16S rRNA Gene Sequence Research Articles

IAA-producing plant growth promoting rhizobacteria from Ceanothus velutinus enhance cutting propagation efficiency and Arabidopsis biomass.

Climate-induced drought impacts plant growth and development. Recurring droughts increase the demand for water for food production and landscaping. Native plants in the Intermountain West region of the US are of keen interest in low water use landscaping as they are acclimatized to dry and cold environments. These native plants do very well at their native locations but are difficult to propagate in landscape. One of the possible reasons is the lack of associated microbiome in the landscaping. Microbiome in the soil contributes to soil health and impacts plant growth and development. Here, we used the bulk soil from the native plant Ceanothus velutinus (snowbrush ceanothus) as inoculant to enhance its propagation. Snowbrush ceanothus is an ornamental plant for low-water landscaping that is hard to propagate asexually. Using 50% native bulk soil as inoculant in the potting mix significantly improved the survival rate of the cuttings compared to no-treated cuttings. Twenty-four plant growth-promoting rhizobacteria (PGPR) producing indole acetic acid (IAA) were isolated from the rhizosphere and roots of the survived snowbrush. Seventeen isolates had more than 10µg/mL of IAA were shortlisted and tested for seven different plant growth-promoting (PGP) traits; 76% showed nitrogen-fixing ability on Norris Glucose Nitrogen free media,70% showed phosphate solubilization activity, 76% showed siderophore production, 36% showed protease activity, 94% showed ACC deaminase activity on DF-ACC media, 76% produced catalase and all of isolates produced ammonia. Eight of seventeen isolates, CK-6, CK-22, CK-41, CK-44, CK-47, CK-50, CK-53, and CK-55, showed an increase in shoot biomass in Arabidopsis thaliana. Seven out of eight isolates were identified as Pseudomonas, except CK-55, identified as Sphingobium based on 16S rRNA gene sequencing. The shortlisted isolates are being tested on different grain and vegetable crops to mitigate drought stress and promote plant growth.

Bacterial hosts of clinically significant beta-lactamase genes in Croatian wastewaters.

Wastewater treatment plants (WWTPs) provide a suitable environment for the interaction of antibiotic resistant bacteria and antibiotic-resistance genes (ARGs) from human, animal, and environmental sources. The aim was to study the influent and effluent of two WWTPs in Croatia to identify bacterial hosts of clinically important beta-lactamase genes (blaTEM, blaVIM, blaOXA-48-like) and observe how their composition changes during the treatment process. A culture-independent epicPCR (Emulsion, Paired isolation and Concatenation Polymerase Chain Reaction) was used to identify the ARG hosts, and 16S rRNA amplicon sequencing to study the entire bacterial community. Different wastewater sources contributed to the significant differences in bacterial composition of the wastewater between the two WWTPs studied. A total of 167 genera were detected by epicPCR, with the Arcobacter genus, in which all ARGs studied were present, dominating in both WWTPs. In addition, the clinically important genera Acinetobacter and Aeromonas contained all ARGs examined. The blaOXA-48-like gene had the highest number of hosts, followed by blaVIM, while blaTEM had the narrowest host range. Based on 16S rRNA gene sequencing, ARG hosts were detected in both abundant and rare taxa. The number of hosts carrying investigated ARGs was reduced by wastewater treatment. EpicPCR provided valuable insights into the bacterial hosts of horizontally transmissible beta-lactamase genes in Croatian wastewater.

Development and evaluation of the inactivated vaccine against Aeromonas schubertii in hybrid snakehead

Aeromonas schubertii is a global pathogen of fish that causes internal nodular diseases and death in severe cases. In the present study, we isolated nine pathogenic strains from diseased hybrid snakehead (Channa argus♂ × Channa maculata♀) which were formally identified as A. schubertii by molecular identification, including 16S rRNA and gyrB gene sequencing. Subsequently, we determined the extracellular enzyme activity of six isolates and compared pathogenicity to investigate potential relationships with geographic characteristics. Two highly pathogenic strains, AS-14 and AS-16, were finally identified as inactivated vaccine candidates. Subsequently, we evaluated different concentrations of the antigen for each vaccine by performing experiments in hybrid snakehead; fish were inoculated with inactivated vaccine via the intraperitoneal route and a booster injection was administered 14 days later. Relative percent survival (RPS) for fish immunized with high doses of the two vaccines (1 × 108 CFU/fish) were 54.4% and 57.4%, respectively; these values were higher than other groups of fish receiving different doses (1 × 106 and 1 × 107 CFU/fish). The bacterial load of tissues harvested from the fish immunized with high doses of the vaccine groups were significantly lower than those of fish immunized with low doses. Titers of specific antibodies against A. schubertii in fish immunized with a high dose of AS-16 vaccine were maintained at high levels when tested six weeks after the booster injection. Furthermore, immune-related genes in the spleen, including MHC I, MHC II, CD4, CD8α and IgM, all exhibited high levels of expression, thus suggesting that hybrid snakehead underwent an adaptive immune response post-vaccination. Collectively, our findings enrich our understanding of the specific causative agents underlying nodular diseases in hybrid snakehead and provide scientific reference guidelines for the development of vaccines against A. schubertii. The development of such vaccines will be conducive to the sustainable development of hybrid snakehead in commercial aquaculture.

Comprehensive genome analysis of five novel flavobacteria: Flavobacterium piscisymbiosum sp. nov., Flavobacterium pisciphilum sp. nov., Flavobacterium flavipigmentatum sp. nov., Flavobacterium lipolyticum sp. nov. and Flavobacterium cupriresistens sp. nov.

Eight isolates were obtained through a study on culture-dependent bacteria from fish farms and identified as members of the genus Flavobacterium based on pairwise analysis of the 16S rRNA gene sequences. The highest pairwise identity values were calculated as 98.8 % for strain F-30 T and Flavobacterium bizetiae, 99.0 % for strain F-65 T and Flavobacterium branchiarum, 98.7 % for strain F-126 T and Flavobacterium tructae, 98.2 % for strain F-323 T and Flavobacterium cupreum while 99.7 % identity level was detected for strain F-70 T and Flavobacterium geliluteum. In addition, strains F-33, Fl-77, and F-70 T shared 100 % identical 16S rRNA genes, while strains F-323 T and Fl-318 showed 99.9 % identity. A polyphasic approach including comparative analysis of whole-genome data was employed to ascertain the taxonomic provenance of the strains. In addition to the morphological, physiological, biochemical and chemotaxonomic characteristics of the strains, the overall genome-relatedness indices of dDDH and ANI below the established thresholds confirmed the classification of the strains as five novel species within the genus Flavobacterium. The comprehensive genome analyses of the strains were also conducted to determine the biosynthetic gene clusters, virulence features and ecological distribution patterns. Based on the polyphasic characterisations, including comparative genome analyses, it is concluded that strains F-30 T, F-65 T, F-70 T, F126T and F-323 T represent five novel species within the genus Flavobacterium for which Flavobacterium piscisymbiosum sp. nov. F-30 T (=JCM 34194 T = KCTC 82254 T), Flavobacterium pisciphilum sp. nov. F-65 T (=JCM 34197 T = KCTC 82257 T), Flavobacterium flavipigmentatum sp. nov. F-70 T (Fl-33 = Fl-77 = JCM 34198 T = KCTC 82258 T), Flavobacterium lipolyticum sp. nov. F-126 T (JCM 34199 T = KCTC 82259 T) and Flavobacterium cupriresistens sp. nov. F-323 T (Fl-318 = JCM 34200 T = KCTC 82260 T), are proposed.

Lactobacillus buchneri ameliorates obesity-related disorders induced by high-fat and high-cholesterol diet in mice

Diet-induced obesity is a serious social issue which can cause various metabolic diseases, such as lipid metabolism disorders, chronic inflammation, and liver steatosis. Recently, probiotics have shown promise in preventing and alleviating obesity and related metabolic syndromes. Here, we investigated the effects of Lactobacillus buchneri intervention on obesity-related disorders in mice fed a high-fat and high-cholesterol diet (HFHCD). The administration of L. buchneri to the HFHCD-induced mice reduced body weight gain, fat accumulation, serum triglycerides, and total cholesterol levels. Additionally, L. buchneri treatment restored triglycerides, total cholesterol, total bile acid, aspartate aminotransferase, and alanine aminotransferase to normal levels in the liver, and ameliorated hepatic steatosis in the HFHCD-induced mice. Consistently, qPCR analysis demonstrated that L. buchneri treatment downregulated the expression of lipogenesis Dgat1 and inflammatory IL-1β in the liver. Finally, 16S rRNA gene sequencing revealed that L. buchneri treatment had a mild impact on the gut microbiota community structure, indicating that the amelioration of obesity-related disorders may not be solely attributed to gut microbiota modulation. In conclusion, these findings provide evidence that L. buchneri can be considered a probiotic to ameliorate obesity-related disorders.

Splendidivirga corallicola gen. nov., sp. nov. and Agaribacillus aureus gen. nov., sp. nov., two bacteria isolated from coral Porites lutea, and proposal of Splendidivirgaceae fam. nov.

The Bacteroidota is one of the dominant bacterial phyla in corals. However, the exact taxa of those coral bacteria under the Bacteroidota are still unclear. Two aerobic, Gram-stain-negative, non-motile rods, designated strains BMA10T and BMA12T, were isolated from stony coral Porites lutea collected from Weizhou Island, PR China. Global alignment of 16S rRNA gene sequences indicated that both strains are closest to species of Fulvivirga with the highest identities being lower than 93 %, and the similarity value between these two strains was 92.3 %. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that these two strains form an monophylogenetic lineage alongside the families Fulvivirgaceae, Reichenbachiellaceae, Roseivirgaceae, Marivirgaceae, Cyclobacteriaceae, and Cesiribacteraceae in the order Cytophagales, phylum Bacteroidota. The genomic DNA G+C contents of BMA10T and BMA12T were 38.4 and 41.9 mol%, respectively. The major polar lipids of BMA10T were phosphatidylethanolamine, unidentified aminophospholipid, four unidentified aminolipids, and five unidentified lipids. While those of BMA12T were phosphatidylethanolamine, two unidentified aminolipids, and five unidentified lipids. The major cellular fatty acids detected in both isolates were iso-C15 : 0 and C16 : 1 ω5c. Carbohydrate-active enzyme analysis indicated these two strains may utilize coral mucus or chitin. Based on above characteristics, these two strains are suggested to represent two new species in two new genera of a new family in the order Cytophagales, for which the name Splendidivirga corallicola gen. nov., sp. nov., Agaribacillus aureus gen. nov., sp. nov. and Splendidivirgaceae fam. nov. are proposed. The type strain of S. corallicola is BMA10T (=MCCC 1K08300T=KCTC 102045T), and that for A. aureus is BMA12T (=MCCC 1K08309T=KCTC 102046T).

Comparative characterization of supragingival plaque microbiomes in malocclusion adult female patients undergoing orthodontic treatment with removable aligners or fixed appliances: a descriptive cross-sectional study.

This study aimed to explore the effects of removable aligners and fixed appliances on the supragingival bacterial communities in adult female patients undergoing orthodontic treatment. Supragingival plaque samples from 48 female individuals underwent microbiome analysis (16S rRNA gene sequencing) using PacBio Sequel sequencing. The study included 13 adults without orthodontic treatment needs as the control group (Group C), and 35 patients with comparable initial orthodontic conditions who received treatment at a university clinic in Beijing, China. The treatment involved either traditional fixed brackets (Group B, n = 17) or Invisalign® aligners (Group AT, n = 18). Bioinformatics methods were used for data analysis. From the 48 plaque samples, a total of 334,961 valid reads were obtained, averaging 6,978 sequences per sample. The 16S rDNA sequences were classified into 25,727 amplicon sequence variants (ASVs). Significant variances in alpha and beta diversity among the groups were noted. Group B microbiome exhibited an increased presence of Gram-negative bacteria. At the phylum level, Actinobacteriota was significantly more prevalent in Group C samples, while Bacteroidota was enriched in Group B samples. Family-level relative abundance analysis showed a notable increase in Saccharibacteria (formerly TM7) and Prevotellaceae in Group B. Genus-level analysis revealed a significant rise in Lautropia in Group AT. Fixed orthodontic appliances were linked to oral microbiome changes, notably an enhanced relative abundance of anaerobes, including periodontal pathogens. The observation points to the impact of orthodontic appliance on the oral microbial community, highlighting the difference between traditional braces (Group B) and clear aligners (Group AT)in terms of the predominance of anaerobic and gram negative bacteria. This emphasizes the importance of considering the microbiological effects when choosing orthodontic appliance and underscores the need for tailored oral hygiene practices for individuals undergoing these treatments. This research might provide insights that could assist in the development of innovative cleaning techniques and antibacterial materials.

Molecular characterisation and diagnostics of the red ring nematode, Bursaphelenchus cocophilus, from Mexico

Molecular characterisation and diagnostics of the red ring nematode, Bursaphelenchus cocophilus, from Mexico

Characterization of Bacillus velezensis DCJ 2 isolated from the rhizosphere soil of aglaonema ‘Maria’ and investigation of its plant growth-promoting effects

Aglaonema ‘Maria’ is one of the key foliage plants that has gained high demand in foreign destinations in the last few years. This study was conducted to characterize Bacillus velezensis DCJ 2, assess its plant growth promotion effect and investigate the effectiveness of different delivery methods of the bacterial inoculum for the growth promotion of Aglaonema ‘Maria’. In this context, DCJ 2, isolated from the rhizosphere soil of A. Maria was screened to investigate its potential as a plant growth-promoting bacterium. The pure culture of DCJ 2 maintained on nutrient agar was utilized for morphological, biochemical and physiological examinations. The molecular characterization of the strain was performed with different primer pairs targeting 16SrRNA, gyrA, pgsB and sugar kinase genes of DCJ 2. A pot experiment was carried out to investigate the plant growth promotion effect. It was conducted in the greenhouse as per the complete randomized block design with eight treatments and five replicates. . Healthy plants of A. ‘Maria’ established in field soil and solarized soil were treated with 100 ml of the suspension of the DCJ 2 at the rate of 10 8 CFU/ml either as a soil drench or foliar spray. The partial 16SrRNA, gyrA, pgsB and sugar kinase gene sequences of DCJ 2, BLAST searched in the NCBI database revealed that it has a high similarity to Bacillus velezensis. The pot experiment showed that the application of strain DCJ 2 as a soil drench to solarized soil (Treatment 6) yielded a significant increase in growth parameters at p=0.05. Based on molecular analysis, morphological, biochemical, and physiological reactions, DCJ 2 was identified as Bacillus velezensis. This study revealed that B. velezensis DCJ 2 has the potential to boost the growth of A. Maria and hence serve as a base for developing a biofertilizer.

The Antioxidant Dendrobium officinale Polysaccharide Modulates Host Metabolism and Gut Microbiota to Alleviate High-Fat Diet-Induced Atherosclerosis in ApoE-/- Mice.

The discovery of traditional plants' medicinal and nutritional properties has opened up new avenues for developing pharmaceutical and dietary strategies to prevent atherosclerosis. However, the effect of the antioxidant Dendrobium officinale polysaccharide (DOP) on atherosclerosis is still not elucidated. This study aims to investigate the inhibitory effect and the potential mechanism of DOP on high-fat diet-induced atherosclerosis in Apolipoprotein E knockout (ApoE-/-) mice. The identification of DOP was measured by high-performance gel permeation chromatography (HPLC) and Fourier transform infrared spectroscopy (FTIR). We used high-fat diet (HFD)-induced atherosclerosis in ApoE-/- mice as an animal model. In the DOP intervention stage, the DOP group was treated by gavage with 200 μL of 200 mg/kg DOP at regular times each day and continued for eight weeks. We detected changes in serum lipid profiles, inflammatory factors, anti-inflammatory factors, and antioxidant capacity to investigate the effect of the DOP on host metabolism. We also determined microbial composition using 16S rRNA gene sequencing to investigate whether the DOP could improve the structure of the gut microbiota in atherosclerotic mice. DOP effectively inhibited histopathological deterioration in atherosclerotic mice and significantly reduced serum lipid levels, inflammatory factors, and malondialdehyde (F/B) production. Additionally, the levels of anti-inflammatory factors and the activity of antioxidant enzymes, including superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX), were significantly increased after DOP intervention. Furthermore, we found that DOP restructures the gut microbiota composition by decreasing the Firmicutes/Bacteroidota (F/B) ratio. The Spearman's correlation analysis indicated that serum lipid profiles, antioxidant activity, and pro-/anti-inflammatory factors were associated with Firmicutes, Bacteroidota, Allobaculum, and Coriobacteriaceae_UCG-002. This study suggests that DOP has the potential to be developed as a food prebiotic for the treatment of atherosclerosis in the future.

Mannheimia indoligenes sp. nov., proposed for clade V organisms of Mannheimia.

A set of 25 strains belonging to clade V of Mannheimia mainly isolated from cattle was investigated and is proposed to represent Mannheimia indoligenes sp. nov. The species can be separated from the other validly published species of the genus by pheno- and genotype. Only indole separates M. indoligenes and Mannheimia varigena while two to seven characters separate M. indoligenes from other species of Mannheimia. Thirteen strains belonging to biogroups 6, 7, 8C, 9, 10, 12 and UG5 formed a monophyletic group based on 16S rRNA gene sequence comparisons with 98-100 % similarity. Eight of these strains were further included in the whole genome comparison. Digital DNA-DNA hybridization showed that the similarities between the suggested type strain M14.4T and the other strains of M. indoligenes were 62.9 % or higher. The average nucleotide identity was 95.5 % or higher between M14.4T and the other strains of the species. The rpoB gene sequence similarity was 95-100 % within M. indoligenes. MALDI-TOF allowed a clear separation from other Mannheimia species further supporting classification as a novel species and making it the diagnostic identification tool of choice for M. indoligenes. The type strain is M14.4T (=CCUG 77347T=DSM 116804T) isolated from a cattle tongue in Scotland.

Characterization of thermophilic bacteria from Ie Seum Hot Springs, Aceh Besar, Indonesia as producers of protease enzyme

Abstract. Sabaria E, Yasmin Y, Ismail YS, Bessania MA, Putri I, Fitri L. 2024. Characterization of thermophilic bacteria from Ie Seum Hot Springs, Aceh Besar, Indonesia as producers of protease enzyme. Biodiversitas 25: 1867-1874. Thermophilic bacteria are microorganisms that can survive in high-temperature environments exceeding 75°C. The Ie Seum Hot Springs in Aceh Besar, Indonesia are known to be a place where these thermophilic bacteria inhabit. In such extreme conditions, proteins and enzymes are often denatured, making these bacteria of interest due to their ability to adapt and produce enzymes such as proteases. Proteases are called proteolytic enzymes that can be applied both in the economic and medical fields. This study aimed to isolate and identify thermophilic bacteria species that have the highest potential for protease production in Ie Seum Hot Spring, Aceh Besar by analyzing the 16S rRNA gene and characterizing them using biochemical tests. Based on the result, seven thermophilic bacterial isolates, namely BT1, BT2, BT3, BT4, BT5, BT6, and BT7 were obtained, each showing different colony characteristics. The biochemical tests also revealed differences metabolic activity of each isolate. Of these isolates, BT4 exhibited the highest proteolytic index (4.65). Additionally, the 16S rRNA gene sequence analysis showed that the BT4 strain belongs to the genus Bacillus and has high similarities to Bacillus sp., B. licheniformis and B. sonorensis. These findings suggest that BT4 has significant potential as a source of thermophilic protease enzymes.

Identification of lactic acid bacteria found in traditional Shalgam juice using 16S rRNA sequencing and evaluation of their probiotic potential in vitro

This research focuses on the identification of lactic acid bacteria (LAB) isolated from traditionally produced Shalgam juices collected from different locations in Türkiye and the characterization of their probiotic potential in vitro. LAB isolates were identified by 16 S rRNA gene sequencing. The most common strains belonged to Pediococcus acidilactici (54.2%), Lacticaseibacillus sp. (18.8%), L. paracasei (8.3%) and Enterococcus faecalis (6.3%). According to the test results, LAB isolates survived after exposure to low pH (2.0) except Levilactobacillus brevis TS9 and P. acidilactici TS10. All isolates showed tolerance to bile salts (69.78%–147.84%), pepsin (50.10%–159.43%), pancreatin (46.64%–120.12%) and phenol (58.19%–121.84%) at various levels. The isolates E. faecalis TS2 and Lacticaseibacillus sp. TS3 were more resistant to the target microorganisms. The isolates E. faecalis TS2, L. paracasei TS7, P. acidilactici TS41, and P. acidilactici TS43 were highly resistant to the antibiotics. The hydrophobicity of the isolates toward xylene ranged from 2.32% to 58.56% and P. acidilactici TS42 showed a high hydrophobicity of 58.56%. The ability of auto-aggregation and co-aggregation varied from 3.59% to 23.67% and 0.85–29.37%, respectively. The isolates showing the best probiotic properties (Lacticaseibacillus sp. TS3, Lacticaseibacillus sp. TS11, and L. paracasei TS33) were tested for their ability to produce short-chain fatty acids. The acetate, butyrate and propionate production of the isolates varied between 4040 and 8135, 1025–1255 and 14620-17225 μg/mL, respectively. Butyrate production of the isolates were higher than the control group. These results indicated that LAB originated from Shalgam juice could be proposed as probiotic candidates for use in fermented foods.

Genome-Based Classification of Pedobacter albus sp. nov. and Pedobacter flavus sp. nov. Isolated from Soil

Two rod-shaped, non-spore-forming, Gram-negative bacteria, strain KR3-3T isolated from fresh soil in Korea and strain VNH31T obtained from soil samples from motorbike repair workshop floors in Vietnam, were identified. Phylogenetic analysis utilizing 16S rRNA gene sequences revealed their affiliation with the family Sphingobacteriaceae and their relation to the genus Pedobacter, exhibiting 16S rRNA gene sequence similarities lower than 98.00% with all known species within the genus Pedobacter. Growth of VNH31T and KR3-3T was impeded by NaCl concentrations exceeding >0.5% and 1.5%, respectively, while they both thrived optimally at temperatures ranging between 25 and 30 °C. Notably, neither strain reduced nitrate to nitrite nor produced indole. Negative results were observed for the acidification of D-glucose and hydrolysis of urea, gelatin, casein, and starch. VNH31T exhibited growth on β-galactosidase, sodium acetate, L-serine, and L-proline, whereas KR 3-3T demonstrated growth on D-glucose, D-mannose, D-maltose, N-acetyl-glucosamine, sucrose, sodium acetate, L-serine, 4-Hydroxybenzoic acid, and L-proline. Core genome-based phylogenetic analysis revealed that the two isolates formed distinct clusters within the genus Pedobacter. The DNA G+C contents of KR3-3T and VNH31T were determined to be 44.12 mol% and 32.96 mol%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization relatedness values (67.19–74.19% and 17.6–23.6%, respectively) between the Pedobacter isolates and the closely related type strains fell below the threshold values utilized for species delineation. Following comprehensive genomic, chemotaxonomic, phenotypic, and phylogenetic analyses, the isolated strains are proposed as two novel species within the genus Pedobacter, named Pedobacter albus sp. nov. (type strain KR3-3T = KACC 23486T = NBRC 116682T) and Pedobacter flavus sp. nov. (type strain VNH31T = KACC 23297T = CCTCC AB 2023109T).

Effect of Mineral Fertilizers and Pesticides Application on Bacterial Community and Antibiotic-Resistance Genes Distribution in Agricultural Soils

Soils are a hotspot for the emergence and spread of antibiotic resistance. The effects of agrochemical treatments on the bacterial community of agricultural soils and the content of antibiotic-resistance genes (ARGs) were studied. Treatments included the following: control, mineral fertilizers (NPKs), pesticides, and the combined treatment of soils under soya (Glycine max), sunflower (Helianthus annuus L.), and wheat (Triticum aestivum). Bacterial community taxonomic composition was studied using 16S rRNA gene sequencing. The content of 10 ARGs and 3 integron genes (intI1, intI2, intI3) was determined using quantitative real-time PCR. The results showed that the treatments had little effect on the taxonomic composition and diversity of the soil bacterial community. The most significant factors determining differences in the microbial community were sampling time and soil physico-chemical parameters. A significant role of the bacterial community in ARG distribution in soils was demonstrated. Representatives of the Pseudomonas, Bacillus, Sphingomonas, Arthrobacter genera, and the Nocardioidaceae and Micrococcaceae families were likely ARG hosts. The presence of integron genes of all three classes was detected, the most numerous being intI3. This work provides important information on the role of agricultural soils in ARG transfer, and the findings may be useful for sustainable and safe agricultural development.

Streptomyces camelliae sp. nov., isolated from rhizosphere soil of Camellia oleifera Abel.

A novel actinobacterium strain, designated HUAS 2-6T, was isolated from the rhizosphere soil of Camellia oleifera Abel collected from Taoyuan County, Northwestern Hunan Province, South China. This strain was subjected to a polyphasic taxonomic study. Strain HUAS 2-6T is characterized by morphology typical of members of the genus Streptomyces, with deep purplish vinaceous aerial mycelia and deep dull lavender substrate mycelia. Strain HUAS 2-6T, based on the full-length 16S rRNA gene sequence analysis, exhibited the highest similarities to S. puniciscabiei S77T (99.31%), S. filipinensis NBRC 12860T (99.10%), S. yaanensis CGMCC 4.7035T (99.09%), S. fodineus TW1S1T (99.08%), S. broussonetiae CICC 24819T (98.76%), S. achromogenes JCM 4121T (98.69%), S. barringtoniae JA03T (98.69%), and less than 98.70% with other validly species. In phylogenomic tree, strain HUAS 2-6T was clustered together with S. broussonetiae CICC 24819T, suggesting that they were closely related to each other. However, average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) between them were much less than the species cutoff values (ANI 96.7% and dDDH 70%). Moreover, in phenotypic and chemotaxonomic characteristics, strain HUAS 2-6T is distinct from S. broussonetiae CICC 24819T. On the basis of the polyphasic data, strain HUAS 2-6T is proposed to represent a novel species, Streptomyces camelliae sp. nov. (= MCCC 1K04729T = JCM 35918T).

Comparative analysis of midgut bacterial communities in Chikungunya virus-infected and non-infected Aedes aegypti Thai laboratory strain mosquitoes

Chikungunya virus (CHIKV) poses a significant global health threat, re-emerging as a mosquito-transmitted pathogen that caused high fever, rash, and severe arthralgia. In Thailand, a notable CHIKV outbreak in 2019–2020 affected approximately 20,000 cases across 60 provinces, underscoring the need for effective mosquito control protocols. Previous studies have highlighted the role of midgut bacteria in the interaction between mosquito vectors and pathogen infections, demonstrating their ability to protect the insect from invading pathogens. However, research on the midgut bacteria of Aedes (Ae.) aegypti, the primary vector for CHIKV in Thailand remains limited. This study aims to characterize the bacterial communities in laboratory strains of Ae. aegypti, both infected and non-infected with CHIKV. Female mosquitoes from a laboratory strain of Ae. aegypti were exposed to a CHIKV-infected blood meal through membrane feeding, while the control group received a non-infected blood meal. At 7 days post-infection (dpi), mosquito midguts were dissected for 16S rRNA gene sequencing to identify midgut bacteria, and CHIKV presence was confirmed by E1-nested RT-PCR using mosquito carcasses. The study aimed to compare the bacterial communities between CHIKV-infected and non-infected groups. The analysis included 12 midgut bacterial samples, divided into three groups: CHIKV-infected (exposed and infected), non-infected (exposed but not infected), and non-exposed (negative control). Alpha diversity indices and Bray–Curtis dissimilarity matrix revealed significant differences in bacterial profiles among the three groups. The infected group exhibited an increased abundance of bacteria genus Gluconobacter, while Asaia was prevalent in both non-infected and negative control groups. Chryseobacterium was prominent in the negative control group. These findings highlight potential alterations in the distribution and abundance of gut microbiomes in response to CHIKV infection status. This study provides valuable insights into the dynamic relationship between midgut bacteria and CHIKV, underscoring the potential for alterations in bacterial composition depending on infection status. Understanding the relationships between mosquitoes and their microbiota holds promise for developing new methods and tools to enhance existing strategies for disease prevention and control. This research advances our understanding of the circulating bacterial composition, opening possibilities for new approaches in combating mosquito-borne diseases.

Lactobacillus paracasei Jlus66 relieves DSS-induced ulcerative colitis in a murine model by maintaining intestinal barrier integrity, inhibiting inflammation, and improving intestinal microbiota structure.

Ulcerative colitis (UC) is a serious health problem with increasing morbidity and prevalence worldwide. The pathogenesis of UC is complex, currently believed to be influenced by genetic factors, dysregulation of the host immune system, imbalance in the intestinal microbiota, and environmental factors. Currently, UC is typically managed using aminosalicylates, immunosuppressants, and biologics as adjunctive therapies, with the risk of relapse and development of drug resistance upon discontinuation. Therefore, further research into the pathogenesis of UC and exploration of potential treatment strategies are necessary to improve the quality of life for affected patients. According to previous studies, Lactobacillus paracasei Jlus66 (Jlus66) reduced inflammation and may help prevent or treat UC. We used dextran sulfate sodium (DSS) to induce a mouse model of UC to assess the effect of Jlus66 on the progression of colitis. During the experiment, we monitored mouse body weight, food and water consumption, as well as rectal bleeding. Hematoxylin-eosin staining was performed to assess intestinal pathological damage. Protein imprinting and immunohistochemical methods were used to evaluate the protein levels of nuclear factor-kappa B (NF-κB), mitogen-activated protein kinase (MAPK), and tight junction (TJ) proteins in intestinal tissues. Fecal microbiota was analyzed based on partial 16S rRNA gene sequencing. Jlus66 supplementation reduced the degree of colon tissue damage, such as colon shortening, fecal occult blood, colon epithelial damage, and weight loss. Supplementation with Jlus66 reduced DSS-induced upregulation of cytokine levels such as TNF-α, IL-1β, and IL-6 (p < 0.05). The NF-κB pathway and MAPK pathway were inhibited, and the expression of TJ proteins (ZO-1, Occludin, and Claudin-3) was upregulated. 16S rRNA sequencing of mouse cecal contents showed that Jlus66 effectively regulated the structure of the intestinal biota. In conclusion, these data indicate that Jlus66 can alter the intestinal biota and slow the progression of UC, providing new insights into potential therapeutic strategies for UC.

Imprints of ecological processes in the taxonomic core community: an analysis of naturally replicated microbial communities enclosed in oil.

It is widely assumed that a taxonomic core community emerges among microbial communities from similar habitats because similar environments select for the same taxa bearing the same traits. Yet, a core community itself is no indicator of selection because it may also arise from dispersal and neutral drift, i.e. by chance. Here, we hypothesize that a core community produced by either selection or chance processes should be distinguishable. While dispersal and drift should produce core communities with similar relative taxon abundances, especially when the proportional core community, i.e. the sum of the relative abundances of the core taxa, is large, selection may produce variable relative abundances. We analyzed the core community of 16S rRNA gene sequences of 193 microbial communities occurring in tiny water droplets enclosed in heavy oil from the Pitch Lake, Trinidad and Tobago. These communities revealed highly variable relative abundances along with a large proportional core community (68.0 ± 19.9%). A dispersal-drift null model predicted a negative relationship of proportional core community and compositional variability along a range of dispersal probabilities and was largely inconsistent with the observed data, suggesting a major role of selection for shaping the water droplet communities in the Pitch Lake.

Prevotella copri promotes vascular calcification via lipopolysaccharide through activation of NF-κB signaling pathway

ABSTRACT Emerging evidence indicates that alteration of gut microbiota plays an important role in chronic kidney disease (CKD)-related vascular calcification (VC). We aimed to investigate the specific gut microbiota and the underlying mechanism involved in CKD-VC. We identified an increased abundance of Prevotella copri (P. copri) in the feces of CKD rats (induced by using 5/6 nephrectomy followed by a high calcium and phosphate diet) with aortic calcification via amplicon sequencing of 16S rRNA genes. In patients with CKD, we further confirmed a positive correlation between abundance of P. copri and aortic calcification scores. Moreover, oral administration of live P. copri aggravated CKD-related VC and osteogenic differentiation of vascular smooth muscle cells in vivo, accompanied by intestinal destruction, enhanced expression of Toll-like receptor-4 (TLR4), and elevated lipopolysaccharide (LPS) levels. In vitro and ex vivo experiments consistently demonstrated that P. copri-derived LPS (Pc-LPS) accelerated high phosphate-induced VC and VSMC osteogenic differentiation. Mechanistically, Pc-LPS bound to TLR4, then activated the nuclear factor κB (NF-κB) and nucleotide-binding domain, leucine-rich–containing family, pyrin domain–containing-3 (NLRP3) inflammasome signals during VC. Inhibition of NF-κB reduced NLRP3 inflammasome and attenuated Pc-LPS-induced VSMC calcification. Our study clarifies a novel role of P. copri in CKD-related VC, by the mechanisms involving increased inflammation-regulating metabolites including Pc-LPS, and activation of the NF-κB/NLRP3 signaling pathway. These findings highlight P. copri and its-derived LPS as potential therapeutic targets for VC in CKD.