients, 76% were found to have prostate cancer. Beta diversity indices differed significantly between the perineum, voided urine, and prostate tissue. There were no beta diversity differences between cancerous or benign tissue, or between pre- and postbiopsy urines. There appear to be unique genera more abundant in cancerous versus benign tissue. There were no differences in alpha diversity indices relative to clinical findings including cancer status, grade, and risk group. We demonstrate a rigorous method to better characterize the prostate microbiome using transperineal biopsy and to limit contamination. These findings provide a framework for future large-scale studies of the microbiome of prostate cancer.

Gastric microbiome composition in obese patients and normal weight subjects with functional dyspepsia.

Despite the numerous studies demonstrating gut microbiota dysbiosis in obese subjects, there is no data on the association between obesity and gastric microbiota. The aim of this study was to address this gap in literature by comparing the composition of gastric microbiota in obese patients and a control group which included normal weight volunteers diagnosed with functional dyspepsia (FD). A total of 19 obese patients, and 18 normal weight subjects with FD and normal endoscopy results were included in the study. The gastric tissue samples were collected from participants in both groups by bariatric surgery and endoscopy, respectively, and profiled using 16S ribosomal RNA gene sequencing. There was no significant difference in the α-diversity scores, while distinct gastric microbial compositions were detected in both groups. Significantly lower levels of Bacteroidetes and Fusobacteria, and higher Firmicutes/Bacteroidetes ratio were recorded in the obese patients. A total of 15 bacterial genera exhibited significant difference in gastric abundance with Prevotella_7, Veillonella, Cupriavidus, and Acinetobacter, present in frequencies higher than 3% in at least one subject group. Our study suggests a significant association between obesity and gastric microbiome composition. Future studies with larger sample size and gastric samples from subjects without any gastrointestinal complications are required to confirm our conclusions.

Short-read full-length 16S rRNA amplicon sequencing for characterisation of the respiratory bacteriome of captive and free-ranging African elephants (Loxodonta africana)

Hypervariable region sequencing of the 16S ribosomal RNA (rRNA) gene plays a critical role in microbial ecology by offering insights into bacterial communities within specific niches. While providing valuable genus-level information, its reliance on data from targeted genetic regions limits its overall utility. Recent advances in sequencing technologies have enabled characterisation of the full-length 16S rRNA gene, enhancing species-level classification. Although current short-read platforms are cost-effective and precise, they lack full-length 16S rRNA amplicon sequencing capability. This study aimed to evaluate the feasibility of a modified 150 bp paired-end full-length 16S rRNA amplicon short-read sequencing technique on the Illumina iSeq 100 and 16S rRNA amplicon assembly workflow by utilising a standard mock microbial community and subsequently performing exploratory characterisation of captive (zoo) and free-ranging African elephant (Loxodonta africana) respiratory microbiota. Our findings demonstrate that, despite generating assembled amplicons averaging 869 bp in length, this sequencing technique provides taxonomic assignments consistent with the theoretical composition of the mock community and respiratory microbiota of other mammals. Tentative bacterial signatures, potentially representing distinct respiratory tract compartments (trunk and lower respiratory tract) were visually identified, necessitating further investigation to gain deeper insights into their implication for elephant physiology and health.

Real-time PCR-based quantitative microbiome profiling elucidates the microbial dynamic succession in backslopping fermentation of Taiwanese pickled cabbage.

Microbiota succession determines the flavor and quality of fermented foods. Quantitative PCR-based quantitative microbiome profiling (QMP) has been applied broadly for microbial analysis from absolute abundance perspectives, transforming microbiota ratios into counts by normalizing 16S ribosomal RNA (16S rRNA) gene sequencing data with gene copies quantified by quantitative PCR. However, the application of QMP in fermented foods is still limited. QMP elucidated microbial succession of Taiwanese pickled cabbage. In the spontaneous first-round fermentation (FR), the 16S rRNA gene copies of total bacteria increased from 6.1 to 10 log copies mL-1. The dominant lactic acid bacteria genera were successively Lactococcus, Leuconostoc and Lactiplantibacillus. Despite the decrease in the proportion of Lactococcus during the succession, the absolute abundance of Lactococcus still increased. In the backslopping second-round fermentation (SR), the total bacteria 16S rRNA gene copies increased from 7.6 to 9.9 log copies mL-1. The addition of backslopping starter and vinegar rapidly led to a homogenous microbial community dominated by Lactiplantibacillus. The proportion of Lactiplantibacillus remained consistently around 90% during SR, whereas its absolute abundance exhibited a continuous increase. In SR without vinegar, Leuconostoc consistently dominated the fermentation. The present study highlights that compositional analysis would misinterpret microbial dynamics, whereas QMP reflected the real succession profiles and unveiled the essential role of vinegar in promoting Lactiplantibacillus dominance in backslopping fermentation of Taiwanese pickled cabbage. Quantitative microbiome profiling (QMP) was found to be a more promising approach for the detailed observation of microbiome succession in food fermentation compared to compositional analysis. © 2024 Society of Chemical Industry.

The Prevalence of Cryptosporidium spp. and Giardia duodenalis in Marmota himalayana (Rodentia: Sciuridae) in the Qinghai Tibetan Plateau area, China.

Cryptosporidium and Giardia are well-known important intestinal zoonotic pathogens that can infect various hosts and cause diarrhoeal diseases. We aimed to determine the epidemiological prevalence and molecular characterization of Cryptosporidium and Giardia species in Himalayan marmot (Marmota himalayana, class Marmota) in the Qinghai Tibetan Plateau Area of Qinghai Province, Northwest China. Overall, 243 Himalayan marmot fecal samples were collected in 2017 and in 2019 and a two-step nested PCR technique was performed to amplify the fragments of the SSU rRNA gene of Cryptosporidium and 18S ribosomal RNA gene of Giardia. Molecular characterization of Cryptosporidium was performed with the primary primers NDIAGF2 and N-DIAGR2, the secondary primers CPB-DIAGF and CPB-DIAGR. Similarly, molecular characterization of Giardia was used the first primers Gia2029 and Gia2150c, the secondary primers RH11 and RH4. The positive PCR products were sequenced and the sequences were processed by Clustal Omega and BLAST. Phylogenetic analysis was achieved by NJ method in MEGA. The infection rate of Cryptosporidium spp. and G. duodenalis was 4.9% (12/243) and 0.8% (2/243) in M. himalayana, respectively. Cryptosporidium spp. are characterized as novel genotypes Cryptosporidium marmot genotype I (n=3) and Cryptosporidium marmot genotype II (n=9); G. duodenalis assemblage A (n=2) was found in M. himalayana. This is the first report of Cryptosporidium spp. and G. duodenalis infections in M. himalayana in Qinghai of Northwest China. The results indicate the existence of Cryptosporidium species and G. duodenalis infections that may have a potential public health significance.

Identification of phytoplasmas associated with Bunchy Top disease of papaya in Colima, Mexico

Phytoplasmas, rickettsiae and viruses have been detected in papaya plants with Bunchy Top disease (BT). In 2019, papaya plants with BT-like symptoms were observed in agroecosystems of Colima, Mexico. In order to determine the BT-associated phytoplasmas species or subgroups, asymptomatic and symptomatic plants were collected from papaya agroecosystems in four papaya producer municipalities, as well as papaya-associated weeds and insects. Phytoplasma detection and identification was conducted by PCR, sequencing and phylogenetics of translocase subunit SecA (secA) and 16S ribosomal RNA (16Sr) genes, and PCR-RFLPs in vitro and in silico for 16Sr gene. In papaya, phytoplasma groups 16SrI (subgroup AF), 16SrX, and 16SrXIII were identified in 2.08% (4 out of 192) symptomatic samples. The results of RFLPs in silico analysis showing the presence of 16SrX and 16SrXIII (sub)groups. In papaya-associated weeds and insects, phytoplasmas of group 16SrI (subgroups AF and B) were identified in 1.7% (3 out of 174) and 1.1% (2 out of 185) evaluated samples, respectively. Phytoplasma-carrying weeds were Amaranthus palmeri and Echinochloa colona; positive insects were Micrutalis calva and Balclutha mexicana. It is the first time that phytoplasmas 16SrI-AF, 16SrX y 16SrXIII are associated with Bunchy Top disease of papaya in agroecosystems from Colima, Mexico. Phytoplasmas 16SrX y 16SrXIII are first reported in papaya plants at the world level and in Mexico, respectively. Phytoplasma-carrying weeds and insects are new records as natural reservoirs and potential vectors.

Molecular tracing of Biomphalaria straminea in China

To investigate the origin of Biomphalaria straminea in China, so as to provide insights into assessment of schistosomiasis mansoni transmission risk and B. straminea control. Guanlan River, Dasha River, Shenzhen Reservoir, upper and lower reaches of Kuiyong River, and Xinzhen River in Shenzhen, China, were selected as sampling sites. Ten Biomphalaria samples were collected from each site, and genomic DNA was extracted from Biomphalaria samples. DNA samples were obtained from 15 B. straminea sampled from 5 sampling sites in Minas Gerais State, Pará State, Federal District, Pernambuco State, and Sao Paulo State in Brazil, South America. Cytochrome c oxidase I (COI) and mitochondrial 16S ribosomal RNA (16S rRNA) genes were sampled using the above DNA templates, and the amplified products were sequenced. The COI and 16S rRNA gene sequences were downloaded from GenBank, and the sampling sites were acquired. All COI and 16S rRNA gene sequences were aligned and evolutionary trees of B. straminea were created based on COI and 16S rRNA gene sequences to identify the genetic similarity and evolutionary relationship between B. straminea samples from China and South America. A total of 60 COI gene sequences with a length of 529 bp and 3 haplotypes were obtained from B. straminea sampled from China. There were 165 COI gene sequences of B. straminea retrieved from GenBank, and following alignment with the above 60 gene sequences, a total of 33 haplotypes were obtained. Phylogenetic analysis showed that the three haplotypes of B. straminea from China were clustered into one clade, among which the haplotype China11 and three B. straminea samples from Brazil retrieved from GenBank belonged to the same haplotype. Geographical evolution analysis showed that the B. straminea samples from three sampling sites along eastern coasts of Brazil had the same haplotype with China11, and B. straminea samples from other two sampling sites were closely, genetically related to China11. A total of 60 16S rDNA gene sequences with approximately 322 bp in length were amplified from B. straminea in China, with 2 haplotypes identified. A total of 70 16S rDNA gene sequences of B. straminea were captured from GenBank. Phylogenetic analysis showed that Biomphalaria snails collected from China were clustered into a clade, and the haplotype China64 and the haplotype 229BS from Brazil shared the same haplotype. The 49 16S rDNA gene sequences of B. straminea from 25 sampling sites in southern Brazil, which were captured from GenBank, were included in the present analysis, and the B. straminea from 3 sampling sites shared the same haplotype with China64 in China. Geographical evolution analysis based on COI and 16S rRNA gene sequences showed that B. straminea sampled from eastern coastal areas of Brazil shared the same haplotypes in two gene fragment sequences with Biomphalaria snails collected from China. The Biomphalaria snails in China are characterized as B. straminea, which have a low genetic diversity. The Biomphalaria snails in China have a high genetic similarity with B. straminea sampled from eastern coastal areas of Brazil, which may have originated from the eastern coastal areas of Brazil.

Bacterial Spermosphere Inoculants Alter N. benthamiana-Plant Physiology and Host Bacterial Microbiome.

In this study, we investigated the interplay between the spermosphere inoculum, host plant physiology, and endophytic compartment (EC) microbial community. Using 16S ribosomal RNA gene sequencing of root, stem, and leaf endophytic compartment communities, we established a baseline microbiome for Nicotiana sp. Phenotypic differences were observed due to the addition of some bacterial inoculants, correlated with endogenous auxin loads using transgenic plants expressing the auxin reporter pB-GFP::P87. When applied as spermosphere inoculants, select bacteria were found to create reproducible variation within the root EC microbiome and, more systematically, the host plant physiology. Our findings support the assertion that the spermosphere of plants is a zone that can influence the EC microbiome when applied in a greenhouse setting.

Key aspects of papillomavirus infection influence the host cervicovaginal microbiome in a preclinical murine papillomavirus (MmuPV1) infection model.

Human papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States and are a major etiological agent of cancers in the anogenital tract and oral cavity. Growing evidence suggests changes in the host microbiome are associated with the natural history and ultimate outcome of HPV infection. We sought to define changes in the host cervicovaginal microbiome during papillomavirus infection, persistence, and pathogenesis using the murine papillomavirus (MmuPV1) cervicovaginal infection model. Cervicovaginal lavages were performed over a time course of MmuPV1 infection in immunocompetent female FVB/N mice and extracted DNA was analyzed by qPCR to track MmuPV1 viral copy number. 16S ribosomal RNA (rRNA) gene sequencing was used to determine the composition and diversity of microbial communities throughout this time course. We also sought to determine whether specific microbial communities exist across the spectrum of MmuPV1-induced neoplastic disease. We, therefore, performed laser-capture microdissection to isolate regions of disease representing all stages of neoplastic disease progression (normal, low- and high-grade dysplasia, and cancer) from female reproductive tract tissue sections from MmuPV1-infected mice and performed 16S rRNA sequencing. Consistent with other studies, we found that the natural murine cervicovaginal microbiome is highly variable across different experiments. Despite these differences in initial microbiome composition between experiments, we observed that MmuPV1 persistence, viral load, and severity of disease influenced the composition of the cervicovaginal microbiome. These studies demonstrate that papillomavirus infection can alter the cervicovaginal microbiome.IMPORTANCEHuman papillomaviruses (HPVs) are the most common sexually transmitted infection in the United States. A subset of HPVs that infect the anogenital tract (cervix, vagina, anus) and oral cavity cause at least 5% of cancers worldwide. Recent evidence indicates that the community of microbial organisms present in the human cervix and vagina, known as the cervicovaginal microbiome, plays a role in HPV-induced cervical cancer. However, the mechanisms underlying this interplay are not well-defined. In this study, we infected the female reproductive tract of mice with a murine papillomavirus (MmuPV1) and found that key aspects of papillomavirus infection and disease influence the host cervicovaginal microbiome. This is the first study to define changes in the host microbiome associated with MmuPV1 infection in a preclinical animal model of HPV-induced cervical cancer. These results pave the way for using MmuPV1 infection models to further investigate the interactions between papillomaviruses and the host microbiome.

Association between gut microbiota and CpG island methylator phenotype in colorectal cancer

ABSTRACT The intestinal microbiota is an important environmental factor implicated in CRC development. Intriguingly, modulation of DNA methylation by gut microbiota has been reported in preclinical models, although the relationship between tumor-infiltrating bacteria and CIMP status is currently unexplored. In this study, we investigated tumor-associated bacteria in 203 CRC tumor cases and validated the findings using The Cancer Genome Atlas datasets. We assessed the abundance of Bacteroides fragilis, Escherichia coli, Fusobacterium nucleatum, and Klebsiella pneumoniae through qPCR analysis and observed enrichment of all four bacterial species in CRC samples. Notably, except for E. coli, all exhibited significant enrichment in cases of CIMP. This enrichment was primarily driven by a subset of cases distinguished by high levels of these bacteria, which we labeled as “Superhigh”. The bacterial Superhigh status showed a significant association with CIMP (odds ratio 3.1, p-value = 0.013) and with MLH1 methylation (odds ratio 4.2, p-value = 0.0025). In TCGA CRC cases (393 tumor and 45 adj. normal), bacterial taxa information was extracted from non-human whole exome sequencing reads, and the bacterial Superhigh status was similarly associated with CIMP (odds ratio 2.9, p < 0.001) and MLH1 methylation (odds ratio 3.5, p < 0.001). Finally, 16S ribosomal RNA gene sequencing revealed high enrichment of Bergeyella spp. C. concisus, and F. canifelinum in CIMP-Positive tumor cases. Our findings highlight that specific bacterial taxa may influence DNA methylation, particularly in CpG islands, and contribute to the development and progression of CIMP in colorectal cancer.

Disseminated septic arthritis caused by Ureaplasma urealyticum in an immunocompromised patient with hypogammaglobulinemia after rituximab therapy

Abstract Purpose Ureaplasma urealyticum is a rare pathogen associated with septic arthritis that predominantly affects patients with hypogammaglobulinemia. Bacterial identification of fastidious organisms is challenging because they are undetectable by routine culture testing. To the best of our knowledge, this is the first report of septic arthritis induced by U. urealyticum infection in Japan. Case description We describe the case of a 23-year-old Japanese female with secondary hypogammaglobulinemia (serum immunoglobulin level &lt; 500 mg/dL), identified 8 years after treatment with rituximab. The patient presented with persistent fever and polyarthritis that were unresponsive to ceftriaxone and prednisolone. Contrast-enhanced computed tomography and gallium-67 scintigraphy revealed effusion and inflammation in the left sternoclavicular, hip, wrist, knee, and ankle joints. Although Gram staining and bacterial culture of the drainage fluid from the left hip joint were negative, the condition exhibited characteristics of purulent bacterial infection. The patient underwent empirical treatment with doxycycline, and her symptoms promptly resolved. Subsequent 16S ribosomal RNA (rRNA) gene sequencing of the joint fluid confirmed the presence of U. urealyticum, leading to the diagnosis of septic arthritis. Combination therapy with doxycycline and azithromycin yielded a favorable recovery from the inflammatory status and severe arthritic pain. Conclusion This case highlights U. urealyticum as a potential causative agent of disseminated septic arthritis, particularly in patients with hypogammaglobulinaemia. The 16S rRNA gene analysis proved beneficial for identifying pathogens in culture-negative specimens, such as synovial fluid, in suspected bacterial infections.

Sex-dependent effects of carbohydrate source and quantity on caspase-1 activity in the mouse central nervous system

BackgroundMounting evidence links glucose intolerance and diabetes as aspects of metabolic dysregulation that are associated with an increased risk of developing dementia. Inflammation and inflammasome activation have emerged as a potential link between these disparate pathologies. As diet is a key factor in both the development of metabolic disorders and inflammation, we hypothesize that long term changes in dietary factors can influence nervous system function by regulating inflammasome activity and that this phenotype would be sex-dependent, as sex hormones are known to regulate metabolism and immune processes.Methods5-week-old male and female transgenic mice expressing a caspase-1 bioluminescent reporter underwent cranial window surgeries and were fed control (65% complex carbohydrates, 15% fat), high glycemic index (65% carbohydrates from sucrose, 15% fat), or ketogenic (1% complex carbohydrates, 79% fat) diet from 6 to 26 weeks of age. Glucose regulation was assessed with a glucose tolerance test following a 4-h morning fast. Bioluminescence in the brain was quantified using IVIS in vivo imaging. Blood cytokine levels were measured using cytokine bead array. 16S ribosomal RNA gene amplicon sequencing of mouse feces was performed to assess alterations in the gut microbiome. Behavior associated with these dietary changes was also evaluated.ResultsThe ketogenic diet caused weight gain and glucose intolerance in both male and female mice. In male mice, the high glycemic diet led to increased caspase-1 biosensor activation over the course of the study, while in females the ketogenic diet drove an increase in biosensor activation compared to their respective controls. These changes correlated with an increase in inflammatory cytokines present in the serum of test mice and the emergence of anxiety-like behavior. The microbiome composition differed significantly between diets; however no significant link between diet, glucose tolerance, or caspase-1 signal was established.ConclusionsOur findings suggest that diet composition, specifically the source and quantity of carbohydrates, has sex-specific effects on inflammasome activation in the central nervous system and behavior. This phenotype manifested as increased anxiety in male mice, and future studies are needed to determine if this phenotype is linked to alterations in microbiome composition.

A Survey of Zoonotic Bacteria in the Spleen of Six Species of Rodents in Panama

Emerging zoonotic diseases are one of the main threats to human and animal health. Among the agents with the potential for zoonoses, those of bacterial origin have great relevance in Public Health. Rodents are considered one of the main reservoirs of pathogens that represent a risk to human health or animal species. We used massive 16S ribosomal RNA gene amplicon sequencing to survey bacteria present in the spleen of six species of rodents in Panama in order to identify bacterial taxa with zoonotic potential in the country. We found 3352 bacterial Amplicon Sequence Variants (ASVs, i.e., phylogenetic species) in the spleen of six rodent species surveyed (Liomys adspersus, Melanomys caliginosus, Mus musculus, Proechimys semispinosus, Rattus rattus, Zygodontomys brevicauda). This bacterial community was represented by 25 phyla, 55 classes, 140 orders, 268 families, and 508 genera. The three predominant phyla were Actinobacteria, Firmicutes, and Proteobacteria, and the five predominant classes were Actinobacteria, Alpha- and Gammaproteobacteria, Bacilli, and Clostridia. There were seven high-abundance genera: Acinetobacter, Bartonella, Cutibacterium, Enterococcus, Sarcina, Staphylococcus, and Wolbachia. Genera found with less abundance included Bradyrhizobium, Chryseobacterium, Clostridium, Corynebacterium, Lactobacillus, Pseudonocardia, Rhodococcus, and Sphingomonas. Some of these genera (high or low abundance) have clinical importance. The identification of bacterial taxa with zoonotic potential in rodent species performed here allows us to have surveillance mechanisms for these pathogens and to be able to recognize localities to be prioritized for prevention of transmission and outbreaks, thus being of value for public health in Panama.

First Report of White Mucus Disease Caused by Fuligo gyrosa on Agrocybe chaxingu in China.

Agrocybe chaxingu is an edible and medicinal mushroom widely cultivated in China (Liu et al. 2021). Agrocybe chaxingu is extremely well-liked for the unique flavor and nutritional value. In May 2021, a serious white mucus disease was observed in the farms of A. chaxingu in the Ganxian district of Ganzhou City, Jiangxi Province, China, with an approximate disease incidence of 20%. In the years of 2022 and 2023, the same white mucus disease on A. chaxingu was observed in the farms in Nanchang City, Jiujiang City and Guangchang County, Jiangxi Province, China. The disease generally occurs on the media, stipe or pileus of A. chaxingu under condition of high humidity. The plasmodial slime molds migrated from the surface of culture media (78% hardwood sawdust, 15% wheat bran, 5% tea seed shell, 1% lime, and 1% gypsum) to the base of fruiting bodies, stipes and finally to pilei, showing as moist, sticky, and white reticulated structures. The infected fruiting bodies of A. chaxingu were completely covered by reticulated plasmodia, displaying a white or pale-yellow color. This resulted in the growth cessation, wilting and eventual death of fruiting body. Microscopic observation found that the plasmodia of slime mold enveloped the hyphae of A. chaxingu, resulting in the fragmentation of the hyphae. The disease can spread quickly, resulting in a 30% reduction in production. Slime mold cultures were isolated by transferring diseased fruiting bodies of A. chaxingu onto oat-agar medium (2% agar and 1% oatmeal) at 25 ℃. The isolates can be obtained after being subcultured for two to three generations. Purified plasmodia were placed on the semi-defined medium (1% tryptone, 1% glucose, 0.15% yeast extract, chick embryo extract and a balanced salt solution) to confirm the absence of bacteria (Daniel et al. 1964) and thus obtained the pure culture. Specimen of the voucher has been deposited in the Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences as number IAAM-W0002. The vegetative plasmodia have a large and well-developed scalloped structure that were white or milky white in colour. The white plasmodium became opaque pale yellow when exposed to light before fruiting. The veins merged and thickened. Fruiting bodies can be formed on the lid or side of the Petri dish under light condition. The fruiting bodies formed papillae with irregular shape, and then the color changed from translucent yellow to greyish black. Spores were usually spherical or subglobose, free, greyish brown in mass, purplish brown, 7-12 μm in diameter under light microscopy. These morphological characteristics were found to be consistent with those of Fuligo gyrosa (Synonym: Physarum gyrosum) (Kim et al. 2009; Shi et al. 2005; Jahn 1902). The identity of the isolates was further confirmed by sequence analysis of the 18S ribosomal RNA gene with primer SMNUR101/NS4 (Rusk et al. 1995; White et al. 1990). Using BLASTn searches, the sequence of 18S rRNA gene (GenBank accession number OR186216) matched the sequence of F. gyrosa (GenBank accession number LC744593) with the identity of 99.91% and coverage of 97%. A phylogenetic tree based on the 18S rRNA gene also demonstrated that the slime mold clustered with F. gyrosa. Over ten isolates have been obtained from the diseased A. chaxingu samples in different factories and identified as F. gyrosa. To test the pathogenicity of F. gyrosa, five healthy young fruiting bodies (three to five days of primordium) of A. chaxingu cultivated in mushroom-growing room were gently inoculated by a 12 mm diameter oat-agar medium with plasmodia at 24 ± 2 ℃ and then were kept with relative humidity of 90%-95%. Five fruiting bodies inoculated with a 12 mm oat-agar medium served as controls. After 5 days, white mucus characteristics and three fifths of death symptoms were observed on the fruiting bodies inoculated with the plasmodia, while the controls remained asymptomatic. The slime mold on the inoculated fruiting bodies was morphologically identical to F. gyrosa that was observed on the initial diseased fruiting bodies. It was also observed the envelopment A. chaxingu hyphae by the plasmodia of slime mold and fragmentation of the hyphae, and the fragmentation was not observed in the controls. Reisolations were prepared from the inoculated fruiting bodies and confirmed to be F. gyrosa based on morphological characteristics and 18S rRNA sequence, thus fulfilling Koch's postulates. Fuligo gyrosa has been reported to cause severe disease in oriental melon in Korea (Kim et al. 2009). This is the first report of F. gyrosa causing white mucus disease in cultivated A. chaxingu. The findings will provide important information on prevention and control of the disease, and be helpful for the development of A. chaxingu industry.

Bacterial community and cyanotoxin gene distribution of the Winam Gulf, Lake Victoria, Kenya.

The Winam Gulf (Kenya) is frequently impaired by cyanobacterial harmful algal blooms (cHABs) due to inadequate wastewater treatment and excess agricultural nutrient input. While phytoplankton in Lake Victoria have been characterized using morphological criteria, our aim is to identify potential toxin-producing cyanobacteria using molecular approaches. The Gulf was sampled over two successive summer seasons, and 16S and 18S ribosomal RNA gene sequencing was performed. Additionally, key genes involved in production of cyanotoxins were examined by quantitative PCR. Bacterial communities were spatially variable, forming distinct clusters in line with regions of the Gulf. Taxa associated with diazotrophy were dominant near Homa Bay. On the eastern side, samples exhibited elevated cyrA abundances, indicating genetic capability of cylindrospermopsin synthesis. Indeed, near the Nyando River mouth in 2022, cyrA exceeded 10 million copies L-1 where there were more than 6000 Cylindrospermopsis spp. cells mL-1. In contrast, the southwestern region had elevated mcyE gene (microcystin synthesis) detections near Homa Bay where Microcystis and Dolichospermum spp. were observed. These findings show that within a relatively small embayment, composition and toxin synthesis potential of cHABs can vary dramatically. This underscores the need for multifaceted management approaches and frequent cyanotoxin monitoring to reduce human health impacts.

Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water.

The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.

Gut microbiota alterations after acute coronary syndrome: a single center, case-control pilot study

Abstract Funding Acknowledgements Type of funding sources: Public Institution(s). Main funding source(s): National Research Council of Thailand Background Decreasing of gut microbiota diversity has been reported in coronary artery disease. However, the data of gut microbiota alterations after acute coronary syndrome (ACS) are still limited. Objective To determine the stool microbiota differences between ACS and controls. Also determine stool microbiota changes between ACS onset and 3 months apart. Methods We conducted a single-center, case-control pilot study. Ten ACS patients, aged between 18 to 80 years old, were consented. Echocardiogram, blood and fecal samples were obtained within 24 hours of hospitalization, then additionally 3 months apart. Ten of controls were also enrolled and collected the data. 16S ribosomal RNA gene was used to identify fecal bacteria. Results The mean age and gender were similar between both groups. The abundance of stool Clostridial was significantly decreased in ACS compared with controls (mean 8.476 ±0.570 vs. 9.254 ±0.829 Log10 copies/uL, p=0.025) and remained unchanged after 3 months (mean 8.256 ±0.787 Log10 copies/uL, p=0.483). The gut dysbiosis was not correlated with left ventricular function and medications. Conclusion Gut dysbiosis was observed in ACS patients and persisted afterward, regardless of LVEF and treatment. Gut dysbiosis might be an ACS risk marker in high cardiovascular risk patients. Further studies are warranted.Bacterial composition of fecal samples

Generation of an induced pluripotent stem cell line (KEIUi008-A) from a hearing loss patient with an A1555G mutation in mitochondrial DNA

We report the establishment of a human induced pluripotent stem cell (iPSC) line from a 54-year-old male patient with an A1555G mutation in the mitochondrial 12S ribosomal RNA gene (MTRNR1), associated with sensorineural hearing loss. The established iPSC line expressed stemness markers or undifferentiated state markers. We also demonstrated the capacity of the cells to differentiate into the three germ layers, suggesting its pluripotency and utility in the pathological study of sensorineural hearing loss and drug screening for ear disorders.