16S rRNA Gene Sequence Analysis Research Articles

Massilia luteola sp. nov., a novel indole-producing and cellulose-degrading bacterium isolated from soil.

A Gram-stain-negative, rod-shaped, indole-producing, and cellulose-degrading bacterial strain, designated NEAU-G-C5T, was isolated from soil collected from a forest in Dali city, Yunnan province, south China. 16S rRNA gene sequence analysis showed that strain NEAU-G-C5T was assigned to the genus Massilia and showed high sequence similarities to Massilia phosphatilytica 12-OD1T (98.32 %) and Massilia putida 6 NM-7T (98.41 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-G-C5T formed a lineage related to M. phosphatilytica 12-OD1T and M. putida 6 NM-7T. The major fatty acids of the strain were C16 : 0, C16 : 1 ω7c, and C17 : 0 cyclo. The respiratory quinone was Q-8. The polar lipid profile of the strain showed the presence of diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. In addition, the average nucleotide identity values between strain NEAU-G-C5T and its reference strains M. phosphatilytica 12-OD1T, M. putida 6 NM-7T, M. norwichensis NS9T, and M. kyonggiensis TSA1T were 89.7, 88.2, 81.3, and 88.0 %, respectively, and the levels of digital DNA-DNA hybridization between them were found to be 58.5 % (54.9-62.0 %), 53.2 % (49.8-56.7 %), 31.9 % (28.6-35.5 %), and 57.7 % (54.1-61.2 %), respectively, which were lower than the accepted threshold values of 95-96 % and 70 %, respectively. The DNA G+C content of strain NEAU-G-C5T was 66.5 mol%. The strain could produce indoleacetic acid and cellulase. On the basis of the phenotypic, genotypic, and chemotaxonomic characteristics, we conclude that strain NEAU-G-C5T represents a novel species of the genus Massilia, for which the name Massilia luteola sp. nov. is proposed. The type strain is NEAU-G-C5T (=MCCC 1K08668T=KCTC 8080T).

The contribution of small heterodimer partner to the occurrence and progression of cholestatic liver injury.

Small heterodimer partner (SHP, encoded by NR0B2) plays an important role in maintaining bile acid homeostasis. The loss of the hepatic farnesoid X receptor (FXR)/SHP signal can cause severe cholestatic liver injury (CLI). FXR and SHP have overlapping and nonoverlapping functions in bile acid homeostasis. However, the key role played by SHP in CLI is unclear. In this study, an alpha-naphthylisothiocyanate (ANIT)-induced cholestasis mouse model was established. The effect of SHP knockout (SHP-KO) on liver and ileal pathology was evaluated. 16S rRNA gene sequencing analysis combined with untargeted metabolomics was applied to reveal the involvement of SHP in the pathogenesis of CLI. The results showed that ANIT (75mg/kg) induced cholestasis in WT mice. No significant morphological changes were found in the liver and ileal tissue of SHP-KO mice. However, the serum metabolism and intestinal flora characteristics were significantly changed. Moreover, compared with the WT+ANIT group, the serum levels of ALT and AST in the SHP-KO+ANIT group were significantly increased, and punctate necrosis in the liver tissue was more obvious. The ileum villi showed obvious shedding, thinning, and shortening. In addition, SHP-KO-associated differential intestinal flora and differential biomarkers were significantly associated. In this study, we elucidated the serum metabolic characteristics and intestinal flora changes related to the aggravation of CLI in SHP-KO mice induced by ANIT.

Proposal of Helicobacter higonensis sp. nov. isolated from a human clinical specimen, and emended description of Helicobacter valdiviensis Collado, 2014.

We have previously isolated a gram-negative microaerophilic strain, PAGU2000T from a patient presenting with a fever in Kumamoto Prefecture, Japan. The present study aimed to comprehensively analyze the taxonomy of the isolated strain using a polyphasic approach. The 16S rRNA gene sequence analysis indicated that the strain was a member of enterohepatic Helicobacter. The strain PAGU2000T shared a 97.5% 16S rRNA gene nucleotide identity with Helicobacter valdiviensis, and this taxonomic position was confirmed by phylogenetic analysis of the GyrA amino acid sequences. The proposed strain PAGU2000T has a 1.482 Mbp chromosome with a DNA G + C content of 31.3 mol% and encodes 1520 predicted coding sequences. The average nucleotide identity between the strain PAGU2000T and type strain of H. valdiviensis was 70.3%, which was lower than the recommended threshold of 95% for species delineation. The strain PAGU2000T was a motile, non-spore-forming, and spiral-shaped bacterium, exhibiting catalase and oxidase activities but not urease and nitrate reduction. This study demonstrates that the isolate represents a novel species within enterohepatic Helicobacter, for which the name Helicobacter higonensis is proposed (type strain: PAGU2000T = GTC 16811T = LMG 33095T). In this study, we describe the phenotypic and morphological features of this strain and propose an emended description of some biochemical traits of H. valdiviensis.

Oral-to-rectum microbial transmission in orthopedic patients without a history of intestinal disorders

The enrichment of oral taxa in the gut has recently been reported as a notable alteration in the microbial balance in patients with intestinal disorders. However, translocation in populations without such diseases remains controversial. In this study, we examined 49 pairs of tongue and rectal samples collected from orthopedic patients without a history of intestinal disorders to verify the presence of oral taxa in the rectal microbiota. The bacterial composition of each sample was determined using 16S rRNA gene sequencing and amplicon sequence variant (ASV) analysis. Although the bacterial compositions of the tongue and rectal microbiota were distinctly different, tongue ASVs were detected in 67.3% of the participants and accounted for 0.0%–9.37% of the rectal microbiota. Particularly, Streptococcus salivarius, Fusobacterium nucleatum, and Streptococcus parasanguinis were abundant in the rectal microbiota. According to the network analysis, tongue taxa, such as S. salivarius and S. parasanguinis, formed a cohabiting group with Klebsiella pneumoniae and Alistipes finegoldii in the rectal microbiota. The total abundance of tongue ASVs in the rectal microbiota was significantly higher in participants with older age, hypertension, and proton pump inhibitor (PPI) use. Our study presents an extensive translocation of oral taxa to the rectum of a population without intestinal disorders and suggests that aging, hypertension, and PPI use are associated with an increased abundance of oral taxa and potential pathogenic bacteria in the rectal microbiota.

Endometrial microbiota alteration in female patients with endometrial polyps based on 16S rRNA gene sequencing analysis

IntroductionThe potential role of the endometrial microbiota in the pathogenesis of endometrial polyps (EPs) warrants further investigation, given the current landscape of limited and inconclusive research findings. We aimed to explore the microecological characteristics of the uterine cavity in patients with EPs and investigate the potential of endometrial microbiota species as novel biomarkers for identifying EPs.MethodsEndometrial samples were collected from 225 patients who underwent hysteroscopies, of whom 167 had EPs, whereas 58 had non- hyperproliferative endometrium status. The endometrial microbiota was assessed using 16S rRNA gene sequencing. We characterized the endometrial microbiota and identified microbial biomarkers for predicting EPs.ResultsThe endometrial microbial diversity and composition were significantly different between the EP and control groups. Predictive functional analyses of the endometrial microbiota demonstrated significant alterations in pathways involved in sphingolipid metabolism, steroid hormone biosynthesis, and apoptosis between the two groups. Moreover, a classification model based on endometrial microbial ASV-based biomarkers along with the presence of abnormal uterine bleeding symptoms achieved powerful classification potential in identifying EPs in both the discovery and validation cohorts.ConclusionOur study indicates a potential association between altered endometrial microbiota and EPs. Endometrial microbiota-based biomarkers may prove valuable for the diagnosis of EPs.Clinical trial registrationChinese Clinical Trial Registry (ChiCTR2100052746).

Enhancement of benzo[a]pyrene mineralization: symbiotic biodegradation by Acinetobacter sp. strain HAP1 in Association with Cyanobacteriota sp. S66

The ability of Acinetobacter sp. strain HAP1, isolated from petroleum refinery effluent, to eliminate different concentrations (20, 40, 60, 80 and 100 mg/L) of Benzo[a]Pyrene degradation (BaP) was studied. A test to improve this degradation capacity was carried out by culturing the bacterial strain in association with a cyanobacteria. The results show a highly significant effect of the concentration of (BaP) and a very highly significant effect of the symbiosis between the bacterial strain and the cyanobacteria. This combination was able to significantly improve the (BaP) degradation rate by up to 18%. This degradation and especially in association leads to a complete mineralization of (BaP) and there is a difference in yield that can go up to 15%. Through molecular identification based on 16S rRNA gene sequence analysis, strains HAP1 and S66 were recognized as Acinetobacter sp. strain HAP1 and Cyanobacteriota sp. S66, respectively. Comparison of the retrieved sequences with the NCBI GenBank database was done, and the closest matches were found to be Acinetobacter pittii strain JD-10 for bacteria and Pseudochroococcus couteii strain PMC 885.14 for cyanobacteria.

Saccharopolyspora ipomoeae sp. nov., an Actinomycete Isolated from Sweet Potato Field Soils.

During the course of the isolation of actinobacteria from sweet potato field soils collected from Phra Nakhon Si Ayutthaya province of Thailand, strain TS4A08T was isolated and subjected to a polyphasic taxonomic approach. The 16S rRNA gene sequence analysis of strain TS4A08T revealed that it is closely related to the type strains of Saccharopolyspora aridisoli, and Saccharopolyspora endophytica with 98.7%, and 98.6% similarity, respectively. However, phylogenetic analyses using 16S rRNA gene and genome sequences indicated that strain TS4A08T clustered with Saccharopolyspora flava AS4.1520T (98.2% similarity), well-supported by bootstrap values, and formed distinct line from the two closest strains. The average nucleotide identity (ANI) values and digital DNA-DNA hybridization (dDDH) values between the genome sequences of strain TS4A08T and the closest type strains of S. aridisoli, S. endophytica, and S. flava, were 86.1-93.2% and 33.1-49.6%, respectively, which were less than the threshold for the species delineation. The genome size and the DNA G + C content of strain TS4A08T were 6.6 Mbp and 70.5%, respectively. The strain grew well at 25-37°C, pH range of 7-9, and NaCl concentration of 0-5% (w/v). Whole-cell hydrolysates contained meso-diaminopimelic acid. The major fatty acids were iso-C16:0, anteiso-C17:0, and iso-C15:0. Strain TS4A08T exhibited phosphatidylcholine in its polar lipid profile, with MK-9(H4) being the predominant isoprenologue. The strain exhibits typical chemotaxonomic properties of the genus Saccharopolyspora, including arabinose, galactose, and ribose as whole-cell sugars. Strain TS4A08T represents a novel species within the genus Saccharopolyspora, for which the name Saccharopolyspora ipomoeae sp. nov. is proposed. The type strain is TS4A08T (= TBRC 17271T = NBRC 115967T).

Marinobacter azerbaijanicus sp. nov., a moderately halophilic bacterium from Urmia Lake, Iran.

A novel moderately halophilic, Gram-stain-negative and facultatively anaerobic bacterium, designated as strain TBZ242T, was isolated from water of Urmia Lake in the Azerbaijan region of Iran. The cells were found to be rod-shaped and motile by a single polar flagellum, producing circular and yellowish colonies. The strain could grow in the presence of 0.5-10 % (w/v) NaCl (optimum, 2.5-5 %). The temperature and pH ranges for growth were 15-45 °C (optimum 30 °C) and pH 7.0-11.0 (optimum pH 8.0) on marine agar. The 16S rRNA gene sequence analysis revealed that strain TBZ242T belonged to the genus Marinobacter, showing the highest similarities to Marinobacter algicola DG893T (98.8 %), Marinobacter vulgaris F01T (98.8 %), Marinobacter salarius R9SW1T (98.5 %), Marinobacter panjinensis PJ-16T (98.4 %), Marinobacter orientalis W62T (98.0 %) and Marinobacter denitrificans JB2H27T (98.0 %). The 16S rRNA and core-genome phylogenetic trees showed that strain TBZ242T formed a distinct branch, closely related to a subclade accommodating M. vulgaris, M. orientalis, M. panjinensis, M. denitrificans, M. algicola, M. salarius and M. iranensis, within the genus Marinobacter. Average nucleotide identity and digital DNA-DNA hybridization values between strain TBZ242T and the type strains of the related species of Marinobacter were ≤85.0 and 28.6 %, respectively, confirming that strain TBZ242T represents a distinct species. The major cellular fatty acids of strain TBZ242T were C16 : 0 and C16 : 1  ω7c/C16 : 1 ω6c and the quinone was ubiquinone Q-9. The genomic DNA G+C content of strain TBZ242T is 57.2 mol%. Based on phenotypic, chemotaxonomic and genomic data, strain TBZ242T represents a novel species within the genus Marinobacter, for which the name Marinobacter azerbaijanicus sp. nov. is proposed. The type strain is TBZ242T (= CECT 30649T = IBRC-M 11466T). Genomic fragment recruitment analysis showed that this species prefers aquatic saline environments with intermediate salinities, being detected on metagenomic databases of Lake Meyghan (Iran) with 5 and 18 % salinity, respectively.

Micromonospora cathayae sp. nov., isolated from the rhizosphere soil of Cathaya argyrophylla.

A novel actinobacterium, strain HUAS 3T, was isolated from the rhizosphere soil of Cathaya argyrophylla collected in Hunan Province, PR China. Strain HUAS 3T contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The dominant menaquinones were MK-9(H4), MK-9(H6), MK-10(H2) and MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phospholipids, phosphatidylethanolamine, phosphatidylglycerol, phosphotidylinositol and phosphatidylinositol mannosides. The main cellular fatty acids (>5.0 %) were C17 : 1 ω8c, iso-C16 : 0, C18 : 1 ω9c, iso-C15 : 0, C16 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The DNA G+C content of the novel strain's genome sequence, consisting of 7 196 442 bp, was 72.8 mol%. The full-length 16S rRNA gene sequence analysis indicated that strain HUAS 3T belonged to the genus Micromonospora and showed highest similarities to Micromonospora fluminis A38T (99.44 %), Micromonospora echinospora DSM 43816T (99.23 %), Micromonospora tulbaghiae DSM 45142T (99.23 %), Micromonospora solifontis PPF5-17T (99.16 %) and Micromonospora endolithica DSM 44398T (98.96 %). Phylogenetic trees based on 16S rRNA gene sequences showed that strain HUAS 3T was closely related to M. fluminis A38T, M. tulbaghiae DSM 45142T and M. solifontis PPF5-17T. The phylogenomic tree revealed that strain HUAS 3T was closely related to Micromonospora pallida DSM 43817T. However, the average nucleotide identity (ANIb/ANIm) and the digital DNA-DNA hybridization values between them were 84.75 /88.16 and 30.80 %, respectively, far less than the 95-96 and 70 % cut-off points recommended for delineating species. Furthermore, strain HUAS 3T was distinct from the type strain of M. pallida in terms of phenotypic and chemotaxonomic characteristics. In summary, strain HUAS 3T represents a novel Micromonospora species, for which the name Micromonospora cathayae sp. nov. is proposed. The type strain is HUAS 3T (=MCCC 1K08599T=JCM 36275T).

Microbial and metabolomic profiles of type 1 diabetes with depression: A case-control study.

Depression is the most common psychological disorder in patients with type 1 diabetes (T1D). However, the characteristics of microbiota and metabolites in these patients remain unclear. This study aimed to investigate microbial and metabolomic profiles and identify novel biomarkers for T1D with depression. A case-control study was conducted in a total of 37 T1D patients with depression (TD+), 35 T1D patients without depression (TD-), and 29 healthy controls (HCs). 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) metabolomics analysis were conducted to investigate the characteristics of microbiota and metabolites. The association between altered microbiota and metabolites was explored by Spearman's rank correlation and visualized by a heatmap. The microbial signatures to discriminate TD+ from TD- were identified by a random forest (RF) classifying model. In microbiota, 15 genera enriched in TD- and 2 genera enriched in TD+, and in metabolites, 14 differential metabolites (11 upregulated and 3 downregulated) in TD+ versus TD- were identified. Additionally, 5 genera (including Phascolarctobacterium, Butyricimonas, and Alistipes from altered microbiota) demonstrated good diagnostic power (area under the curve [AUC] = 0.73; 95% CI, 0.58-0.87). In the correlation analysis, Butyricimonas was negatively correlated with glutaric acid (r = -0.28, p = 0.015) and malondialdehyde (r = -0.30, p = 0.012). Both Phascolarctobacterium (r = 0.27, p = 0.022) and Alistipes (r = 0.31, p = 0.009) were positively correlated with allopregnanolone. T1D patients with depression were characterized by unique profiles of gut microbiota and serum metabolites. Phascolarctobacterium, Butyricimonas, and Alistipes could predict the risk of T1D with depression. These findings provide further evidence that the microbiota-gut-brain axis is involved in T1D with depression.

16S amplicon sequencing and untargeted metabolomics reveal changes in rumen microorganisms and metabolic pathways involved in the reduction of methane by cordycepin

As a major contributor to methane production in agriculture, there is a need for a suitable methane inhibitor to reduce ruminant methane emissions and minimize the impact on the climate. This work aimed to explore the influence of cordycepin on rumen fermentation, gas production, microbiome and their metabolites. A total of 0.00, 0.08, 0.16, 0.32, and 0.64 g L-1 cordycepin were added into fermentation bottles containing 2g total mixed ration for in vitro ruminal fermentation, and then the gas produced and fermentation parameters were measured for each bottle. Samples from the 0.00 and 0.64 g L-1 cordycepin addition were selected for 16S rRNA gene sequencing and metabolome analysis. The result of this experiment indicated that the addition of cordycepin could linearly increase the concentration of total volatile fatty acid, ammonia nitrogen, the proportion of propionate, valerate, and isovalerate, and linearly reduce ruminal pH and methane, carbon dioxide, hydrogen and total gas production, as well as the methane proportion, carbon dioxide proportion and proportion of butyrate. In addition, there was a quadratic relationship between hydrogen and cordycepin addition. At the same time, the relative abundance of Succiniclasticum, Prevotella, Rikenellaceae_RC9_gut_group, NK4A214_group, Christensenellaceae_R_7_group, unclassified_F082, Veillonellaceae_UCG_001, Dasytricha, Ophryoscolex, Isotricha, unclassified_Eukaryota, Methanobrevibacter, and Piromyces decreased significantly after adding the maximum dose of cordycepin. In contrast, the relative abundance of Succinivibrio, unclassified_Succinivibrionaceae, Prevotellaceae_UCG_001, unclassified_Lachnospiraceae, Lachnospira, Succinivibrionaceae_UCG_002, Pseudobutyrivibrio, Entodinium, Polyplastron, unclassified_Methanomethylophilaceae, Methanosphaera, and Candidatus_Methanomethylophilus increased significantly. Metabolic pathways such as biosynthesis of unsaturated fatty acids and purine metabolism and metabolites such as arachidonic acid, adenine, and 2′-deoxyguanosine were also affected by the addition of cordycepin. Based on this, we conclude that cordycepin is an effective methane emission inhibitor that can change the rumen metabolites and fermentation parameters by influencing the rumen microbiome, thus regulating rumen methane production. This experiment may provide a potential theoretical reference for developing Cordyceps byproduct or additives containing cordycepin as methane inhibitors.

First Report of Pectobacterium aroidearum Causing Soft Rot on Ficus carica in Korea

In July 2021, symptoms of soft rot were observed on the stems of <i>Ficus carica</i> in Yeongam, Jeollanamdo, Korea. To accurately diagnose the cause, infected stem was collected and bacterial strain was isolated. Among these, the pathogenic strain KNUB-08-21 was identified as <i>Pectobacterium aroidearum</i> through 16S rRNA gene sequencing and phylogenetic analysis based on the concatenated sequences of the <i>dnaX</i>, <i>leuS</i>, and <i>recA</i> genes. The affiliation of the isolate with this bacterial species was also confirmed by its biochemical characteristics obtained using API ID 32 GN system. Artificial inoculation confirmed the strain’s pathogenicity in figs, causing significant damage to both stems and fruits. To our knowledge, this is the first report of <i>P. aroidearum</i> causing soft rot disease in <i>F. carica</i> in Korea.

Attenuation of biofilm formation of Listeria monocytogenes by bacteriocin producing Pediococcus pentosaceus DS1 on selected biotic and abiotic surfaces

The present study explores the antilisterial activities of potentially probiotic strain Pediococcus pentosaceus DS1 isolated from fermented bamboo shoot. 16s rRNA gene sequence analysis confirmed the identity of the strains. Class IIA bacteriocin pediocin expressing YGNGV motif was identified and its antilisterial activity was validated by well diffusion assay. When cocultured with P. pentosaceus DS1, in case of L. monocytogenes AMDK2, maximum biofilm exclusion (55.54 ± 3.44%) was observed which could be visually observed by Scanning electron micrographs. P. pentosaceus DS1 showed maximum adhesion inhibition to Caco-2 cell line in case of L. monocytogenes AMDK2 (91.8%) whereas maximum decrease in invasion was observed in case of L. monocytogenes MTCC 839 (52.9%). Coculture in UHT milk also significantly decreased microbial growth parameters of Listeria suggesting the efficiency of P. pentosaceus DS1 in the removal of Listeria contamination from food.

Isolation and molecular characterization of cellulase-producing bacteria from waste dump site

Cellulases are collections of extracellular enzymes and a complex mixture of enzyme proteins with various specificities. Cellulases work together to hydrolyze glycosidic bonds and generate monomers of glucose for fermentation. This investigation aims to isolate and molecularly characterize Bacillus species with cellulolytic ability. Bacillus species were isolated from soil samples retrieved from a dump site and screened for cellulolytic ability on carboxyl methylcellulose (CMC) agar. The percentage hydrolysis efficiency of isolates was determined and cellulase produced was quantified using CMC assay method. Biochemical identification was by Analytical Profile Index (API) Kit 50CHB/20E and API web software while molecular characterization employed 16S rRNA gene sequencing and blast search analysis. Bacillus megaterium (FSP1) and Bacillus zanthoxyli (FSP4) exhibited their cellulolytic potentials by presenting zones of clearance of about 21 ± 2.08 and 7 ± 1.00 mm on CMCA with hydrolysis efficiency of 250 and 600 % respectively. Quantification of crude cellulase revealed cellulase activity of 85 and 74μmol/ml for both bacteria species. Biochemically, the cellulolytic bacteria were identified as Bacillus megaterium (FSP1) and Bacillus zanthoxyli (FSP4) while molecularly, they were identified as Bacillus megaterium 14581 (FSP1) and Bacillus zanthoxyli 1433 (FSP4) with Reference Sequence (RefSeq) accession numbers NR_116873 and NR_164882, and showing maximum sequence similarity of 99 and 96 % respectively. Results obtained from this investigation, suggests that both bacteria species characterised, possesses good cellulolytic ability and hence can be utilized for the production of the enzyme cellulase which has a wide range of industrial application.

Polystyrene-degrading bacteria in the gut microbiome of marine benthic polychaetes support enhanced digestion of plastic fragments

Polystyrene foam, which is used as a buoyant material in mariculture, is a common constituent of marine plastic debris. Here, we conduct analyses on polystyrene foam debris collected on the east coast of Xiamen Island, China, and associated plastic-burrowing clamworms. We apply interferometry, mass spectrometry and microscopy to polystyrene foam fragments excreted by the benthic clamworms (Perinereis vancaurica). We find evidence of polystyrene digestion and degradation during passage of the clamworm gut leading to the formation and accumulation of microplastics, with a mean diameter of 0.6 ± 0.2 mm. 16S rRNA gene sequence analysis of clamworm intestines indicated diverse bacterial gut microbiome, dominated by Acinetobacter and Ruegeria bacteria. Further characterization confirmed that polystyrene was degraded by representative gut isolates of Acinetobacter johnsonii, Brevibacterium casei, and Ruegeria arenilitoris. During a 30-day incubation, we observed a very slight decrease in polystyrene weight, changes in chemical group and thermal characteristic, and production of polystyrene metabolic intermediates. Our findings indicate that polystyrene-degrading bacteria in the gut microbiome of clamworms may influence plastic fragmentation and degradation in marine ecosystems.

Effects of Bacillus coagulans TBC169 on gut microbiota and metabolites in gynecological laparoscopy patients.

The primary objective of this study is to investigate the mechanism by which Bacillus coagulans TBC169 accelerates intestinal function recovery in patients who have undergone gynecological laparoscopic surgery, using metabolomics and gut microbiota analysis. A total of 20 subjects were selected and randomly divided into two groups: the intervention group (n = 10) receiving Bacillus coagulans TBC169 Tablets (6 pills, 1.05 × 108 CFU), and the control group (n = 10) receiving placebos (6 pills). After the initial postoperative defecation, fecal samples were collected from each subject to analyze their gut microbiota and metabolic profiles by high-throughput 16S rRNA gene sequencing analysis and untargeted metabonomic. There were no statistically significant differences observed in the α-diversity and β-diversity between the two groups; however, in the intervention group, there was a significant reduction in the relative abundance of unclassified_Enterobacteriaceae at the genus level. Furthermore, the control group showed increased levels of Holdemanella and Enterobacter, whereas the intervention group exhibited elevated levels of Intestinimonas. And administration of Bacillus coagulans TBC169 led to variations in 2 metabolic pathways: D-glutamine and D-glutamate metabolism, and arginine biosynthesis. This study demonstrated that consuming Bacillus coagulans TBC169 after gynecological laparoscopic surgery might inhibit the proliferation of harmful Enterobacteriaceae; mainly influence 2 pathways including D-glutamine and D-glutamate metabolism, and arginine biosynthesis; and regulate metabolites related to immunity and intestinal motility; which can help regulate immune function, maintain intestinal balance, promote intestinal peristalsis, and thus accelerate the recovery of intestinal function.

Proposal of Streptomyces bellus Margalith and Beretta 1960 as a Later Heterotypic Synonym of Streptomyces coeruleorubidus (Preobrazhenskaya 1957) Pridham et al. 1958 and an Emended Description of Streptomyces coeruleorubidus.

In the present work, the taxonomic relationship between Streptomyces coeruleorubidus and Streptomyces bellus was reevaluated by a comprehensive comparison of phenotypic, chemotaxonomic and genomic characteristics, as well as phylogeny. In 1957 and 1960, Streptomyces coeruleorubidus and Streptomyces bellus were described as two novel Streptomyces species. The full-length 16S rRNA gene sequence analysis indicated that Streptomyces bellus JCM 4292T shared highest sequence identity with Streptomyces coerulescens ISP 5146T (100%). Phylogenetic analysis of 16S rRNA gene sequence showed that S. bellus JCM 4292T was most closely related to Streptomyces coerulescens ISP 5146T. Phylogenetic analysis of five housekeeping gene sequences demonstrated that S. bellus JCM 4292T was most closely related to S. coeruleorubidus ATCC 13740T. Nevertheless, the ANIm (average nucleotide identity based on MuMmer ultra-rapid aligning tool) and dDDH (digital DNA-DNA hybridization) values between them were 97.71% and 81.9%, respectively, greater than the threshold of 96.7% and 70% for the delineation of Streptomyces species, suggesting that they represent the same genomic species. In addition, phenotypic and chemotaxonomic characteristics, as well as phylogeny and genomic DNA-DNA correlation analysis also confirmed the above conclusion. Consequently, we proposed that S. bellus Margalith and Beretta 1960 is a later heterotypic synonym of S. coeruleorubidus (Preobrazhenskaya 1957) Pridham et al. 1958.

Pathogenicity of Streptococcus iniae causing mass mortalities of yellow catfish (Tachysurus fulvidraco) and its induced host immune response.

The outbreak of mass mortality occurred in Tachysurus fulvidraco farm in Hubei province of China. The pathogenic strain of Streptococcus iniae (termed 2022SI08) was isolated and identified from diseased T. fulvidraco, based on morphological, physiological, and biochemical characteristics, as well as 16S rRNA gene sequence and phylogenetic analysis. Further, the whole genome of isolate S. iniae was sequenced and predicted to contain one single circular chromosome of 1,776,777 bp with a GC content of 37.14%. The genomic sequence analysis showed that 2022SI08 was positive for 204 virulent and 127 antibiotic resistant genes. The experimental challenge demonstrated the high pathogenicity of the retrieved isolate of S. iniae, with a median lethal dosage (LD50) 9.53 × 105 CFU/g. Histopathological examination indicated that the 2022SI08 strain could induce extensive tissue cell degeneration, necrosis, hemorrhage, and inflammation in the skin, gill, fin, spleen, liver, kidney, intestine, eye, and brain. Moreover, the innate immune enzyme activities in serum such as acid phosphatase and alkaline phosphatase were increased significantly at 24 and 48 h post infection (hpi) and then decreased at 168 hpi. The transcriptional profile of immune associated gene in T. fulvidraco following bacterial infection was detected at each point of time, and the results revealed clear transcriptional activation of those genes, which proving their reacting and regulatory role during the response of the host against S. iniae infection. The results revealed that S. iniae was an etiological agent in the mass mortalities of T. fulvidraco and this research will be conducive for increasing our understanding on pathogenesis and host defensive system in S. iniae invasion.

Membrane-anchoring selenophene viologens for antibacterial photodynamic therapy against periodontitis via restoring subgingival flora and alleviating inflammation

Antibacterial photodynamic therapy (aPDT) has emerged as a promising strategy for treating periodontitis. However, the weak binding of most photosensitizers to bacteria and the hypoxic environment of periodontal pockets severely hamper the therapeutic efficacy. Herein, two novel oxygen-independent photosensitizers are developed by introducing selenophene into viologens and modifying with hexane chains (HASeV) or quaternary ammonium chains (QASeV), which improve the adsorption to bacteria through anchoring to the negatively charged cell membrane. Notably, QASeV binds only to the bacterial surface of Porphyromonas gingivalis and Fusobacterium nucleatum due to electrostatic binding, but HASeV can insert into their membrane by strong hydrophobic interactions. Therefore, HASeV exhibits superior antimicrobial activity and more pronounced plaque biofilm disruption than QASeV when combined with light irradiation (MVL-210 photoreactor, 350–600 nm, 50 mW/cm2), and a better effect on reducing the diversity and restoring the structure of subgingival flora in periodontitis rat model was found through 16S rRNA gene sequencing analysis. The histological and Micro-CT analyses reveal that HASeV-based aPDT has a better therapeutic effect in reducing periodontal tissue inflammation and alveolar bone resorption. This work provides a new strategy for the development of viologen-based photosensitizers, which may be a favorable candidate for the aPDT against periodontitis.

Species-level Microbiota of Biting Midges and Ticks from Poyang Lake.

The purpose of this study was to investigate the bacterial communities of biting midges and ticks collected from three sites in the Poyang Lake area, namely, Qunlu Practice Base, Peach Blossom Garden, and Huangtong Animal Husbandry, and whether vectors carry any bacterial pathogens that may cause diseases to humans, to provide scientific basis for prospective pathogen discovery and disease prevention and control. Using a metataxonomics approach in concert with full-length 16S rRNA gene sequencing and operational phylogenetic unit (OPU) analysis, we characterized the species-level microbial community structure of two important vector species, biting midges and ticks, including 33 arthropod samples comprising 3,885 individuals, collected around Poyang Lake. A total of 662 OPUs were classified in biting midges, including 195 known species and 373 potentially new species, and 618 OPUs were classified in ticks, including 217 known species and 326 potentially new species. Surprisingly, OPUs with potentially pathogenicity were detected in both arthropod vectors, with 66 known species of biting midges reported to carry potential pathogens, including Asaia lannensis and Rickettsia bellii, compared to 50 in ticks, such as Acinetobacter lwoffii and Staphylococcus sciuri. We found that Proteobacteria was the most dominant group in both midges and ticks. Furthermore, the outcomes demonstrated that the microbiota of midges and ticks tend to be governed by a few highly abundant bacteria. Pantoea sp7 was predominant in biting midges, while Coxiella sp1 was enriched in ticks. Meanwhile, Coxiella spp., which may be essential for the survival of Haemaphysalis longicornis Neumann, were detected in all tick samples. The identification of dominant species and pathogens of biting midges and ticks in this study serves to broaden our knowledge associated to microbes of arthropod vectors. Biting midges and ticks carry large numbers of known and potentially novel bacteria, and carry a wide range of potentially pathogenic bacteria, which may pose a risk of infection to humans and animals. The microbial communities of midges and ticks tend to be dominated by a few highly abundant bacteria.